Starting phenix.real_space_refine
on Tue Jul 29 08:26:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ce1_16597/07_2025/8ce1_16597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ce1_16597/07_2025/8ce1_16597.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ce1_16597/07_2025/8ce1_16597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ce1_16597/07_2025/8ce1_16597.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ce1_16597/07_2025/8ce1_16597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ce1_16597/07_2025/8ce1_16597.cif"
  }
  resolution = 3.47
  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=   0.009 sd=   0.110
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      58      5.16       5
     C    7496      2.51       5
     N    1974      2.21       5
     O    1910      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11438
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "a"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1595
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 6, 'TRANS': 196}
    Chain: "b"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1656
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 202}
    Chain: "c"
      Number of atoms: 1930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1930
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 11, 'TRANS': 229}
    Chain: "d"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 538
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 65}
    Chain: "A"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1595
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 6, 'TRANS': 196}
    Chain: "B"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1656
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 202}
    Chain: "C"
      Number of atoms: 1930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1930
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 11, 'TRANS': 229}
    Chain: "D"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 538
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 65}
  Time building chain proxies: 7.47, per 1000 atoms: 0.65
  Number of scatterers: 11438
  At special positions: 0
  Unit cell: (83.52, 120.93, 107.88, 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      58     16.00
     O    1910      8.00
     N    1974      7.00
     C    7496      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.96
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2704

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 5 sheets defined
      73.5% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'a' and resid 42 through 50
    Processing helix  chain 'a' and resid 70 through 75
    Processing helix  chain 'a' and resid 92 through 100
      removed outlier: 3.931A  pdb=" N   TYR a 100 " --> pdb=" O   ASN a  96 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 111 through 116
      removed outlier: 3.720A  pdb=" N   ALA a 116 " --> pdb=" O   ALA a 112 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 125 through 129
    Processing helix  chain 'a' and resid 130 through 141
      removed outlier: 3.830A  pdb=" N   VAL a 137 " --> pdb=" O   GLN a 133 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ALA a 138 " --> pdb=" O   GLN a 134 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 142 through 144
      No H-bonds generated for 'chain 'a' and resid 142 through 144'
    Processing helix  chain 'a' and resid 160 through 177
      removed outlier: 3.874A  pdb=" N   GLN a 177 " --> pdb=" O   GLN a 173 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 3 through 17
      removed outlier: 3.662A  pdb=" N   PHE b   7 " --> pdb=" O   PHE b   3 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   HIS b  17 " --> pdb=" O   VAL b  13 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 18 through 20
      No H-bonds generated for 'chain 'b' and resid 18 through 20'
    Processing helix  chain 'b' and resid 21 through 40
      removed outlier: 4.396A  pdb=" N   LEU b  25 " --> pdb=" O   ILE b  21 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE b  35 " --> pdb=" O   VAL b  31 " (cutoff:3.500A)
      Proline residue:  b  36  - end of helix
    Processing helix  chain 'b' and resid 42 through 66
      Proline residue:  b  51  - end of helix
    Processing helix  chain 'b' and resid 66 through 77
      removed outlier: 4.330A  pdb=" N   PHE b  70 " --> pdb=" O   LEU b  66 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ASP b  72 " --> pdb=" O   ARG b  68 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   ASP b  73 " --> pdb=" O   LEU b  69 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU b  74 " --> pdb=" O   PHE b  70 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLN b  75 " --> pdb=" O   ARG b  71 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 77 through 84
      removed outlier: 3.920A  pdb=" N   GLN b  81 " --> pdb=" O   GLY b  77 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 88 through 119
      removed outlier: 3.587A  pdb=" N   VAL b  92 " --> pdb=" O   PRO b  88 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   LEU b 106 " --> pdb=" O   MET b 102 " (cutoff:3.500A)
      Proline residue:  b 107  - end of helix
      Proline residue:  b 113  - end of helix
      removed outlier: 3.503A  pdb=" N   LEU b 119 " --> pdb=" O   VAL b 115 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 122 through 151
      Proline residue:  b 138  - end of helix
      Proline residue:  b 146  - end of helix
    Processing helix  chain 'b' and resid 159 through 169
      Proline residue:  b 167  - end of helix
    Processing helix  chain 'b' and resid 169 through 185
      removed outlier: 3.594A  pdb=" N   MET b 185 " --> pdb=" O   ASP b 181 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 189 through 220
      Proline residue:  b 208  - end of helix
      removed outlier: 4.405A  pdb=" N   ALA b 213 " --> pdb=" O   PHE b 209 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ALA b 214 " --> pdb=" O   ALA b 210 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 6 through 9
    Processing helix  chain 'c' and resid 10 through 41
      Proline residue:  c  23  - end of helix
    Processing helix  chain 'c' and resid 50 through 54
      removed outlier: 3.592A  pdb=" N   SER c  53 " --> pdb=" O   GLN c  50 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR c  54 " --> pdb=" O   GLY c  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'c' and resid 50 through 54'
    Processing helix  chain 'c' and resid 55 through 83
      removed outlier: 3.986A  pdb=" N   LEU c  59 " --> pdb=" O   ARG c  55 " (cutoff:3.500A)
      Proline residue:  c  62  - end of helix
      removed outlier: 3.853A  pdb=" N   SER c  67 " --> pdb=" O   ALA c  63 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   TYR c  71 " --> pdb=" O   SER c  67 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 86 through 120
      removed outlier: 3.698A  pdb=" N   ASN c  90 " --> pdb=" O   MET c  86 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA c  94 " --> pdb=" O   ASN c  90 " (cutoff:3.500A)
      Proline residue:  c  98  - end of helix
      Proline residue:  c 117  - end of helix
    Processing helix  chain 'c' and resid 126 through 149
      removed outlier: 3.568A  pdb=" N   PHE c 149 " --> pdb=" O   LEU c 145 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 151 through 184
      Proline residue:  c 171  - end of helix
    Processing helix  chain 'c' and resid 198 through 229
      removed outlier: 3.882A  pdb=" N   LEU c 202 " --> pdb=" O   MET c 198 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG c 222 " --> pdb=" O   LEU c 218 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 232 through 242
      removed outlier: 3.846A  pdb=" N   SER c 236 " --> pdb=" O   ARG c 232 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 7 through 12
      removed outlier: 3.911A  pdb=" N   PHE d  12 " --> pdb=" O   TRP d   8 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 17 through 69
      removed outlier: 4.292A  pdb=" N   VAL d  21 " --> pdb=" O   TYR d  17 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TRP d  22 " --> pdb=" O   ALA d  18 " (cutoff:3.500A)
      Proline residue:  d  31  - end of helix
    Processing helix  chain 'A' and resid 41 through 50
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 92 through 100
      removed outlier: 3.926A  pdb=" N   TYR A 100 " --> pdb=" O   ASN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 3.616A  pdb=" N   ALA A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 129
    Processing helix  chain 'A' and resid 130 through 141
      removed outlier: 3.817A  pdb=" N   VAL A 137 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ALA A 138 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 145
      removed outlier: 3.504A  pdb=" N   THR A 145 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 142 through 145'
    Processing helix  chain 'A' and resid 160 through 177
      removed outlier: 3.790A  pdb=" N   GLN A 177 " --> pdb=" O   GLN A 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 17
      removed outlier: 3.598A  pdb=" N   PHE B   7 " --> pdb=" O   PHE B   3 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   HIS B  17 " --> pdb=" O   VAL B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 21
    Processing helix  chain 'B' and resid 22 through 40
      removed outlier: 3.880A  pdb=" N   PHE B  35 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      Proline residue:  B  36  - end of helix
    Processing helix  chain 'B' and resid 42 through 66
      Proline residue:  B  51  - end of helix
    Processing helix  chain 'B' and resid 66 through 77
      removed outlier: 4.263A  pdb=" N   PHE B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   ASP B  72 " --> pdb=" O   ARG B  68 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   ASP B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU B  74 " --> pdb=" O   PHE B  70 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLN B  75 " --> pdb=" O   ARG B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 84
      removed outlier: 3.656A  pdb=" N   GLN B  81 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 120
      removed outlier: 3.544A  pdb=" N   VAL B  92 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   LEU B 106 " --> pdb=" O   MET B 102 " (cutoff:3.500A)
      Proline residue:  B 107  - end of helix
      Proline residue:  B 113  - end of helix
      removed outlier: 3.563A  pdb=" N   GLY B 120 " --> pdb=" O   ALA B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 151
      Proline residue:  B 138  - end of helix
      Proline residue:  B 146  - end of helix
    Processing helix  chain 'B' and resid 158 through 185
      removed outlier: 4.101A  pdb=" N   SER B 162 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
      Proline residue:  B 167  - end of helix
      Proline residue:  B 171  - end of helix
      removed outlier: 3.616A  pdb=" N   MET B 185 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 220
      Proline residue:  B 208  - end of helix
      removed outlier: 4.120A  pdb=" N   ALA B 213 " --> pdb=" O   PHE B 209 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA B 214 " --> pdb=" O   ALA B 210 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 8
    Processing helix  chain 'C' and resid 10 through 41
      Proline residue:  C  23  - end of helix
    Processing helix  chain 'C' and resid 50 through 54
      removed outlier: 3.645A  pdb=" N   SER C  53 " --> pdb=" O   GLN C  50 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   TYR C  54 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 50 through 54'
    Processing helix  chain 'C' and resid 55 through 83
      removed outlier: 4.094A  pdb=" N   LEU C  59 " --> pdb=" O   ARG C  55 " (cutoff:3.500A)
      Proline residue:  C  62  - end of helix
      removed outlier: 3.788A  pdb=" N   SER C  67 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   TYR C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 120
      removed outlier: 3.740A  pdb=" N   ASN C  90 " --> pdb=" O   MET C  86 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA C  94 " --> pdb=" O   ASN C  90 " (cutoff:3.500A)
      Proline residue:  C  98  - end of helix
      Proline residue:  C 117  - end of helix
    Processing helix  chain 'C' and resid 126 through 149
      removed outlier: 3.645A  pdb=" N   PHE C 149 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 181
      Proline residue:  C 171  - end of helix
    Processing helix  chain 'C' and resid 199 through 229
      removed outlier: 3.806A  pdb=" N   ARG C 222 " --> pdb=" O   LEU C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 242
      removed outlier: 3.734A  pdb=" N   SER C 236 " --> pdb=" O   ARG C 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 12
      removed outlier: 3.885A  pdb=" N   PHE D  12 " --> pdb=" O   TRP D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 69
      Proline residue:  D  31  - end of helix
      removed outlier: 3.742A  pdb=" N   HIS D  43 " --> pdb=" O   SER D  39 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 26
      removed outlier: 6.864A  pdb=" N   LEU a  18 " --> pdb=" O   GLU a  12 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   GLU a  12 " --> pdb=" O   LEU a  18 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER a  20 " --> pdb=" O   LEU a  10 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   LEU a  10 " --> pdb=" O   SER a  20 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   LEU a  22 " --> pdb=" O   GLU a   8 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU a   4 " --> pdb=" O   LEU a  26 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   LEU a   9 " --> pdb=" O   ALA a  57 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   ALA a  57 " --> pdb=" O   LEU a   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'a' and resid 32 through 34
    Processing sheet with id=AA3, first strand: chain 'a' and resid 78 through 81
      removed outlier: 6.211A  pdb=" N   LEU a  79 " --> pdb=" O   ILE a 151 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ASP a 153 " --> pdb=" O   LEU a  79 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE a  81 " --> pdb=" O   ASP a 153 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   TRP a 150 " --> pdb=" O   ILE a 182 " (cutoff:3.500A)
      removed outlier: 8.378A  pdb=" N   THR a 184 " --> pdb=" O   TRP a 150 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU a 152 " --> pdb=" O   THR a 184 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 16 through 25
      removed outlier: 6.787A  pdb=" N   LEU A  18 " --> pdb=" O   GLU A  12 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   GLU A  12 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   SER A  20 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   LEU A  10 " --> pdb=" O   SER A  20 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   LEU A  22 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU A   9 " --> pdb=" O   ALA A  57 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA A  57 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 81
      removed outlier: 6.214A  pdb=" N   LEU A  79 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   ASP A 153 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ILE A  81 " --> pdb=" O   ASP A 153 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   VAL A  32 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)

    720 hydrogen bonds defined for protein.
    2136 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: 3.11

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2570
        1.33 -     1.45: 2490
        1.45 -     1.57: 6560
        1.57 -     1.69: 0
        1.69 -     1.81: 110
  Bond restraints: 11730
  Sorted by residual:
  bond pdb=" CA  MET C 198 "
       pdb=" C   MET C 198 "
    ideal  model  delta    sigma   weight residual
    1.523  1.474  0.049 1.61e-02 3.86e+03 9.24e+00
  bond pdb=" CA  ALA C 197 "
       pdb=" C   ALA C 197 "
    ideal  model  delta    sigma   weight residual
    1.522  1.487  0.035 1.33e-02 5.65e+03 6.92e+00
  bond pdb=" CB  TRP C  39 "
       pdb=" CG  TRP C  39 "
    ideal  model  delta    sigma   weight residual
    1.498  1.570 -0.072 3.10e-02 1.04e+03 5.33e+00
  bond pdb=" C   ILE c  22 "
       pdb=" N   PRO c  23 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.97e+00
  bond pdb=" N   MET C 198 "
       pdb=" CA  MET C 198 "
    ideal  model  delta    sigma   weight residual
    1.460  1.428  0.032 1.45e-02 4.76e+03 4.89e+00
  ... (remaining 11725 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 15550
        2.91 -     5.83: 379
        5.83 -     8.74: 64
        8.74 -    11.66: 10
       11.66 -    14.57: 3
  Bond angle restraints: 16006
  Sorted by residual:
  angle pdb=" N   MET C 198 "
        pdb=" CA  MET C 198 "
        pdb=" C   MET C 198 "
      ideal   model   delta    sigma   weight residual
     110.44   96.70   13.74 1.20e+00 6.94e-01 1.31e+02
  angle pdb=" N   GLN c  16 "
        pdb=" CA  GLN c  16 "
        pdb=" CB  GLN c  16 "
      ideal   model   delta    sigma   weight residual
     110.30  118.21   -7.91 1.54e+00 4.22e-01 2.64e+01
  angle pdb=" CA  TRP C  39 "
        pdb=" CB  TRP C  39 "
        pdb=" CG  TRP C  39 "
      ideal   model   delta    sigma   weight residual
     113.60  122.59   -8.99 1.90e+00 2.77e-01 2.24e+01
  angle pdb=" N   GLN C  16 "
        pdb=" CA  GLN C  16 "
        pdb=" CB  GLN C  16 "
      ideal   model   delta    sigma   weight residual
     110.30  117.56   -7.26 1.54e+00 4.22e-01 2.22e+01
  angle pdb=" N   ALA C 197 "
        pdb=" CA  ALA C 197 "
        pdb=" C   ALA C 197 "
      ideal   model   delta    sigma   weight residual
     113.56  107.21    6.35 1.39e+00 5.18e-01 2.09e+01
  ... (remaining 16001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 5888
       16.10 -    32.21: 729
       32.21 -    48.31: 193
       48.31 -    64.41: 25
       64.41 -    80.51: 7
  Dihedral angle restraints: 6842
    sinusoidal: 2660
      harmonic: 4182
  Sorted by residual:
  dihedral pdb=" CA  ASN C 181 "
           pdb=" C   ASN C 181 "
           pdb=" N   THR C 182 "
           pdb=" CA  THR C 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.68   24.32     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  THR C 182 "
           pdb=" C   THR C 182 "
           pdb=" N   LEU C 183 "
           pdb=" CA  LEU C 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.42   23.58     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  LEU A 110 "
           pdb=" C   LEU A 110 "
           pdb=" N   GLU A 111 "
           pdb=" CA  GLU A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.50   23.50     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 6839 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1357
       0.057 -    0.114: 401
       0.114 -    0.171: 96
       0.171 -    0.228: 12
       0.228 -    0.285: 4
  Chirality restraints: 1870
  Sorted by residual:
  chirality pdb=" CB  VAL a  70 "
            pdb=" CA  VAL a  70 "
            pdb=" CG1 VAL a  70 "
            pdb=" CG2 VAL a  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CB  VAL A  70 "
            pdb=" CA  VAL A  70 "
            pdb=" CG1 VAL A  70 "
            pdb=" CG2 VAL A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CA  TRP b  55 "
            pdb=" N   TRP b  55 "
            pdb=" C   TRP b  55 "
            pdb=" CB  TRP b  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1867 not shown)

  Planarity restraints: 1978
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE b  35 "   -0.074 5.00e-02 4.00e+02   1.10e-01 1.93e+01
        pdb=" N   PRO b  36 "    0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO b  36 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO b  36 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  89 "    0.063 5.00e-02 4.00e+02   9.45e-02 1.43e+01
        pdb=" N   PRO B  90 "   -0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO B  90 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B  90 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU b  89 "   -0.061 5.00e-02 4.00e+02   9.06e-02 1.31e+01
        pdb=" N   PRO b  90 "    0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO b  90 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO b  90 "   -0.050 5.00e-02 4.00e+02
  ... (remaining 1975 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 515
        2.73 -     3.27: 11691
        3.27 -     3.82: 19175
        3.82 -     4.36: 22688
        4.36 -     4.90: 38499
  Nonbonded interactions: 92568
  Sorted by model distance:
  nonbonded pdb=" OH  TYR c  54 "
            pdb=" O   SER c 193 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR C  54 "
            pdb=" O   SER C 193 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   VAL B 159 "
            pdb=" OG  SER B 162 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OE2 GLU B  10 "
            pdb=" NH2 ARG B  68 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   VAL b 159 "
            pdb=" OG  SER b 162 "
     model   vdw
     2.349 3.040
  ... (remaining 92563 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'a'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'b'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'c'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'd'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             34.960
  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:             0.020
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.530
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.050
  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:3.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   69.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
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      :  0.006   0.072  11730  Z= 0.252
  Angle     :  1.081  14.571  16006  Z= 0.548
  Chirality :  0.058   0.285   1870
  Planarity :  0.010   0.110   1978
  Dihedral  : 15.030  80.514   4138
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.70 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  7.36 %
    Favored  : 92.22 %
  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: -0.68 (0.21), residues: 1446
  helix: -0.03 (0.16), residues: 962
  sheet: -0.84 (0.83), residues: 48
  loop : -1.09 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP c  20 
 HIS   0.012   0.002   HIS A 174 
 PHE   0.022   0.002   PHE B 142 
 TYR   0.021   0.003   TYR C  54 
 ARG   0.015   0.001   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11540 (  720)
  hydrogen bonds       : angle       6.43138 ( 2136)
  covalent geometry    : bond        0.00586 (11730)
  covalent geometry    : angle       1.08077 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 149
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 ILE cc_start: 0.7607 (mt) cc_final: 0.7387 (mm)
  outliers start: 5
  outliers final: 4
  residues processed: 151
  average time/residue: 0.3704
  time to fit residues: 82.4335
Evaluate side-chains
  130 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 3.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  121 THR
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  198 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 111 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 82 optimal weight:   10.0000
   chunk 128 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
c 169 ASN
A 174 HIS
B  17 HIS
B 100 HIS
** C  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.182016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.157562 restraints weight = 13556.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 1.77
r_work: 0.3714 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3578 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11730  Z= 0.141
  Angle     :  0.655   9.161  16006  Z= 0.323
  Chirality :  0.042   0.157   1870
  Planarity :  0.007   0.085   1978
  Dihedral  :  5.381  58.977   1580
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.07 %
    Favored  : 87.82 %
  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:  0.65 (0.22), residues: 1446
  helix:  1.03 (0.16), residues: 974
  sheet: -0.08 (0.92), residues: 44
  loop : -0.80 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP c  20 
 HIS   0.005   0.001   HIS A 174 
 PHE   0.013   0.001   PHE b   7 
 TYR   0.010   0.001   TYR A 100 
 ARG   0.006   0.001   ARG d  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  720)
  hydrogen bonds       : angle       4.65119 ( 2136)
  covalent geometry    : bond        0.00349 (11730)
  covalent geometry    : angle       0.65547 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 1.209 
Fit side-chains
REVERT: a   59 GLU cc_start: 0.7615 (pm20) cc_final: 0.7196 (pm20)
REVERT: C   59 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8110 (mp)
REVERT: C  198 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8531 (tmm)
  outliers start: 25
  outliers final: 16
  residues processed: 141
  average time/residue: 0.2750
  time to fit residues: 57.3470
Evaluate side-chains
  140 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue    2 MET
Chi-restraints excluded: chain b residue  170 ILE
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain b residue  219 ILE
Chi-restraints excluded: chain c residue   21 PHE
Chi-restraints excluded: chain c residue   30 VAL
Chi-restraints excluded: chain c residue  182 THR
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  198 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 106 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 131 optimal weight:    0.0370
   chunk 72 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    2.8066

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

Flipped N/Q/H residues before XYZ refinement:
b  81 GLN
d  38 HIS
** C  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.169313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.144046 restraints weight = 13898.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 1.74
r_work: 0.3527 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  11730  Z= 0.249
  Angle     :  0.745   9.333  16006  Z= 0.363
  Chirality :  0.046   0.185   1870
  Planarity :  0.006   0.077   1978
  Dihedral  :  5.273  58.029   1577
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 12.27 %
    Favored  : 84.60 %
  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:  0.73 (0.22), residues: 1446
  helix:  1.07 (0.17), residues: 968
  sheet: -1.64 (0.73), residues: 56
  loop : -0.40 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP c  20 
 HIS   0.006   0.001   HIS C 174 
 PHE   0.015   0.002   PHE B  70 
 TYR   0.015   0.002   TYR A 100 
 ARG   0.006   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04408 (  720)
  hydrogen bonds       : angle       4.69705 ( 2136)
  covalent geometry    : bond        0.00631 (11730)
  covalent geometry    : angle       0.74515 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 132
  time to evaluate  : 1.132 
Fit side-chains
REVERT: c   80 ILE cc_start: 0.9269 (mm) cc_final: 0.8998 (mt)
REVERT: c  204 TRP cc_start: 0.8369 (m100) cc_final: 0.8063 (m100)
REVERT: A   61 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7909 (mt)
REVERT: A  154 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7152 (pt0)
REVERT: C  204 TRP cc_start: 0.8189 (m100) cc_final: 0.7856 (m100)
REVERT: D   54 ARG cc_start: 0.7686 (mmt90) cc_final: 0.7483 (mpt-90)
  outliers start: 37
  outliers final: 22
  residues processed: 152
  average time/residue: 0.2161
  time to fit residues: 48.3530
Evaluate side-chains
  148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   20 SER
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue  104 THR
Chi-restraints excluded: chain b residue  185 MET
Chi-restraints excluded: chain b residue  205 THR
Chi-restraints excluded: chain b residue  219 ILE
Chi-restraints excluded: chain c residue   21 PHE
Chi-restraints excluded: chain c residue   30 VAL
Chi-restraints excluded: chain c residue  182 THR
Chi-restraints excluded: chain d residue   50 VAL
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  181 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 106 optimal weight:    0.3980
   chunk 97 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 113 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 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 = 0.4068 r_free = 0.4068 target = 0.174133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.149354 restraints weight = 13719.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 1.72
r_work: 0.3590 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11730  Z= 0.130
  Angle     :  0.617   9.383  16006  Z= 0.298
  Chirality :  0.041   0.158   1870
  Planarity :  0.006   0.072   1978
  Dihedral  :  4.571  22.149   1572
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.55 %
    Favored  : 82.91 %
  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:  1.18 (0.23), residues: 1446
  helix:  1.47 (0.17), residues: 982
  sheet: -1.77 (0.70), residues: 56
  loop : -0.40 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  55 
 HIS   0.003   0.001   HIS C 174 
 PHE   0.009   0.001   PHE b   7 
 TYR   0.009   0.001   TYR A 100 
 ARG   0.003   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  720)
  hydrogen bonds       : angle       4.34280 ( 2136)
  covalent geometry    : bond        0.00319 (11730)
  covalent geometry    : angle       0.61676 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 1.188 
Fit side-chains
REVERT: a    1 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6903 (ptp)
REVERT: a  160 ASP cc_start: 0.8523 (p0) cc_final: 0.8288 (p0)
REVERT: b  156 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7771 (mtm-85)
REVERT: c   80 ILE cc_start: 0.9193 (mm) cc_final: 0.8947 (mt)
REVERT: c  204 TRP cc_start: 0.8268 (m100) cc_final: 0.7983 (m100)
REVERT: A  154 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7084 (pt0)
REVERT: C   80 ILE cc_start: 0.9237 (mm) cc_final: 0.9002 (mt)
REVERT: C  198 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7211 (tmt)
  outliers start: 30
  outliers final: 17
  residues processed: 144
  average time/residue: 0.2302
  time to fit residues: 47.8996
Evaluate side-chains
  146 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    1 MET
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   20 SER
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue    9 LEU
Chi-restraints excluded: chain b residue  106 LEU
Chi-restraints excluded: chain b residue  185 MET
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain c residue   38 ILE
Chi-restraints excluded: chain c residue  182 THR
Chi-restraints excluded: chain A residue    3 MET
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  198 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0020
   chunk 116 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
C  90 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.172054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.146786 restraints weight = 13820.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.76
r_work: 0.3558 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11730  Z= 0.139
  Angle     :  0.603   9.337  16006  Z= 0.291
  Chirality :  0.041   0.160   1870
  Planarity :  0.005   0.072   1978
  Dihedral  :  4.359  21.132   1572
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.97 %
    Favored  : 82.40 %
  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:  1.41 (0.23), residues: 1446
  helix:  1.67 (0.17), residues: 982
  sheet: -0.71 (1.02), residues: 36
  loop : -0.59 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  55 
 HIS   0.004   0.001   HIS C 184 
 PHE   0.009   0.001   PHE b   7 
 TYR   0.009   0.001   TYR A 100 
 ARG   0.004   0.000   ARG D  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  720)
  hydrogen bonds       : angle       4.19050 ( 2136)
  covalent geometry    : bond        0.00347 (11730)
  covalent geometry    : angle       0.60322 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 1.127 
Fit side-chains
REVERT: a    1 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6870 (ptp)
REVERT: b  156 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7811 (mtm-85)
REVERT: c   80 ILE cc_start: 0.9148 (mm) cc_final: 0.8905 (mt)
REVERT: c  204 TRP cc_start: 0.8302 (m100) cc_final: 0.7997 (m100)
REVERT: c  230 LYS cc_start: 0.8294 (pttp) cc_final: 0.7947 (ttpt)
REVERT: A    1 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6582 (ptp)
REVERT: A   61 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7666 (mt)
REVERT: A  154 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7089 (pt0)
REVERT: B   49 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7875 (mt)
REVERT: C   80 ILE cc_start: 0.9213 (mm) cc_final: 0.9003 (mt)
REVERT: C  198 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.7392 (tmt)
  outliers start: 31
  outliers final: 18
  residues processed: 150
  average time/residue: 0.2288
  time to fit residues: 49.6634
Evaluate side-chains
  153 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    1 MET
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue  106 LEU
Chi-restraints excluded: chain b residue  185 MET
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain b residue  219 ILE
Chi-restraints excluded: chain c residue   21 PHE
Chi-restraints excluded: chain c residue  182 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  228 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 140 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 84 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 135 optimal weight:    0.9990
   chunk 127 optimal weight:    4.9990
   chunk 123 optimal weight:    5.9990
   chunk 10 optimal weight:    0.1980
   overall best weight:    1.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.170185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.143952 restraints weight = 14044.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 1.66
r_work: 0.3560 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  11730  Z= 0.159
  Angle     :  0.613   9.517  16006  Z= 0.296
  Chirality :  0.042   0.157   1870
  Planarity :  0.005   0.070   1978
  Dihedral  :  4.315  20.636   1572
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.24 %
    Favored  : 81.30 %
  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:  1.42 (0.23), residues: 1446
  helix:  1.67 (0.17), residues: 986
  sheet: -0.77 (1.01), residues: 36
  loop : -0.59 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  55 
 HIS   0.003   0.001   HIS C 174 
 PHE   0.009   0.001   PHE D   5 
 TYR   0.010   0.001   TYR A 100 
 ARG   0.004   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (  720)
  hydrogen bonds       : angle       4.17540 ( 2136)
  covalent geometry    : bond        0.00403 (11730)
  covalent geometry    : angle       0.61285 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 1.202 
Fit side-chains
REVERT: a    1 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6946 (ptp)
REVERT: b  156 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7863 (mtm-85)
REVERT: c   80 ILE cc_start: 0.9145 (mm) cc_final: 0.8912 (mt)
REVERT: c  204 TRP cc_start: 0.8337 (m100) cc_final: 0.8008 (m-10)
REVERT: c  230 LYS cc_start: 0.8380 (pttp) cc_final: 0.7981 (ttpt)
REVERT: A   30 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7274 (mt-10)
REVERT: A   61 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7626 (mt)
REVERT: A  154 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7074 (pt0)
REVERT: C   80 ILE cc_start: 0.9222 (mm) cc_final: 0.9006 (mt)
REVERT: C  198 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7927 (ttt)
  outliers start: 29
  outliers final: 22
  residues processed: 154
  average time/residue: 0.3222
  time to fit residues: 70.8456
Evaluate side-chains
  160 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    1 MET
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue    9 LEU
Chi-restraints excluded: chain b residue  106 LEU
Chi-restraints excluded: chain b residue  185 MET
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain b residue  219 ILE
Chi-restraints excluded: chain c residue   21 PHE
Chi-restraints excluded: chain c residue  182 THR
Chi-restraints excluded: chain A residue    3 MET
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  228 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 65 optimal weight:    0.4980
   chunk 107 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 141 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0870
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5360

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.162104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.136563 restraints weight = 13955.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.58
r_work: 0.3406 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11730  Z= 0.112
  Angle     :  0.577  10.932  16006  Z= 0.276
  Chirality :  0.039   0.148   1870
  Planarity :  0.005   0.070   1978
  Dihedral  :  4.149  20.045   1572
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.84 %
    Favored  : 81.05 %
  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:  1.81 (0.23), residues: 1446
  helix:  1.98 (0.17), residues: 982
  sheet: -1.39 (0.67), residues: 66
  loop : -0.24 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP c  20 
 HIS   0.002   0.000   HIS a 186 
 PHE   0.009   0.001   PHE b   7 
 TYR   0.006   0.001   TYR A 100 
 ARG   0.005   0.000   ARG D  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03148 (  720)
  hydrogen bonds       : angle       4.00240 ( 2136)
  covalent geometry    : bond        0.00270 (11730)
  covalent geometry    : angle       0.57733 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.947 
Fit side-chains
REVERT: a    1 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6727 (ptp)
REVERT: b  156 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7806 (mtm-85)
REVERT: c   80 ILE cc_start: 0.9157 (mm) cc_final: 0.8924 (mt)
REVERT: c  204 TRP cc_start: 0.8269 (m100) cc_final: 0.8007 (m-10)
REVERT: A    1 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6356 (ptp)
REVERT: A   30 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7327 (mt-10)
REVERT: A  154 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7184 (pt0)
REVERT: C   80 ILE cc_start: 0.9210 (mm) cc_final: 0.8997 (mt)
REVERT: C  198 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8409 (tmm)
  outliers start: 25
  outliers final: 18
  residues processed: 146
  average time/residue: 0.2349
  time to fit residues: 49.3753
Evaluate side-chains
  151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    1 MET
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue    9 LEU
Chi-restraints excluded: chain b residue  106 LEU
Chi-restraints excluded: chain b residue  185 MET
Chi-restraints excluded: chain b residue  219 ILE
Chi-restraints excluded: chain c residue   21 PHE
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  228 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0570
   chunk 48 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 129 optimal weight:    3.9990
   chunk 127 optimal weight:    4.9990
   chunk 116 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 130 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    2.1902

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.156261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.130287 restraints weight = 13796.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.61
r_work: 0.3331 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  11730  Z= 0.192
  Angle     :  0.643  11.027  16006  Z= 0.309
  Chirality :  0.043   0.164   1870
  Planarity :  0.005   0.069   1978
  Dihedral  :  4.269  20.470   1572
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.43 %
    Favored  : 80.20 %
  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:  1.47 (0.23), residues: 1446
  helix:  1.74 (0.17), residues: 982
  sheet: -0.85 (1.01), residues: 36
  loop : -0.60 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP c  20 
 HIS   0.004   0.001   HIS C 174 
 PHE   0.010   0.001   PHE D   5 
 TYR   0.012   0.001   TYR A 100 
 ARG   0.008   0.000   ARG D  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03767 (  720)
  hydrogen bonds       : angle       4.18973 ( 2136)
  covalent geometry    : bond        0.00489 (11730)
  covalent geometry    : angle       0.64262 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 1.238 
Fit side-chains
REVERT: a    1 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6842 (ptp)
REVERT: b  156 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7835 (mtm-85)
REVERT: c   38 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8199 (mm)
REVERT: c   80 ILE cc_start: 0.9200 (mm) cc_final: 0.8953 (mt)
REVERT: c   88 MET cc_start: 0.8925 (mmm) cc_final: 0.8673 (mmp)
REVERT: c   91 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7674 (mp)
REVERT: c  204 TRP cc_start: 0.8354 (m100) cc_final: 0.8116 (m-10)
REVERT: c  230 LYS cc_start: 0.8405 (pttp) cc_final: 0.8127 (ttpt)
REVERT: A   30 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7314 (mt-10)
REVERT: A  154 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7269 (pt0)
REVERT: C   80 ILE cc_start: 0.9292 (mm) cc_final: 0.9054 (mt)
REVERT: C  198 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7277 (tmt)
REVERT: C  204 TRP cc_start: 0.8260 (m100) cc_final: 0.7960 (m100)
  outliers start: 28
  outliers final: 20
  residues processed: 152
  average time/residue: 0.2377
  time to fit residues: 52.0201
Evaluate side-chains
  161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    1 MET
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue    9 LEU
Chi-restraints excluded: chain b residue  106 LEU
Chi-restraints excluded: chain b residue  185 MET
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain b residue  219 ILE
Chi-restraints excluded: chain c residue   21 PHE
Chi-restraints excluded: chain c residue   38 ILE
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain A residue    3 MET
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  228 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 77 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 74 optimal weight:   10.0000
   chunk 101 optimal weight:    0.0980
   chunk 85 optimal weight:    6.9990
   chunk 94 optimal weight:    0.7980
   chunk 135 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.159970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.134248 restraints weight = 13846.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.58
r_work: 0.3386 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11730  Z= 0.121
  Angle     :  0.590  10.633  16006  Z= 0.283
  Chirality :  0.040   0.156   1870
  Planarity :  0.005   0.069   1978
  Dihedral  :  4.168  19.828   1572
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.43 %
    Favored  : 80.20 %
  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:  1.69 (0.23), residues: 1446
  helix:  1.91 (0.17), residues: 982
  sheet: -0.68 (1.03), residues: 36
  loop : -0.55 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP c  20 
 HIS   0.002   0.000   HIS a 101 
 PHE   0.008   0.001   PHE b   7 
 TYR   0.007   0.001   TYR A 100 
 ARG   0.006   0.000   ARG D  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  720)
  hydrogen bonds       : angle       4.03772 ( 2136)
  covalent geometry    : bond        0.00298 (11730)
  covalent geometry    : angle       0.58976 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 1.485 
Fit side-chains
REVERT: a    1 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6789 (ptp)
REVERT: b  156 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7845 (mtm-85)
REVERT: c   80 ILE cc_start: 0.9179 (mm) cc_final: 0.8928 (mt)
REVERT: c  204 TRP cc_start: 0.8322 (m100) cc_final: 0.8080 (m-10)
REVERT: A   30 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7274 (mt-10)
REVERT: A   61 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7683 (mt)
REVERT: A  154 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7217 (pt0)
REVERT: C   80 ILE cc_start: 0.9219 (mm) cc_final: 0.8987 (mt)
REVERT: C  198 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8310 (tmm)
  outliers start: 28
  outliers final: 20
  residues processed: 149
  average time/residue: 0.2803
  time to fit residues: 59.8983
Evaluate side-chains
  153 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 1.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    1 MET
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   20 SER
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue    9 LEU
Chi-restraints excluded: chain b residue  106 LEU
Chi-restraints excluded: chain b residue  185 MET
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain b residue  219 ILE
Chi-restraints excluded: chain c residue   21 PHE
Chi-restraints excluded: chain A residue    3 MET
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  227 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 83 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 134 optimal weight:    5.9990
   chunk 112 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.156172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.130593 restraints weight = 13869.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.65
r_work: 0.3334 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11730  Z= 0.177
  Angle     :  0.632  10.338  16006  Z= 0.304
  Chirality :  0.042   0.171   1870
  Planarity :  0.005   0.069   1978
  Dihedral  :  4.244  20.428   1572
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.77 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.44 (0.23), residues: 1446
  helix:  1.70 (0.17), residues: 994
  sheet: -0.78 (1.02), residues: 36
  loop : -0.65 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP c  20 
 HIS   0.004   0.001   HIS C 174 
 PHE   0.009   0.001   PHE B 175 
 TYR   0.012   0.001   TYR A 100 
 ARG   0.007   0.000   ARG D  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  720)
  hydrogen bonds       : angle       4.14860 ( 2136)
  covalent geometry    : bond        0.00449 (11730)
  covalent geometry    : angle       0.63200 (16006)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 1.734 
Fit side-chains
REVERT: a    1 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7016 (ptp)
REVERT: b  156 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7865 (mtm-85)
REVERT: c   80 ILE cc_start: 0.9199 (mm) cc_final: 0.8950 (mt)
REVERT: c   91 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7672 (mp)
REVERT: c  204 TRP cc_start: 0.8348 (m100) cc_final: 0.8113 (m-10)
REVERT: c  230 LYS cc_start: 0.8314 (pttp) cc_final: 0.8097 (ttpt)
REVERT: A   30 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7307 (mt-10)
REVERT: A   61 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7765 (mt)
REVERT: A  154 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7269 (pt0)
REVERT: C   80 ILE cc_start: 0.9284 (mm) cc_final: 0.9047 (mt)
REVERT: C  198 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7174 (tmt)
REVERT: C  204 TRP cc_start: 0.8292 (m100) cc_final: 0.8000 (m100)
  outliers start: 27
  outliers final: 21
  residues processed: 147
  average time/residue: 0.3232
  time to fit residues: 68.5323
Evaluate side-chains
  157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue    1 MET
Chi-restraints excluded: chain a residue    3 MET
Chi-restraints excluded: chain a residue   32 VAL
Chi-restraints excluded: chain a residue  171 MET
Chi-restraints excluded: chain a residue  181 VAL
Chi-restraints excluded: chain b residue    9 LEU
Chi-restraints excluded: chain b residue  106 LEU
Chi-restraints excluded: chain b residue  185 MET
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain b residue  219 ILE
Chi-restraints excluded: chain c residue   21 PHE
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain A residue    3 MET
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  171 MET
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  228 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 40 optimal weight:    0.7980
   chunk 131 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 113 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 111 optimal weight:    0.7980
   chunk 115 optimal weight:    0.0040
   chunk 140 optimal weight:    2.9990
   overall best weight:    0.9196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.159955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.134341 restraints weight = 13827.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.56
r_work: 0.3382 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11730  Z= 0.125
  Angle     :  0.595  10.097  16006  Z= 0.289
  Chirality :  0.041   0.200   1870
  Planarity :  0.005   0.070   1978
  Dihedral  :  4.162  20.169   1572
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.85 %
    Favored  : 79.86 %
  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:  1.66 (0.23), residues: 1446
  helix:  1.89 (0.17), residues: 992
  sheet: -0.70 (1.02), residues: 36
  loop : -0.63 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP c  20 
 HIS   0.002   0.000   HIS a 186 
 PHE   0.008   0.001   PHE b   7 
 TYR   0.009   0.001   TYR C  58 
 ARG   0.006   0.000   ARG D  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03314 (  720)
  hydrogen bonds       : angle       4.04186 ( 2136)
  covalent geometry    : bond        0.00303 (11730)
  covalent geometry    : angle       0.59513 (16006)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6255.01 seconds
wall clock time: 114 minutes 36.62 seconds (6876.62 seconds total)