Starting phenix.real_space_refine
on Wed Feb  4 10:06:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9umz_64333/02_2026/9umz_64333.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9umz_64333/02_2026/9umz_64333.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9umz_64333/02_2026/9umz_64333.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9umz_64333/02_2026/9umz_64333.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9umz_64333/02_2026/9umz_64333.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9umz_64333/02_2026/9umz_64333.map"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      28      5.49       5
     S      54      5.16       5
     C    6294      2.51       5
     N    1664      2.21       5
     O    1978      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10018
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1886
          Classifications: {'peptide': 245}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 232}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 1895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1895
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 12, 'TRANS': 232}
    Chain: "C"
      Number of atoms: 1895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1895
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 12, 'TRANS': 232}
    Chain: "D"
      Number of atoms: 1895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1895
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 12, 'TRANS': 232}
    Chain: "E"
      Number of atoms: 1887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1887
          Classifications: {'peptide': 244}
          Link IDs: {'PTRANS': 12, 'TRANS': 231}
    Chain: "K"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 560
          Classifications: {'RNA': 28}
          Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 5, 'rna3p': 22}
  Time building chain proxies: 1.89, per 1000 atoms: 0.19
  Number of scatterers: 10018
  At special positions: 0
  Unit cell: (71.25, 110.2, 120.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     P      28     15.00
     O    1978      8.00
     N    1664      7.00
     C    6294      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 116 " - pdb=" SG  CYS C 146 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 116 " - pdb=" SG  CYS E 146 " distance=2.03

  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: 0.59
  Conformation dependent library (CDL) restraints added in 497.6 milliseconds
  

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2298

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 0 sheets defined
      74.3% alpha, 0.0% beta
      0 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 11
    Processing helix  chain 'A' and resid 12 through 14
      No H-bonds generated for 'chain 'A' and resid 12 through 14'
    Processing helix  chain 'A' and resid 17 through 28
    Processing helix  chain 'A' and resid 34 through 46
      removed outlier: 3.688A  pdb=" N   ILE A  39 " --> pdb=" O   PRO A  35 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LYS A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   LEU A  42 " --> pdb=" O   ILE A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 64
      removed outlier: 3.659A  pdb=" N   LYS A  55 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE A  57 " --> pdb=" O   ASP A  53 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A  59 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 75
      removed outlier: 3.641A  pdb=" N   GLY A  73 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 91
      removed outlier: 3.569A  pdb=" N   ARG A  82 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 111
      removed outlier: 3.550A  pdb=" N   VAL A 107 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 122
      removed outlier: 4.378A  pdb=" N   ALA A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 147 through 152
      removed outlier: 4.101A  pdb=" N   GLY A 150 " --> pdb=" O   MET A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 182
      removed outlier: 3.585A  pdb=" N   TRP A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 197 through 206
      removed outlier: 3.623A  pdb=" N   LEU A 201 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 222
      removed outlier: 3.975A  pdb=" N   ARG A 215 " --> pdb=" O   PRO A 211 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 244
      removed outlier: 3.552A  pdb=" N   GLU A 236 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG A 243 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 11
      removed outlier: 4.094A  pdb=" N   PHE B  11 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 22
    Processing helix  chain 'B' and resid 22 through 27
      removed outlier: 3.702A  pdb=" N   ARG B  26 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLU B  27 " --> pdb=" O   ASP B  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 22 through 27'
    Processing helix  chain 'B' and resid 36 through 47
      removed outlier: 3.632A  pdb=" N   LYS B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LYS B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 64
      removed outlier: 3.710A  pdb=" N   LYS B  55 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   PHE B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 73
    Processing helix  chain 'B' and resid 76 through 91
    Processing helix  chain 'B' and resid 103 through 110
      removed outlier: 3.575A  pdb=" N   ALA B 108 " --> pdb=" O   PRO B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 122
      removed outlier: 3.586A  pdb=" N   THR B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ALA B 117 " --> pdb=" O   THR B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 133
    Processing helix  chain 'B' and resid 141 through 145
      removed outlier: 3.851A  pdb=" N   MET B 145 " --> pdb=" O   PRO B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 153
    Processing helix  chain 'B' and resid 159 through 182
      removed outlier: 4.191A  pdb=" N   TRP B 173 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLN B 174 " --> pdb=" O   TYR B 170 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LYS B 179 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 207
      removed outlier: 3.960A  pdb=" N   PHE B 197 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ASP B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
      Proline residue:  B 200  - end of helix
      removed outlier: 3.510A  pdb=" N   ALA B 203 " --> pdb=" O   ASP B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 222
      removed outlier: 3.613A  pdb=" N   LYS B 217 " --> pdb=" O   ASP B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 244
      removed outlier: 3.680A  pdb=" N   GLU B 236 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASN B 244 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 14
      removed outlier: 3.726A  pdb=" N   ARG C   6 " --> pdb=" O   SER C   2 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 29
    Processing helix  chain 'C' and resid 34 through 46
      removed outlier: 3.561A  pdb=" N   THR C  45 " --> pdb=" O   LYS C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 64
      removed outlier: 4.240A  pdb=" N   VAL C  59 " --> pdb=" O   LYS C  55 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE C  60 " --> pdb=" O   PHE C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 73
    Processing helix  chain 'C' and resid 76 through 91
      removed outlier: 4.034A  pdb=" N   ARG C  82 " --> pdb=" O   SER C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 111
      removed outlier: 3.639A  pdb=" N   LEU C 111 " --> pdb=" O   VAL C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 122
      removed outlier: 3.529A  pdb=" N   ALA C 121 " --> pdb=" O   ALA C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 126
    Processing helix  chain 'C' and resid 129 through 134
    Processing helix  chain 'C' and resid 141 through 145
    Processing helix  chain 'C' and resid 148 through 152
    Processing helix  chain 'C' and resid 159 through 182
      removed outlier: 3.903A  pdb=" N   TRP C 173 " --> pdb=" O   ALA C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 186
      removed outlier: 3.550A  pdb=" N   ARG C 186 " --> pdb=" O   VAL C 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 183 through 186'
    Processing helix  chain 'C' and resid 189 through 197
      removed outlier: 3.653A  pdb=" N   ASN C 195 " --> pdb=" O   THR C 191 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   PHE C 197 " --> pdb=" O   VAL C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 206
    Processing helix  chain 'C' and resid 211 through 222
      removed outlier: 3.592A  pdb=" N   ARG C 215 " --> pdb=" O   PRO C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 244
      removed outlier: 4.079A  pdb=" N   GLU C 236 " --> pdb=" O   SER C 232 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL C 237 " --> pdb=" O   ARG C 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 14
      removed outlier: 3.735A  pdb=" N   ARG D   6 " --> pdb=" O   SER D   2 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU D  10 " --> pdb=" O   ARG D   6 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLN D  14 " --> pdb=" O   GLU D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 28
    Processing helix  chain 'D' and resid 34 through 47
      removed outlier: 3.515A  pdb=" N   LEU D  42 " --> pdb=" O   ILE D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 64
      removed outlier: 4.162A  pdb=" N   LYS D  55 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE D  56 " --> pdb=" O   LYS D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 73
      removed outlier: 3.778A  pdb=" N   GLY D  73 " --> pdb=" O   VAL D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 91
    Processing helix  chain 'D' and resid 103 through 111
    Processing helix  chain 'D' and resid 111 through 122
    Processing helix  chain 'D' and resid 123 through 126
      removed outlier: 3.721A  pdb=" N   LEU D 126 " --> pdb=" O   LYS D 123 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 123 through 126'
    Processing helix  chain 'D' and resid 129 through 137
      removed outlier: 3.652A  pdb=" N   LEU D 135 " --> pdb=" O   ALA D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 146 through 153
      removed outlier: 3.602A  pdb=" N   PHE D 149 " --> pdb=" O   CYS D 146 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY D 150 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER D 151 " --> pdb=" O   ALA D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 182
      removed outlier: 3.641A  pdb=" N   THR D 165 " --> pdb=" O   ALA D 161 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TRP D 173 " --> pdb=" O   ALA D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 189 through 206
      removed outlier: 3.966A  pdb=" N   PHE D 197 " --> pdb=" O   VAL D 193 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ASP D 199 " --> pdb=" O   ASN D 195 " (cutoff:3.500A)
      Proline residue:  D 200  - end of helix
    Processing helix  chain 'D' and resid 211 through 222
      removed outlier: 3.700A  pdb=" N   LYS D 217 " --> pdb=" O   ASP D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 244
      removed outlier: 3.609A  pdb=" N   ASN D 244 " --> pdb=" O   ALA D 240 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 14
      removed outlier: 3.700A  pdb=" N   ALA E   8 " --> pdb=" O   TRP E   4 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN E  14 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 29
      removed outlier: 3.552A  pdb=" N   GLU E  27 " --> pdb=" O   ASP E  23 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 34 through 46
      removed outlier: 3.514A  pdb=" N   ILE E  38 " --> pdb=" O   ASP E  34 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY E  46 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 49 through 64
      removed outlier: 3.963A  pdb=" N   LYS E  55 " --> pdb=" O   VAL E  51 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE E  56 " --> pdb=" O   LYS E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 67 through 73
      removed outlier: 3.557A  pdb=" N   GLY E  73 " --> pdb=" O   VAL E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 91
      removed outlier: 3.701A  pdb=" N   ARG E  82 " --> pdb=" O   SER E  78 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 111
    Processing helix  chain 'E' and resid 111 through 122
      removed outlier: 3.588A  pdb=" N   ALA E 119 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA E 120 " --> pdb=" O   CYS E 116 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA E 121 " --> pdb=" O   ALA E 117 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU E 122 " --> pdb=" O   ALA E 118 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 129 through 134
    Processing helix  chain 'E' and resid 141 through 145
      removed outlier: 3.549A  pdb=" N   MET E 144 " --> pdb=" O   PRO E 141 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 152
    Processing helix  chain 'E' and resid 159 through 182
      removed outlier: 3.715A  pdb=" N   LEU E 172 " --> pdb=" O   GLU E 168 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   TRP E 173 " --> pdb=" O   ALA E 169 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLN E 174 " --> pdb=" O   TYR E 170 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA E 176 " --> pdb=" O   LEU E 172 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 189 through 196
    Processing helix  chain 'E' and resid 197 through 207
      removed outlier: 3.512A  pdb=" N   ALA E 203 " --> pdb=" O   ASP E 199 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA E 204 " --> pdb=" O   PRO E 200 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 211 through 222
      removed outlier: 3.588A  pdb=" N   VAL E 216 " --> pdb=" O   ASN E 212 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 232 through 244
      removed outlier: 3.663A  pdb=" N   GLU E 236 " --> pdb=" O   SER E 232 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASN E 244 " --> pdb=" O   ALA E 240 " (cutoff:3.500A)

    496 hydrogen bonds defined for protein.
    1434 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3069
        1.34 -     1.46: 1603
        1.46 -     1.58: 5436
        1.58 -     1.70: 55
        1.70 -     1.82: 98
  Bond restraints: 10261
  Sorted by residual:
  bond pdb=" CA  GLU B  31 "
       pdb=" CB  GLU B  31 "
    ideal  model  delta    sigma   weight residual
    1.526  1.556 -0.030 1.70e-02 3.46e+03 3.15e+00
  bond pdb=" CG  ARG B  26 "
       pdb=" CD  ARG B  26 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CB  GLU E  88 "
       pdb=" CG  GLU E  88 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.20e-01
  bond pdb=" CB  GLN D  87 "
       pdb=" CG  GLN D  87 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.74e-01
  bond pdb=" C   GLY D  79 "
       pdb=" O   GLY D  79 "
    ideal  model  delta    sigma   weight residual
    1.239  1.245 -0.006 7.10e-03 1.98e+04 7.71e-01
  ... (remaining 10256 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 13744
        1.75 -     3.50: 208
        3.50 -     5.25: 41
        5.25 -     7.00: 8
        7.00 -     8.74: 6
  Bond angle restraints: 14007
  Sorted by residual:
  angle pdb=" C   GLU A 138 "
        pdb=" N   ASN A 139 "
        pdb=" CA  ASN A 139 "
      ideal   model   delta    sigma   weight residual
     121.54  127.34   -5.80 1.91e+00 2.74e-01 9.24e+00
  angle pdb=" CB  MET D 133 "
        pdb=" CG  MET D 133 "
        pdb=" SD  MET D 133 "
      ideal   model   delta    sigma   weight residual
     112.70  121.44   -8.74 3.00e+00 1.11e-01 8.50e+00
  angle pdb=" CB  MET A 167 "
        pdb=" CG  MET A 167 "
        pdb=" SD  MET A 167 "
      ideal   model   delta    sigma   weight residual
     112.70  121.15   -8.45 3.00e+00 1.11e-01 7.94e+00
  angle pdb=" CB  MET C  84 "
        pdb=" CG  MET C  84 "
        pdb=" SD  MET C  84 "
      ideal   model   delta    sigma   weight residual
     112.70  121.05   -8.35 3.00e+00 1.11e-01 7.75e+00
  angle pdb=" CA  LYS B  89 "
        pdb=" CB  LYS B  89 "
        pdb=" CG  LYS B  89 "
      ideal   model   delta    sigma   weight residual
     114.10  119.54   -5.44 2.00e+00 2.50e-01 7.41e+00
  ... (remaining 14002 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 5651
       17.96 -    35.92: 523
       35.92 -    53.88: 104
       53.88 -    71.84: 44
       71.84 -    89.81: 11
  Dihedral angle restraints: 6333
    sinusoidal: 2781
      harmonic: 3552
  Sorted by residual:
  dihedral pdb=" CA  TYR B  30 "
           pdb=" C   TYR B  30 "
           pdb=" N   GLU B  31 "
           pdb=" CA  GLU B  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.07   17.93     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ASP E  34 "
           pdb=" CB  ASP E  34 "
           pdb=" CG  ASP E  34 "
           pdb=" OD1 ASP E  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -91.00   61.00     1      2.00e+01 2.50e-03 1.24e+01
  dihedral pdb=" CB  GLU D  20 "
           pdb=" CG  GLU D  20 "
           pdb=" CD  GLU D  20 "
           pdb=" OE1 GLU D  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.34  -88.34     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 6330 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1420
       0.057 -    0.114: 190
       0.114 -    0.171: 13
       0.171 -    0.228: 0
       0.228 -    0.285: 1
  Chirality restraints: 1624
  Sorted by residual:
  chirality pdb=" CB  ILE A 102 "
            pdb=" CA  ILE A 102 "
            pdb=" CG1 ILE A 102 "
            pdb=" CG2 ILE A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  VAL A 158 "
            pdb=" N   VAL A 158 "
            pdb=" C   VAL A 158 "
            pdb=" CB  VAL A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  ILE D 153 "
            pdb=" N   ILE D 153 "
            pdb=" C   ILE D 153 "
            pdb=" CB  ILE D 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 1621 not shown)

  Planarity restraints: 1686
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 141 "    0.029 5.00e-02 4.00e+02   4.49e-02 3.22e+00
        pdb=" N   PRO C 142 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO C 142 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 142 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  26 "   -0.123 9.50e-02 1.11e+02   5.55e-02 2.52e+00
        pdb=" NE  ARG B  26 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  26 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  26 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  26 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 111 "   -0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO E 112 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO E 112 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E 112 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1683 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 174
        2.67 -     3.23: 10148
        3.23 -     3.79: 15803
        3.79 -     4.34: 20710
        4.34 -     4.90: 32153
  Nonbonded interactions: 78988
  Sorted by model distance:
  nonbonded pdb=" O   LEU C  28 "
            pdb=" NH2 ARG D  64 "
     model   vdw
     2.114 3.120
  nonbonded pdb=" OE2 GLU A  27 "
            pdb=" OG  SER B  78 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OD2 ASP C 199 "
            pdb=" O2'   U K  15 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O   THR D  98 "
            pdb=" OG  SER D 101 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   SER E 159 "
            pdb=" OG1 THR E 162 "
     model   vdw
     2.237 3.040
  ... (remaining 78983 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 2 through 245)
  selection = (chain 'B' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 5 through 245))
  selection = (chain 'C' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 5 through 245))
  selection = (chain 'D' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 5 through 245))
  selection = (chain 'E' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 5 through 245))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.520
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
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      :  0.002   0.034  10263  Z= 0.107
  Angle     :  0.570   8.745  14011  Z= 0.283
  Chirality :  0.038   0.285   1624
  Planarity :  0.004   0.056   1686
  Dihedral  : 15.104  89.806   4029
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.23), residues: 1214
  helix: -0.49 (0.18), residues: 745
  sheet:  None (None), residues: 0
  loop :  0.38 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B  26 
 TYR   0.021   0.001   TYR B 170 
 PHE   0.023   0.002   PHE E 197 
 TRP   0.023   0.002   TRP C 114 
 HIS   0.001   0.000   HIS D 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (10261)
  covalent geometry    : angle       0.56940 (14007)
  SS BOND              : bond        0.00306 (    2)
  SS BOND              : angle       1.16625 (    4)
  hydrogen bonds       : bond        0.29379 (  496)
  hydrogen bonds       : angle       8.06804 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7960 (tpp80)
REVERT: B  134 ASN cc_start: 0.8791 (m110) cc_final: 0.8579 (m-40)
REVERT: E  144 MET cc_start: 0.7805 (ppp) cc_final: 0.7318 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0926
  time to fit residues: 32.1041
Evaluate side-chains
  199 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:   10.0000
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  87 GLN
A 244 ASN
B  17 ASN
B 202 HIS
C 212 ASN
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.170060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.140617 restraints weight = 16631.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.145283 restraints weight = 10405.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.148688 restraints weight = 7375.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.151162 restraints weight = 5661.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.152694 restraints weight = 4621.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10263  Z= 0.147
  Angle     :  0.612   8.703  14011  Z= 0.316
  Chirality :  0.041   0.149   1624
  Planarity :  0.004   0.047   1686
  Dihedral  : 12.231  79.790   1759
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.92 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.23), residues: 1214
  helix: -0.26 (0.17), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.21 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  26 
 TYR   0.016   0.002   TYR A 194 
 PHE   0.029   0.002   PHE B  11 
 TRP   0.018   0.002   TRP D  50 
 HIS   0.001   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10261)
  covalent geometry    : angle       0.61137 (14007)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       1.37484 (    4)
  hydrogen bonds       : bond        0.04832 (  496)
  hydrogen bonds       : angle       5.17973 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 211
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.7420 (ttm) cc_final: 0.7197 (ttm)
REVERT: B  134 ASN cc_start: 0.8835 (m110) cc_final: 0.8581 (m-40)
REVERT: B  174 GLN cc_start: 0.8634 (mp10) cc_final: 0.8314 (mp10)
REVERT: C   17 ASN cc_start: 0.8593 (t0) cc_final: 0.8277 (t0)
REVERT: C  185 MET cc_start: 0.7739 (tpt) cc_final: 0.7444 (tpt)
REVERT: D  147 MET cc_start: 0.7995 (tpt) cc_final: 0.7379 (tpt)
REVERT: E  144 MET cc_start: 0.7882 (ppp) cc_final: 0.6981 (ppp)
REVERT: E  242 TYR cc_start: 0.7487 (t80) cc_final: 0.7269 (t80)
  outliers start: 18
  outliers final: 8
  residues processed: 221
  average time/residue: 0.0902
  time to fit residues: 28.6969
Evaluate side-chains
  198 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 190
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain C residue   23 ASP
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  193 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 21 optimal weight:    0.1980
   chunk 31 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 73 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B  17 ASN
C 109 GLN
D  15 GLN
** E  87 GLN ** 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 = 0.4110 r_free = 0.4110 target = 0.172996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.143965 restraints weight = 16719.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.148756 restraints weight = 10341.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.152153 restraints weight = 7246.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.154594 restraints weight = 5539.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.156392 restraints weight = 4509.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10263  Z= 0.117
  Angle     :  0.560   9.939  14011  Z= 0.283
  Chirality :  0.040   0.175   1624
  Planarity :  0.004   0.048   1686
  Dihedral  : 12.286  82.759   1759
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.13 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.23), residues: 1214
  helix: -0.13 (0.18), residues: 786
  sheet:  None (None), residues: 0
  loop :  0.29 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 233 
 TYR   0.015   0.002   TYR C 170 
 PHE   0.023   0.002   PHE B  11 
 TRP   0.015   0.002   TRP D 114 
 HIS   0.001   0.000   HIS E 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10261)
  covalent geometry    : angle       0.55936 (14007)
  SS BOND              : bond        0.00418 (    2)
  SS BOND              : angle       1.21162 (    4)
  hydrogen bonds       : bond        0.04033 (  496)
  hydrogen bonds       : angle       4.77762 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 225
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.8035 (t80) cc_final: 0.7537 (t80)
REVERT: A  144 MET cc_start: 0.7388 (ttm) cc_final: 0.6498 (ttt)
REVERT: B   88 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7766 (tm-30)
REVERT: B  116 CYS cc_start: 0.7717 (m) cc_final: 0.7497 (m)
REVERT: B  134 ASN cc_start: 0.8816 (m110) cc_final: 0.8551 (m-40)
REVERT: B  174 GLN cc_start: 0.8495 (mp10) cc_final: 0.8184 (mp10)
REVERT: C   17 ASN cc_start: 0.8526 (t0) cc_final: 0.8217 (t0)
REVERT: D  147 MET cc_start: 0.7831 (tpt) cc_final: 0.7484 (tpt)
REVERT: E   75 MET cc_start: 0.4899 (ttt) cc_final: 0.4048 (ttt)
REVERT: E  144 MET cc_start: 0.7751 (ppp) cc_final: 0.7009 (ppp)
REVERT: E  210 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7699 (m-80)
REVERT: E  220 LYS cc_start: 0.7877 (mmtp) cc_final: 0.7628 (mmtp)
REVERT: E  242 TYR cc_start: 0.7612 (t80) cc_final: 0.7392 (t80)
  outliers start: 26
  outliers final: 13
  residues processed: 238
  average time/residue: 0.0896
  time to fit residues: 30.5765
Evaluate side-chains
  217 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 202
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  212 ASN
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  210 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 95 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 48 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 116 optimal weight:    2.9990
   chunk 110 optimal weight:    0.4980
   chunk 104 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
B  17 ASN
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.170381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.140259 restraints weight = 16911.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.144975 restraints weight = 10626.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.148362 restraints weight = 7541.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.150740 restraints weight = 5839.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.152551 restraints weight = 4802.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10263  Z= 0.135
  Angle     :  0.584  10.220  14011  Z= 0.295
  Chirality :  0.040   0.201   1624
  Planarity :  0.004   0.049   1686
  Dihedral  : 12.329  83.218   1759
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.24 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.23), residues: 1214
  helix: -0.05 (0.18), residues: 799
  sheet:  None (None), residues: 0
  loop :  0.26 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 233 
 TYR   0.018   0.002   TYR D 242 
 PHE   0.025   0.002   PHE B  60 
 TRP   0.015   0.002   TRP A 114 
 HIS   0.001   0.000   HIS E 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10261)
  covalent geometry    : angle       0.58270 (14007)
  SS BOND              : bond        0.00423 (    2)
  SS BOND              : angle       2.13033 (    4)
  hydrogen bonds       : bond        0.03793 (  496)
  hydrogen bonds       : angle       4.67431 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 213
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.8022 (t80) cc_final: 0.7418 (t80)
REVERT: A  144 MET cc_start: 0.7451 (ttm) cc_final: 0.6791 (ttt)
REVERT: A  217 LYS cc_start: 0.8985 (pttm) cc_final: 0.8687 (pttp)
REVERT: B   57 ILE cc_start: 0.7975 (mm) cc_final: 0.7733 (mm)
REVERT: B  134 ASN cc_start: 0.8821 (m110) cc_final: 0.8550 (m-40)
REVERT: C   17 ASN cc_start: 0.8606 (t0) cc_final: 0.8276 (t0)
REVERT: C   26 ARG cc_start: 0.8826 (mtm180) cc_final: 0.8560 (ttp-110)
REVERT: C  133 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7154 (ttp)
REVERT: C  170 TYR cc_start: 0.8344 (t80) cc_final: 0.7897 (t80)
REVERT: C  185 MET cc_start: 0.7884 (tpt) cc_final: 0.7598 (tpt)
REVERT: C  236 GLU cc_start: 0.7522 (pm20) cc_final: 0.7312 (pm20)
REVERT: E   75 MET cc_start: 0.5062 (ttt) cc_final: 0.4188 (ttt)
REVERT: E  144 MET cc_start: 0.7777 (ppp) cc_final: 0.7008 (ppp)
REVERT: E  168 GLU cc_start: 0.8870 (tp30) cc_final: 0.8175 (tp30)
REVERT: E  210 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7602 (m-80)
REVERT: E  242 TYR cc_start: 0.7650 (t80) cc_final: 0.7253 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 228
  average time/residue: 0.1027
  time to fit residues: 32.9621
Evaluate side-chains
  222 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 203
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain E residue   38 ILE
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  210 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 78 optimal weight:    0.1980
   chunk 49 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 212 ASN
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.171727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.142425 restraints weight = 16590.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.147000 restraints weight = 10343.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.150408 restraints weight = 7338.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152912 restraints weight = 5627.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.154525 restraints weight = 4579.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10263  Z= 0.116
  Angle     :  0.554  10.800  14011  Z= 0.279
  Chirality :  0.039   0.185   1624
  Planarity :  0.004   0.048   1686
  Dihedral  : 12.309  84.601   1759
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.14 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.23), residues: 1214
  helix:  0.02 (0.18), residues: 793
  sheet:  None (None), residues: 0
  loop :  0.30 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 233 
 TYR   0.016   0.001   TYR D 242 
 PHE   0.026   0.002   PHE B  60 
 TRP   0.014   0.002   TRP E   4 
 HIS   0.001   0.000   HIS E 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (10261)
  covalent geometry    : angle       0.55398 (14007)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       1.31023 (    4)
  hydrogen bonds       : bond        0.03557 (  496)
  hydrogen bonds       : angle       4.54669 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 201
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7938 (t80) cc_final: 0.7483 (t80)
REVERT: A  144 MET cc_start: 0.7501 (ttm) cc_final: 0.6472 (ttm)
REVERT: A  210 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6630 (m-80)
REVERT: B   57 ILE cc_start: 0.7915 (mm) cc_final: 0.7678 (mm)
REVERT: B  134 ASN cc_start: 0.8775 (m110) cc_final: 0.8517 (m-40)
REVERT: C   17 ASN cc_start: 0.8566 (t0) cc_final: 0.8260 (t0)
REVERT: C   26 ARG cc_start: 0.8784 (mtm180) cc_final: 0.8559 (ttp-110)
REVERT: C  133 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7218 (ttp)
REVERT: C  170 TYR cc_start: 0.8390 (t80) cc_final: 0.8035 (t80)
REVERT: E  144 MET cc_start: 0.7716 (ppp) cc_final: 0.7005 (ppp)
REVERT: E  242 TYR cc_start: 0.7728 (t80) cc_final: 0.7443 (t80)
  outliers start: 24
  outliers final: 17
  residues processed: 218
  average time/residue: 0.0943
  time to fit residues: 29.3917
Evaluate side-chains
  209 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 190
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain E residue   38 ILE
Chi-restraints excluded: chain E residue  115 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 75 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 39 optimal weight:    0.2980
   chunk 66 optimal weight:    4.9990
   chunk 111 optimal weight:    7.9990
   chunk 108 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 212 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 = 0.4095 r_free = 0.4095 target = 0.171917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.142527 restraints weight = 16618.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.147177 restraints weight = 10322.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.150584 restraints weight = 7282.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152816 restraints weight = 5588.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.154794 restraints weight = 4594.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10263  Z= 0.120
  Angle     :  0.585  11.590  14011  Z= 0.291
  Chirality :  0.039   0.172   1624
  Planarity :  0.004   0.048   1686
  Dihedral  : 12.288  85.715   1759
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 21.44 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.24), residues: 1214
  helix:  0.08 (0.18), residues: 793
  sheet:  None (None), residues: 0
  loop :  0.32 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 233 
 TYR   0.017   0.001   TYR A 170 
 PHE   0.017   0.002   PHE D 149 
 TRP   0.016   0.002   TRP E   4 
 HIS   0.001   0.000   HIS C 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10261)
  covalent geometry    : angle       0.58459 (14007)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       1.22132 (    4)
  hydrogen bonds       : bond        0.03502 (  496)
  hydrogen bonds       : angle       4.51004 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 208
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7961 (t80) cc_final: 0.7553 (t80)
REVERT: A  144 MET cc_start: 0.7425 (ttm) cc_final: 0.6408 (ttm)
REVERT: A  210 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6608 (m-80)
REVERT: B   57 ILE cc_start: 0.7923 (mm) cc_final: 0.7684 (mm)
REVERT: B  134 ASN cc_start: 0.8779 (m110) cc_final: 0.8524 (m-40)
REVERT: C   26 ARG cc_start: 0.8774 (mtm180) cc_final: 0.8546 (ttp-110)
REVERT: C  133 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7127 (ttp)
REVERT: C  170 TYR cc_start: 0.8402 (t80) cc_final: 0.8126 (t80)
REVERT: C  236 GLU cc_start: 0.7938 (mp0) cc_final: 0.7695 (pm20)
REVERT: E  144 MET cc_start: 0.7824 (ppp) cc_final: 0.7106 (ppp)
REVERT: E  242 TYR cc_start: 0.7591 (t80) cc_final: 0.7320 (t80)
  outliers start: 29
  outliers final: 19
  residues processed: 226
  average time/residue: 0.1025
  time to fit residues: 32.8046
Evaluate side-chains
  213 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   38 ILE
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  174 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 24 optimal weight:    0.4980
   chunk 87 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0010
   chunk 51 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 212 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 = 0.4119 r_free = 0.4119 target = 0.174170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.144741 restraints weight = 16652.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.149404 restraints weight = 10417.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.152770 restraints weight = 7377.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.155089 restraints weight = 5690.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.156933 restraints weight = 4679.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10263  Z= 0.113
  Angle     :  0.588  12.460  14011  Z= 0.290
  Chirality :  0.039   0.160   1624
  Planarity :  0.004   0.048   1686
  Dihedral  : 12.243  89.643   1759
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.44 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.24), residues: 1214
  helix:  0.07 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop :  0.32 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 233 
 TYR   0.018   0.001   TYR A 170 
 PHE   0.013   0.002   PHE E 209 
 TRP   0.018   0.002   TRP E   4 
 HIS   0.001   0.000   HIS E 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10261)
  covalent geometry    : angle       0.58787 (14007)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       0.99712 (    4)
  hydrogen bonds       : bond        0.03351 (  496)
  hydrogen bonds       : angle       4.44967 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 207
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7947 (t80) cc_final: 0.7469 (t80)
REVERT: A  144 MET cc_start: 0.7418 (ttm) cc_final: 0.6359 (ttm)
REVERT: A  198 ARG cc_start: 0.7561 (mpp80) cc_final: 0.7339 (mpp80)
REVERT: A  210 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6546 (m-80)
REVERT: B  134 ASN cc_start: 0.8784 (m110) cc_final: 0.8533 (m-40)
REVERT: C   26 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8566 (ttp-110)
REVERT: C  133 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7248 (ttp)
REVERT: C  170 TYR cc_start: 0.8446 (t80) cc_final: 0.8216 (t80)
REVERT: C  236 GLU cc_start: 0.7978 (mp0) cc_final: 0.7768 (pm20)
REVERT: D  116 CYS cc_start: 0.8418 (m) cc_final: 0.7644 (t)
REVERT: E  144 MET cc_start: 0.7863 (ppp) cc_final: 0.7099 (ppp)
REVERT: E  242 TYR cc_start: 0.7704 (t80) cc_final: 0.7412 (t80)
  outliers start: 29
  outliers final: 17
  residues processed: 227
  average time/residue: 0.0947
  time to fit residues: 30.8415
Evaluate side-chains
  214 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 195
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain E residue   38 ILE
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  174 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 GLN
C 109 GLN
D 139 ASN
D 206 ASN
** E 212 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 = 0.4160 r_free = 0.4160 target = 0.176891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.148283 restraints weight = 16447.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.152951 restraints weight = 10227.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.156277 restraints weight = 7227.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.158700 restraints weight = 5536.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.160190 restraints weight = 4504.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10263  Z= 0.149
  Angle     :  0.639  12.263  14011  Z= 0.313
  Chirality :  0.040   0.147   1624
  Planarity :  0.004   0.048   1686
  Dihedral  : 12.270  91.442   1759
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 23.25 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.24), residues: 1214
  helix:  0.05 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop :  0.27 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 233 
 TYR   0.020   0.002   TYR A 170 
 PHE   0.017   0.002   PHE D 197 
 TRP   0.028   0.002   TRP E   4 
 HIS   0.002   0.001   HIS C 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10261)
  covalent geometry    : angle       0.63883 (14007)
  SS BOND              : bond        0.00280 (    2)
  SS BOND              : angle       1.39270 (    4)
  hydrogen bonds       : bond        0.03547 (  496)
  hydrogen bonds       : angle       4.54747 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.8082 (t80) cc_final: 0.7386 (t80)
REVERT: A  144 MET cc_start: 0.7569 (ttm) cc_final: 0.6850 (ttm)
REVERT: A  147 MET cc_start: 0.7988 (tpt) cc_final: 0.7448 (tpt)
REVERT: A  210 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6625 (m-80)
REVERT: B  134 ASN cc_start: 0.8818 (m110) cc_final: 0.8574 (m-40)
REVERT: C   26 ARG cc_start: 0.8843 (mtm180) cc_final: 0.8616 (ttp-110)
REVERT: C  133 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7317 (ttp)
REVERT: D  116 CYS cc_start: 0.8477 (m) cc_final: 0.7632 (t)
REVERT: D  126 LEU cc_start: 0.8950 (mp) cc_final: 0.8740 (mp)
REVERT: D  143 GLU cc_start: 0.6874 (pm20) cc_final: 0.6555 (pm20)
REVERT: E  144 MET cc_start: 0.7830 (ppp) cc_final: 0.7173 (ppp)
REVERT: E  168 GLU cc_start: 0.8921 (tp30) cc_final: 0.8538 (tp30)
REVERT: E  242 TYR cc_start: 0.7630 (t80) cc_final: 0.7161 (t80)
  outliers start: 27
  outliers final: 18
  residues processed: 227
  average time/residue: 0.0953
  time to fit residues: 31.3419
Evaluate side-chains
  226 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain E residue   38 ILE
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  174 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 76 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 94 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
D 139 ASN
E 212 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.179051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.152784 restraints weight = 15757.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.156993 restraints weight = 10190.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.159950 restraints weight = 7303.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.162013 restraints weight = 5692.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.163532 restraints weight = 4686.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10263  Z= 0.131
  Angle     :  0.628  12.271  14011  Z= 0.308
  Chirality :  0.040   0.148   1624
  Planarity :  0.004   0.049   1686
  Dihedral  : 12.273  92.711   1759
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 24.95 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.24), residues: 1214
  helix: -0.01 (0.18), residues: 794
  sheet:  None (None), residues: 0
  loop :  0.27 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 233 
 TYR   0.021   0.001   TYR A 170 
 PHE   0.020   0.002   PHE E 209 
 TRP   0.028   0.002   TRP E   4 
 HIS   0.001   0.000   HIS C 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10261)
  covalent geometry    : angle       0.62794 (14007)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       1.25235 (    4)
  hydrogen bonds       : bond        0.03441 (  496)
  hydrogen bonds       : angle       4.50336 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 211
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.8003 (t80) cc_final: 0.7319 (t80)
REVERT: A  144 MET cc_start: 0.7520 (ttm) cc_final: 0.6319 (ttm)
REVERT: A  147 MET cc_start: 0.7871 (tpt) cc_final: 0.7444 (tpt)
REVERT: A  198 ARG cc_start: 0.7601 (mpp80) cc_final: 0.7385 (mpp80)
REVERT: B  134 ASN cc_start: 0.8701 (m110) cc_final: 0.8444 (m-40)
REVERT: C   26 ARG cc_start: 0.8729 (mtm180) cc_final: 0.8504 (ttp-110)
REVERT: C  133 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7381 (ttp)
REVERT: D  116 CYS cc_start: 0.8369 (m) cc_final: 0.7612 (t)
REVERT: D  133 MET cc_start: 0.7716 (mmm) cc_final: 0.7380 (mmm)
REVERT: E  144 MET cc_start: 0.7833 (ppp) cc_final: 0.7253 (ppp)
REVERT: E  168 GLU cc_start: 0.8796 (tp30) cc_final: 0.8435 (tp30)
REVERT: E  242 TYR cc_start: 0.7272 (t80) cc_final: 0.6860 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 225
  average time/residue: 0.1002
  time to fit residues: 31.9779
Evaluate side-chains
  218 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 201
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain E residue   38 ILE
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  174 GLN
Chi-restraints excluded: chain E residue  212 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 61 optimal weight:    0.3980
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
E 134 ASN
E 212 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.165873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137910 restraints weight = 16158.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.141758 restraints weight = 10887.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.144521 restraints weight = 8121.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.146383 restraints weight = 6512.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.147847 restraints weight = 5523.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10263  Z= 0.177
  Angle     :  0.684  12.231  14011  Z= 0.341
  Chirality :  0.041   0.141   1624
  Planarity :  0.004   0.049   1686
  Dihedral  : 12.353  92.938   1759
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 25.45 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.24), residues: 1214
  helix: -0.03 (0.18), residues: 787
  sheet:  None (None), residues: 0
  loop :  0.24 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 233 
 TYR   0.025   0.002   TYR C 242 
 PHE   0.024   0.003   PHE E 209 
 TRP   0.027   0.002   TRP E   4 
 HIS   0.002   0.001   HIS C 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (10261)
  covalent geometry    : angle       0.68365 (14007)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       1.48897 (    4)
  hydrogen bonds       : bond        0.03713 (  496)
  hydrogen bonds       : angle       4.65710 ( 1434)

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.8069 (t80) cc_final: 0.7426 (t80)
REVERT: A  144 MET cc_start: 0.7709 (ttm) cc_final: 0.6739 (ttm)
REVERT: A  147 MET cc_start: 0.8147 (tpt) cc_final: 0.7671 (tpt)
REVERT: A  210 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6664 (m-80)
REVERT: B  134 ASN cc_start: 0.8761 (m110) cc_final: 0.8504 (m-40)
REVERT: C   26 ARG cc_start: 0.8862 (mtm180) cc_final: 0.8631 (ttp-110)
REVERT: C  133 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7457 (ttp)
REVERT: C  219 LEU cc_start: 0.8759 (mt) cc_final: 0.8549 (mt)
REVERT: D  116 CYS cc_start: 0.8523 (m) cc_final: 0.7684 (t)
REVERT: D  133 MET cc_start: 0.7858 (mmm) cc_final: 0.7556 (mmm)
REVERT: D  143 GLU cc_start: 0.6781 (pm20) cc_final: 0.6524 (pm20)
REVERT: E  144 MET cc_start: 0.7924 (ppp) cc_final: 0.7325 (ppp)
REVERT: E  168 GLU cc_start: 0.8860 (tp30) cc_final: 0.8440 (tp30)
REVERT: E  242 TYR cc_start: 0.7470 (t80) cc_final: 0.6990 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 220
  average time/residue: 0.0931
  time to fit residues: 29.4827
Evaluate side-chains
  224 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 204
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   38 ILE
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  134 ASN
Chi-restraints excluded: chain E residue  174 GLN
Chi-restraints excluded: chain E residue  212 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 105 optimal weight:    0.0870
   chunk 84 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0060
   chunk 11 optimal weight:    4.9990
   chunk 99 optimal weight:    0.0070
   chunk 46 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   chunk 118 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.3592

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

Flipped N/Q/H residues before XYZ refinement:
E 134 ASN
E 212 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.180940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.155214 restraints weight = 15895.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.159250 restraints weight = 10345.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.162185 restraints weight = 7493.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.164238 restraints weight = 5834.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.165548 restraints weight = 4811.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10263  Z= 0.124
  Angle     :  0.660  12.390  14011  Z= 0.325
  Chirality :  0.040   0.142   1624
  Planarity :  0.004   0.049   1686
  Dihedral  : 12.353  94.567   1759
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 26.95 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.24), residues: 1214
  helix: -0.05 (0.18), residues: 789
  sheet:  None (None), residues: 0
  loop :  0.27 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 233 
 TYR   0.023   0.002   TYR C 242 
 PHE   0.025   0.002   PHE E 209 
 TRP   0.021   0.002   TRP E 173 
 HIS   0.001   0.000   HIS C 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10261)
  covalent geometry    : angle       0.66011 (14007)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       1.11584 (    4)
  hydrogen bonds       : bond        0.03408 (  496)
  hydrogen bonds       : angle       4.53166 ( 1434)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1681.11 seconds
wall clock time: 29 minutes 54.03 seconds (1794.03 seconds total)