Starting phenix.real_space_refine
on Fri Jul 25 20:04:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y26_33586/07_2025/7y26_33586.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y26_33586/07_2025/7y26_33586.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2025/7y26_33586.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2025/7y26_33586.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2025/7y26_33586.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2025/7y26_33586.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.154
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5117      2.51       5
     N    1355      2.21       5
     O    1489      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8014
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2420
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 127
    Chain: "B"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1687
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 4, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 145
          Unresolved non-hydrogen angles: 169
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 8, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 91
    Chain: "C"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 22
          Classifications: {'peptide': 3}
          Modifications used: {'PEPT-D': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'DPN%PEPT-D:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 44
          Classifications: {'peptide': 5}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 4}
    Chain: "D"
      Number of atoms: 1633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1633
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 9, 'TRANS': 212}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "E"
      Number of atoms: 1881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 1881
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 10, 'TRANS': 259}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 279
          Unresolved non-hydrogen angles: 344
          Unresolved non-hydrogen dihedrals: 239
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 127
    Chain: "F"
      Number of atoms: 327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 327
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 44
  Time building chain proxies: 5.28, per 1000 atoms: 0.66
  Number of scatterers: 8014
  At special positions: 0
  Unit cell: (92.02, 128.14, 129.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1489      8.00
     N    1355      7.00
     C    5117      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C   2 " - pdb=" SG  CYS C   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 115 " - pdb=" SG  CYS E 193 " 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
  Links applied
    TRANS
      " DTR C   4 " - " PHE C   3 "
  Time building additional restraints: 2.17
  Conformation dependent library (CDL) restraints added in 974.8 milliseconds
  

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DPN C   1 "
        pdb=" CB  DTR C   4 "
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      37.7% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 26
    Processing helix  chain 'A' and resid 29 through 35
      removed outlier: 3.578A  pdb=" N   ILE A  33 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 31
      removed outlier: 3.942A  pdb=" N   ASN B  22 " --> pdb=" O   MET B  18 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU B  23 " --> pdb=" O   ILE B  19 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   GLU B  28 " --> pdb=" O   ARG B  24 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   LYS B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 55
    Processing helix  chain 'B' and resid 88 through 92
      removed outlier: 3.916A  pdb=" N   ASP B  91 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 145 through 156
      removed outlier: 3.690A  pdb=" N   GLY B 156 " --> pdb=" O   LYS B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 170
      removed outlier: 4.291A  pdb=" N   ARG B 169 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 202
      removed outlier: 4.210A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   SER B 201 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR B 202 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 243
      removed outlier: 3.812A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 56
      removed outlier: 3.879A  pdb=" N   GLY D  56 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 53 through 56'
    Processing helix  chain 'D' and resid 62 through 65
      removed outlier: 3.794A  pdb=" N   LYS D  65 " --> pdb=" O   ASP D  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 62 through 65'
    Processing helix  chain 'E' and resid 42 through 71
    Processing helix  chain 'E' and resid 77 through 93
      removed outlier: 3.858A  pdb=" N   TYR E  81 " --> pdb=" O   ILE E  77 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET E  93 " --> pdb=" O   ASP E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 105
    Processing helix  chain 'E' and resid 112 through 146
      removed outlier: 4.022A  pdb=" N   ARG E 116 " --> pdb=" O   LYS E 112 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   VAL E 117 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE E 127 " --> pdb=" O   GLY E 123 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ILE E 130 " --> pdb=" O   GLN E 126 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU E 142 " --> pdb=" O   ILE E 138 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA E 143 " --> pdb=" O   ASP E 139 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL E 144 " --> pdb=" O   ARG E 140 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 152
      removed outlier: 3.872A  pdb=" N   LYS E 152 " --> pdb=" O   LYS E 149 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 155 through 175
      removed outlier: 3.636A  pdb=" N   THR E 163 " --> pdb=" O   ALA E 159 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   MET E 164 " --> pdb=" O   LYS E 160 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ALA E 165 " --> pdb=" O   MET E 161 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL E 166 " --> pdb=" O   ILE E 162 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   TRP E 167 " --> pdb=" O   THR E 163 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 176 through 178
      No H-bonds generated for 'chain 'E' and resid 176 through 178'
    Processing helix  chain 'E' and resid 203 through 238
      removed outlier: 5.486A  pdb=" N   VAL E 219 " --> pdb=" O   LEU E 215 " (cutoff:3.500A)
      Proline residue:  E 220  - end of helix
      removed outlier: 3.893A  pdb=" N   CYS E 227 " --> pdb=" O   ILE E 223 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TYR E 228 " --> pdb=" O   ILE E 224 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER E 238 " --> pdb=" O   LYS E 234 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 249 through 282
      Proline residue:  E 271  - end of helix
    Processing helix  chain 'E' and resid 287 through 301
      removed outlier: 3.665A  pdb=" N   LYS E 291 " --> pdb=" O   THR E 287 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 302 through 314
      removed outlier: 3.783A  pdb=" N   CYS E 306 " --> pdb=" O   TYR E 302 " (cutoff:3.500A)
      Proline residue:  E 309  - end of helix
    Processing helix  chain 'E' and resid 316 through 318
      No H-bonds generated for 'chain 'E' and resid 316 through 318'
    Processing helix  chain 'E' and resid 319 through 326
      removed outlier: 3.693A  pdb=" N   VAL E 326 " --> pdb=" O   SER E 322 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 12 through 24
      removed outlier: 3.608A  pdb=" N   ASN F  24 " --> pdb=" O   LYS F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 44
      removed outlier: 3.614A  pdb=" N   HIS F  44 " --> pdb=" O   TYR F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 48
      removed outlier: 3.827A  pdb=" N   ASP F  48 " --> pdb=" O   ALA F  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 45 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51
      removed outlier: 3.645A  pdb=" N   ARG A  49 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   CYS A 317 " --> pdb=" O   GLY A 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 63
      removed outlier: 3.538A  pdb=" N   TYR A  59 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ALA A  73 " --> pdb=" O   TYR A  59 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   MET A  61 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   VAL A  71 " --> pdb=" O   MET A  61 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   TRP A  63 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LEU A  69 " --> pdb=" O   TRP A  63 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A  74 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   LYS A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   HIS A  91 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ASP A  83 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LYS A  89 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105
      removed outlier: 3.633A  pdb=" N   THR A 102 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A 115 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   GLY A 116 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   ILE A 120 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ASN A 125 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   VAL A 135 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 153
      removed outlier: 7.053A  pdb=" N   SER A 160 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   CYS A 149 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL A 158 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   PHE A 151 " --> pdb=" O   GLN A 156 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   GLN A 156 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   SER A 161 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   THR A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   THR A 178 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192
      removed outlier: 3.913A  pdb=" N   SER A 189 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLY A 202 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLN A 220 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ASP A 212 " --> pdb=" O   CYS A 218 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   CYS A 218 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 234
      removed outlier: 7.029A  pdb=" N   GLY A 244 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   ILE A 232 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   PHE A 234 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ALA A 240 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   MET A 262 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ASP A 254 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   GLU A 260 " --> pdb=" O   ASP A 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 278
      removed outlier: 4.087A  pdb=" N   SER A 275 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   ASN A 293 " --> pdb=" O   TYR A 289 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLY A 306 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASP A 298 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ARG A 304 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 76
      removed outlier: 3.724A  pdb=" N   PHE B  70 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASP B  85 " --> pdb=" O   PHE B  70 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   ARG B  35 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 9.323A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR B 212 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU B 143 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3
    Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 6
      removed outlier: 3.650A  pdb=" N   ARG D  18 " --> pdb=" O   MET D  83 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60
      removed outlier: 5.163A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG D  98 " --> pdb=" O   PHE D 110 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   PHE D 110 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135
      removed outlier: 3.571A  pdb=" N   THR D 231 " --> pdb=" O   TYR D 215 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TYR D 163 " --> pdb=" O   MET D 218 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE D 177 " --> pdb=" O   TRP D 164 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR D 178 " --> pdb=" O   ASN D 182 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASN D 182 " --> pdb=" O   TYR D 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 182 through 185
      removed outlier: 3.604A  pdb=" N   GLY E 182 " --> pdb=" O   THR E 194 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1155 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2594
        1.34 -     1.46: 2021
        1.46 -     1.58: 3492
        1.58 -     1.70: 0
        1.70 -     1.81: 74
  Bond restraints: 8181
  Sorted by residual:
  bond pdb=" N   MET D 180 "
       pdb=" CA  MET D 180 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.51e+00
  bond pdb=" C   VAL D  64 "
       pdb=" O   VAL D  64 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.011 1.19e-02 7.06e+03 8.10e-01
  bond pdb=" CA  GLU A 130 "
       pdb=" CB  GLU A 130 "
    ideal  model  delta    sigma   weight residual
    1.532  1.545 -0.013 1.51e-02 4.39e+03 6.93e-01
  bond pdb=" C   ALA A 287 "
       pdb=" N   GLY A 288 "
    ideal  model  delta    sigma   weight residual
    1.329  1.340 -0.011 1.39e-02 5.18e+03 6.52e-01
  bond pdb=" CG1 ILE E 174 "
       pdb=" CD1 ILE E 174 "
    ideal  model  delta    sigma   weight residual
    1.513  1.484  0.029 3.90e-02 6.57e+02 5.54e-01
  ... (remaining 8176 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 10763
        1.27 -     2.53: 324
        2.53 -     3.80: 63
        3.80 -     5.07: 20
        5.07 -     6.33: 5
  Bond angle restraints: 11175
  Sorted by residual:
  angle pdb=" CA  GLU A 130 "
        pdb=" CB  GLU A 130 "
        pdb=" CG  GLU A 130 "
      ideal   model   delta    sigma   weight residual
     114.10  120.43   -6.33 2.00e+00 2.50e-01 1.00e+01
  angle pdb=" C   ARG D 179 "
        pdb=" N   MET D 180 "
        pdb=" CA  MET D 180 "
      ideal   model   delta    sigma   weight residual
     121.54  126.79   -5.25 1.91e+00 2.74e-01 7.57e+00
  angle pdb=" C   ILE E 174 "
        pdb=" CA  ILE E 174 "
        pdb=" CB  ILE E 174 "
      ideal   model   delta    sigma   weight residual
     111.29  106.80    4.49 1.64e+00 3.72e-01 7.49e+00
  angle pdb=" CA  MET D 180 "
        pdb=" CB  MET D 180 "
        pdb=" CG  MET D 180 "
      ideal   model   delta    sigma   weight residual
     114.10  119.28   -5.18 2.00e+00 2.50e-01 6.72e+00
  angle pdb=" C   GLY D 197 "
        pdb=" N   THR D 198 "
        pdb=" CA  THR D 198 "
      ideal   model   delta    sigma   weight residual
     122.40  126.07   -3.67 1.45e+00 4.76e-01 6.41e+00
  ... (remaining 11170 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4373
       17.98 -    35.96: 296
       35.96 -    53.94: 55
       53.94 -    71.92: 6
       71.92 -    89.90: 2
  Dihedral angle restraints: 4732
    sinusoidal: 1514
      harmonic: 3218
  Sorted by residual:
  dihedral pdb=" CB  CYS E 115 "
           pdb=" SG  CYS E 115 "
           pdb=" SG  CYS E 193 "
           pdb=" CB  CYS E 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.90   89.90     1      1.00e+01 1.00e-02 9.58e+01
  dihedral pdb=" CB  CYS D 147 "
           pdb=" SG  CYS D 147 "
           pdb=" SG  CYS D 217 "
           pdb=" CB  CYS D 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.60  -88.40     1      1.00e+01 1.00e-02 9.33e+01
  dihedral pdb=" CA  THR D 160 "
           pdb=" C   THR D 160 "
           pdb=" N   TYR D 161 "
           pdb=" CA  TYR D 161 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.71  -16.29     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 4729 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 858
       0.032 -    0.065: 305
       0.065 -    0.097: 107
       0.097 -    0.129: 50
       0.129 -    0.161: 7
  Chirality restraints: 1327
  Sorted by residual:
  chirality pdb=" CB  VAL E 106 "
            pdb=" CA  VAL E 106 "
            pdb=" CG1 VAL E 106 "
            pdb=" CG2 VAL E 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  MET D 180 "
            pdb=" N   MET D 180 "
            pdb=" C   MET D 180 "
            pdb=" CB  MET D 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  ILE D  58 "
            pdb=" N   ILE D  58 "
            pdb=" C   ILE D  58 "
            pdb=" CB  ILE D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.29e-01
  ... (remaining 1324 not shown)

  Planarity restraints: 1418
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F  48 "   -0.026 5.00e-02 4.00e+02   3.88e-02 2.41e+00
        pdb=" N   PRO F  49 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO F  49 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO F  49 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E 214 "    0.008 2.00e-02 2.50e+03   1.51e-02 2.28e+00
        pdb=" C   ILE E 214 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ILE E 214 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU E 215 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  74 "    0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO D  75 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO D  75 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D  75 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1415 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 707
        2.74 -     3.28: 7563
        3.28 -     3.82: 12108
        3.82 -     4.36: 12622
        4.36 -     4.90: 24172
  Nonbonded interactions: 57172
  Sorted by model distance:
  nonbonded pdb=" O   LEU D 153 "
            pdb=" OG1 THR D 160 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NH2 ARG D  67 "
            pdb=" OD2 ASP D  90 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" NZ  LYS D 151 "
            pdb=" O   SER D 152 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" O   GLY A 224 "
            pdb=" NH1 ARG A 251 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" O   TYR B 170 "
            pdb=" NH2 ARG B 188 "
     model   vdw
     2.326 3.120
  ... (remaining 57167 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.970
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
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      :  0.003   0.031   8185  Z= 0.138
  Angle     :  0.566   6.332  11184  Z= 0.315
  Chirality :  0.042   0.161   1327
  Planarity :  0.004   0.043   1417
  Dihedral  : 12.619  70.709   2640
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.25), residues: 1081
  helix:  2.36 (0.27), residues: 372
  sheet:  0.86 (0.32), residues: 254
  loop : -1.50 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  96 
 HIS   0.007   0.001   HIS B 209 
 PHE   0.017   0.002   PHE A 278 
 TYR   0.020   0.002   TYR E  50 
 ARG   0.010   0.000   ARG B 241 

Details of bonding type rmsd
  link_TRANS           : bond        0.00085 (    1)
  link_TRANS           : angle       0.27719 (    3)
  hydrogen bonds       : bond        0.12110 (  402)
  hydrogen bonds       : angle       4.66892 ( 1155)
  SS BOND              : bond        0.00387 (    3)
  SS BOND              : angle       1.19140 (    6)
  covalent geometry    : bond        0.00295 ( 8181)
  covalent geometry    : angle       0.56551 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8419 (mmm) cc_final: 0.8012 (mmm)
REVERT: B  194 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7606 (ttm110)
REVERT: D  159 ASN cc_start: 0.8397 (m-40) cc_final: 0.8138 (m110)
REVERT: E  119 MET cc_start: 0.7646 (mmm) cc_final: 0.7433 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1828
  time to fit residues: 36.6780
Evaluate side-chains
  117 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 63 optimal weight:    0.4980
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
B 146 GLN
B 239 ASN
** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 308 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.170502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.133867 restraints weight = 12829.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 3.43
r_work: 0.3583 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.0846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8185  Z= 0.130
  Angle     :  0.536   6.133  11184  Z= 0.291
  Chirality :  0.042   0.152   1327
  Planarity :  0.003   0.038   1417
  Dihedral  :  4.115  29.386   1179
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  8.96 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1081
  helix:  2.40 (0.27), residues: 374
  sheet:  0.79 (0.32), residues: 266
  loop : -1.33 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 108 
 HIS   0.007   0.002   HIS B 209 
 PHE   0.016   0.001   PHE A 278 
 TYR   0.016   0.001   TYR A 105 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  link_TRANS           : bond        0.00150 (    1)
  link_TRANS           : angle       0.65828 (    3)
  hydrogen bonds       : bond        0.04664 (  402)
  hydrogen bonds       : angle       4.07399 ( 1155)
  SS BOND              : bond        0.00484 (    3)
  SS BOND              : angle       1.04873 (    6)
  covalent geometry    : bond        0.00290 ( 8181)
  covalent geometry    : angle       0.53565 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8540 (mmm) cc_final: 0.8026 (mmm)
REVERT: A  261 LEU cc_start: 0.8339 (mp) cc_final: 0.8119 (mp)
REVERT: B  126 LYS cc_start: 0.8129 (tttp) cc_final: 0.7796 (ttpp)
REVERT: B  194 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7599 (ttm110)
REVERT: D  159 ASN cc_start: 0.8598 (m-40) cc_final: 0.8185 (m110)
REVERT: D  180 MET cc_start: 0.6668 (pmm) cc_final: 0.5920 (pmm)
  outliers start: 7
  outliers final: 5
  residues processed: 128
  average time/residue: 0.1902
  time to fit residues: 33.6411
Evaluate side-chains
  116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain E residue  232 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 62 optimal weight:    0.2980
   chunk 108 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 76 optimal weight:    9.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN
** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.170898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.136809 restraints weight = 13082.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 3.57
r_work: 0.3529 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8185  Z= 0.119
  Angle     :  0.510   5.541  11184  Z= 0.277
  Chirality :  0.042   0.174   1327
  Planarity :  0.003   0.037   1417
  Dihedral  :  3.995  25.273   1179
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.46 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 1081
  helix:  2.38 (0.27), residues: 374
  sheet:  0.73 (0.32), residues: 274
  loop : -1.29 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 108 
 HIS   0.006   0.001   HIS B 209 
 PHE   0.015   0.001   PHE A 199 
 TYR   0.015   0.001   TYR A 105 
 ARG   0.005   0.000   ARG A 219 

Details of bonding type rmsd
  link_TRANS           : bond        0.00104 (    1)
  link_TRANS           : angle       0.78266 (    3)
  hydrogen bonds       : bond        0.04373 (  402)
  hydrogen bonds       : angle       3.94056 ( 1155)
  SS BOND              : bond        0.00451 (    3)
  SS BOND              : angle       0.90751 (    6)
  covalent geometry    : bond        0.00263 ( 8181)
  covalent geometry    : angle       0.50981 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.8504 (mmm) cc_final: 0.8009 (mmm)
REVERT: B  126 LYS cc_start: 0.8181 (tttp) cc_final: 0.7863 (ttpp)
REVERT: B  194 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7556 (ttm110)
REVERT: B  239 ASN cc_start: 0.8744 (t160) cc_final: 0.8495 (t0)
REVERT: D    3 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6813 (mp10)
REVERT: D   68 PHE cc_start: 0.6388 (m-80) cc_final: 0.6090 (m-10)
REVERT: D  180 MET cc_start: 0.6557 (pmm) cc_final: 0.5620 (pmm)
  outliers start: 10
  outliers final: 7
  residues processed: 124
  average time/residue: 0.1782
  time to fit residues: 30.9486
Evaluate side-chains
  115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain E residue  223 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 108 optimal weight:   30.0000
   chunk 32 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 97 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.165861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.132649 restraints weight = 13024.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 3.19
r_work: 0.3481 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8185  Z= 0.189
  Angle     :  0.597   6.551  11184  Z= 0.326
  Chirality :  0.044   0.212   1327
  Planarity :  0.004   0.039   1417
  Dihedral  :  4.446  24.357   1179
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.04 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1081
  helix:  2.14 (0.27), residues: 370
  sheet:  0.55 (0.32), residues: 275
  loop : -1.39 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 332 
 HIS   0.008   0.002   HIS B 209 
 PHE   0.020   0.002   PHE A 241 
 TYR   0.028   0.002   TYR A 105 
 ARG   0.005   0.000   ARG B 241 

Details of bonding type rmsd
  link_TRANS           : bond        0.00098 (    1)
  link_TRANS           : angle       0.83191 (    3)
  hydrogen bonds       : bond        0.05800 (  402)
  hydrogen bonds       : angle       4.29451 ( 1155)
  SS BOND              : bond        0.00551 (    3)
  SS BOND              : angle       1.18753 (    6)
  covalent geometry    : bond        0.00450 ( 8181)
  covalent geometry    : angle       0.59596 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A   82 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.7507 (m-10)
REVERT: A  188 MET cc_start: 0.8488 (mmm) cc_final: 0.7983 (mmm)
REVERT: B  126 LYS cc_start: 0.8241 (tttp) cc_final: 0.7923 (ttpp)
REVERT: B  239 ASN cc_start: 0.8737 (t160) cc_final: 0.8244 (m-40)
REVERT: D  159 ASN cc_start: 0.8687 (m-40) cc_final: 0.8112 (m110)
REVERT: E  108 TRP cc_start: 0.8322 (t-100) cc_final: 0.7930 (t-100)
REVERT: E  217 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8094 (m-80)
  outliers start: 16
  outliers final: 7
  residues processed: 130
  average time/residue: 0.1706
  time to fit residues: 31.6592
Evaluate side-chains
  117 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TRP
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain E residue  217 PHE
Chi-restraints excluded: chain E residue  305 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 80 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 51 optimal weight:    0.1980
   chunk 98 optimal weight:    4.9990
   chunk 71 optimal weight:    0.2980
   chunk 100 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 5 optimal weight:    0.2980
   chunk 82 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 146 HIS
E 308 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.170091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.133383 restraints weight = 12755.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 3.39
r_work: 0.3575 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8185  Z= 0.110
  Angle     :  0.504   5.665  11184  Z= 0.275
  Chirality :  0.041   0.165   1327
  Planarity :  0.003   0.035   1417
  Dihedral  :  4.005  25.725   1179
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.76 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.26), residues: 1081
  helix:  2.34 (0.27), residues: 371
  sheet:  0.49 (0.32), residues: 283
  loop : -1.30 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  36 
 HIS   0.008   0.001   HIS E 146 
 PHE   0.016   0.001   PHE A 199 
 TYR   0.013   0.001   TYR A 105 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  link_TRANS           : bond        0.00099 (    1)
  link_TRANS           : angle       0.78454 (    3)
  hydrogen bonds       : bond        0.04197 (  402)
  hydrogen bonds       : angle       3.93606 ( 1155)
  SS BOND              : bond        0.00404 (    3)
  SS BOND              : angle       0.76232 (    6)
  covalent geometry    : bond        0.00236 ( 8181)
  covalent geometry    : angle       0.50422 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A   58 ILE cc_start: 0.9093 (mm) cc_final: 0.8779 (mm)
REVERT: A   82 TRP cc_start: 0.7655 (OUTLIER) cc_final: 0.7445 (m-10)
REVERT: A  188 MET cc_start: 0.8477 (mmm) cc_final: 0.8247 (mmm)
REVERT: B  126 LYS cc_start: 0.8159 (tttp) cc_final: 0.7847 (ttpp)
REVERT: B  197 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7265 (t80)
REVERT: B  239 ASN cc_start: 0.8681 (t160) cc_final: 0.8129 (m-40)
REVERT: D  159 ASN cc_start: 0.8424 (m-40) cc_final: 0.7815 (m110)
REVERT: E  217 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7974 (m-80)
REVERT: F   48 ASP cc_start: 0.8195 (t70) cc_final: 0.7936 (p0)
  outliers start: 15
  outliers final: 9
  residues processed: 134
  average time/residue: 0.1969
  time to fit residues: 37.7874
Evaluate side-chains
  123 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TRP
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  197 PHE
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain E residue  217 PHE
Chi-restraints excluded: chain F residue   51 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 56 optimal weight:    0.0070
   chunk 0 optimal weight:   60.0000
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** E 125 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 = 0.4149 r_free = 0.4149 target = 0.173908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.137261 restraints weight = 12934.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 3.43
r_work: 0.3581 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8185  Z= 0.094
  Angle     :  0.476   5.564  11184  Z= 0.259
  Chirality :  0.040   0.165   1327
  Planarity :  0.003   0.036   1417
  Dihedral  :  3.651  25.399   1179
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.21 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 1081
  helix:  2.50 (0.28), residues: 373
  sheet:  0.67 (0.32), residues: 282
  loop : -1.31 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  96 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.014   0.001   PHE A 199 
 TYR   0.008   0.001   TYR A 124 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  link_TRANS           : bond        0.00124 (    1)
  link_TRANS           : angle       0.72733 (    3)
  hydrogen bonds       : bond        0.03249 (  402)
  hydrogen bonds       : angle       3.70092 ( 1155)
  SS BOND              : bond        0.00322 (    3)
  SS BOND              : angle       0.50646 (    6)
  covalent geometry    : bond        0.00191 ( 8181)
  covalent geometry    : angle       0.47630 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 2.123 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 TRP cc_start: 0.7548 (OUTLIER) cc_final: 0.7342 (m-10)
REVERT: A  188 MET cc_start: 0.8447 (mmm) cc_final: 0.7973 (mmm)
REVERT: B  126 LYS cc_start: 0.8115 (tttp) cc_final: 0.7858 (ttpp)
REVERT: B  166 GLU cc_start: 0.7587 (tp30) cc_final: 0.7144 (tp30)
REVERT: B  197 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7198 (t80)
REVERT: B  239 ASN cc_start: 0.8630 (t160) cc_final: 0.8118 (m-40)
REVERT: D    3 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6835 (mp10)
REVERT: D  160 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7722 (t)
REVERT: D  180 MET cc_start: 0.6570 (pmm) cc_final: 0.5860 (pmm)
REVERT: E  161 MET cc_start: 0.7806 (tmm) cc_final: 0.7408 (tmm)
REVERT: E  217 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7775 (m-80)
REVERT: F   48 ASP cc_start: 0.8201 (t70) cc_final: 0.7854 (p0)
  outliers start: 10
  outliers final: 4
  residues processed: 135
  average time/residue: 0.2208
  time to fit residues: 42.9678
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TRP
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  197 PHE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain E residue  217 PHE
Chi-restraints excluded: chain F residue   51 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 99 optimal weight:   20.0000
   chunk 84 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 89 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 70 optimal weight:    7.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  88 ASN
** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.170949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.134246 restraints weight = 12856.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 3.41
r_work: 0.3585 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8185  Z= 0.112
  Angle     :  0.512   8.703  11184  Z= 0.275
  Chirality :  0.041   0.141   1327
  Planarity :  0.003   0.037   1417
  Dihedral  :  3.710  24.473   1179
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.07 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.26), residues: 1081
  helix:  2.49 (0.27), residues: 373
  sheet:  0.61 (0.32), residues: 280
  loop : -1.30 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  96 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.016   0.001   PHE A 199 
 TYR   0.016   0.001   TYR E  50 
 ARG   0.002   0.000   ARG B 188 

Details of bonding type rmsd
  link_TRANS           : bond        0.00111 (    1)
  link_TRANS           : angle       0.76585 (    3)
  hydrogen bonds       : bond        0.03907 (  402)
  hydrogen bonds       : angle       3.76000 ( 1155)
  SS BOND              : bond        0.00359 (    3)
  SS BOND              : angle       0.74037 (    6)
  covalent geometry    : bond        0.00247 ( 8181)
  covalent geometry    : angle       0.51204 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9102 (mm) cc_final: 0.8739 (mm)
REVERT: A   82 TRP cc_start: 0.7626 (OUTLIER) cc_final: 0.7398 (m-10)
REVERT: A  188 MET cc_start: 0.8487 (mmm) cc_final: 0.7995 (mmm)
REVERT: B  126 LYS cc_start: 0.8154 (tttp) cc_final: 0.7903 (ttpp)
REVERT: B  166 GLU cc_start: 0.7595 (tp30) cc_final: 0.7168 (tp30)
REVERT: B  197 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7293 (t80)
REVERT: B  239 ASN cc_start: 0.8666 (t160) cc_final: 0.8116 (m-40)
REVERT: D    3 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6824 (mp10)
REVERT: D  160 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7695 (t)
REVERT: D  180 MET cc_start: 0.6748 (pmm) cc_final: 0.5989 (pmm)
REVERT: E  161 MET cc_start: 0.7811 (tmm) cc_final: 0.7405 (tmm)
REVERT: E  217 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7780 (m-80)
REVERT: F   48 ASP cc_start: 0.8214 (t70) cc_final: 0.7862 (p0)
  outliers start: 15
  outliers final: 9
  residues processed: 132
  average time/residue: 0.1920
  time to fit residues: 37.1287
Evaluate side-chains
  128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TRP
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  197 PHE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain D residue  109 ASP
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain E residue  217 PHE
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   51 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 99 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0000
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:   50.0000
   chunk 59 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 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 = 0.4134 r_free = 0.4134 target = 0.172480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.138936 restraints weight = 12996.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 3.43
r_work: 0.3555 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8185  Z= 0.098
  Angle     :  0.493   8.452  11184  Z= 0.263
  Chirality :  0.041   0.145   1327
  Planarity :  0.003   0.037   1417
  Dihedral  :  3.583  24.318   1179
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.81 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1081
  helix:  2.53 (0.27), residues: 373
  sheet:  0.72 (0.33), residues: 271
  loop : -1.24 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  96 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.014   0.001   PHE A 199 
 TYR   0.009   0.001   TYR A 105 
 ARG   0.002   0.000   ARG E 140 

Details of bonding type rmsd
  link_TRANS           : bond        0.00112 (    1)
  link_TRANS           : angle       0.72448 (    3)
  hydrogen bonds       : bond        0.03469 (  402)
  hydrogen bonds       : angle       3.65681 ( 1155)
  SS BOND              : bond        0.00325 (    3)
  SS BOND              : angle       0.62999 (    6)
  covalent geometry    : bond        0.00210 ( 8181)
  covalent geometry    : angle       0.49255 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9116 (mm) cc_final: 0.8761 (mm)
REVERT: A   82 TRP cc_start: 0.7619 (OUTLIER) cc_final: 0.7342 (m-10)
REVERT: A  188 MET cc_start: 0.8465 (mmm) cc_final: 0.7977 (mmm)
REVERT: B  126 LYS cc_start: 0.8105 (tttp) cc_final: 0.7850 (ttpp)
REVERT: B  166 GLU cc_start: 0.7508 (tp30) cc_final: 0.7093 (tp30)
REVERT: B  197 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7229 (t80)
REVERT: B  239 ASN cc_start: 0.8625 (t160) cc_final: 0.8105 (m-40)
REVERT: D   46 GLU cc_start: 0.7708 (tp30) cc_final: 0.7053 (pt0)
REVERT: D  160 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7651 (t)
REVERT: D  180 MET cc_start: 0.6646 (pmm) cc_final: 0.5915 (pmm)
REVERT: E  161 MET cc_start: 0.7867 (tmm) cc_final: 0.7456 (tmm)
REVERT: E  217 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7738 (m-80)
REVERT: F   48 ASP cc_start: 0.8241 (t70) cc_final: 0.7934 (p0)
  outliers start: 16
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1609
  time to fit residues: 30.3982
Evaluate side-chains
  131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TRP
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  197 PHE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain D residue  109 ASP
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain E residue  217 PHE
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   51 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 87 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 108 optimal weight:    0.0670
   chunk 98 optimal weight:    0.9980
   chunk 104 optimal weight:    9.9990
   chunk 97 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7722

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

Flipped N/Q/H residues before XYZ refinement:
** E 125 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 = 0.4142 r_free = 0.4142 target = 0.173267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.140240 restraints weight = 13169.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 3.28
r_work: 0.3575 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8185  Z= 0.097
  Angle     :  0.495   8.374  11184  Z= 0.263
  Chirality :  0.040   0.146   1327
  Planarity :  0.003   0.038   1417
  Dihedral  :  3.505  23.688   1179
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.81 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1081
  helix:  2.55 (0.27), residues: 373
  sheet:  0.81 (0.34), residues: 260
  loop : -1.20 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E 108 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.014   0.001   PHE A 199 
 TYR   0.008   0.001   TYR D 102 
 ARG   0.002   0.000   ARG E 140 

Details of bonding type rmsd
  link_TRANS           : bond        0.00118 (    1)
  link_TRANS           : angle       0.70336 (    3)
  hydrogen bonds       : bond        0.03295 (  402)
  hydrogen bonds       : angle       3.61114 ( 1155)
  SS BOND              : bond        0.00326 (    3)
  SS BOND              : angle       0.51909 (    6)
  covalent geometry    : bond        0.00205 ( 8181)
  covalent geometry    : angle       0.49472 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9148 (mm) cc_final: 0.8752 (mm)
REVERT: A   82 TRP cc_start: 0.7568 (OUTLIER) cc_final: 0.7281 (m-10)
REVERT: A  188 MET cc_start: 0.8436 (mmm) cc_final: 0.7931 (mmm)
REVERT: B  126 LYS cc_start: 0.8110 (tttp) cc_final: 0.7849 (ttpp)
REVERT: B  166 GLU cc_start: 0.7503 (tp30) cc_final: 0.7093 (tp30)
REVERT: B  197 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7230 (t80)
REVERT: B  239 ASN cc_start: 0.8612 (t160) cc_final: 0.8104 (m-40)
REVERT: D   46 GLU cc_start: 0.7697 (tp30) cc_final: 0.7017 (pt0)
REVERT: D  160 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7648 (t)
REVERT: D  180 MET cc_start: 0.6621 (pmm) cc_final: 0.5936 (pmm)
REVERT: E  161 MET cc_start: 0.7852 (tmm) cc_final: 0.7497 (tmm)
REVERT: E  217 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7703 (m-80)
REVERT: F   48 ASP cc_start: 0.8178 (t70) cc_final: 0.7901 (p0)
  outliers start: 16
  outliers final: 11
  residues processed: 131
  average time/residue: 0.2553
  time to fit residues: 47.7080
Evaluate side-chains
  133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TRP
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  197 PHE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain D residue  109 ASP
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain E residue  217 PHE
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   51 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 96 optimal weight:    8.9990
   chunk 39 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 47 optimal weight:   20.0000
   chunk 78 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** E 125 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 = 0.4124 r_free = 0.4124 target = 0.171487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.138365 restraints weight = 12945.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 3.23
r_work: 0.3594 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8185  Z= 0.109
  Angle     :  0.513   8.056  11184  Z= 0.274
  Chirality :  0.041   0.158   1327
  Planarity :  0.003   0.038   1417
  Dihedral  :  3.597  23.383   1179
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.21 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.26), residues: 1081
  helix:  2.53 (0.28), residues: 373
  sheet:  0.64 (0.33), residues: 268
  loop : -1.21 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E 108 
 HIS   0.004   0.001   HIS D 220 
 PHE   0.014   0.001   PHE A 199 
 TYR   0.013   0.001   TYR A 105 
 ARG   0.002   0.000   ARG E 140 

Details of bonding type rmsd
  link_TRANS           : bond        0.00111 (    1)
  link_TRANS           : angle       0.72886 (    3)
  hydrogen bonds       : bond        0.03718 (  402)
  hydrogen bonds       : angle       3.69009 ( 1155)
  SS BOND              : bond        0.00372 (    3)
  SS BOND              : angle       0.69023 (    6)
  covalent geometry    : bond        0.00242 ( 8181)
  covalent geometry    : angle       0.51304 (11175)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9109 (mm) cc_final: 0.8725 (mm)
REVERT: A   82 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.7332 (m-10)
REVERT: A  188 MET cc_start: 0.8430 (mmm) cc_final: 0.7920 (mmm)
REVERT: B  126 LYS cc_start: 0.8155 (tttp) cc_final: 0.7903 (ttpp)
REVERT: B  166 GLU cc_start: 0.7489 (tp30) cc_final: 0.7087 (tp30)
REVERT: B  197 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7279 (t80)
REVERT: B  239 ASN cc_start: 0.8652 (t160) cc_final: 0.8121 (m-40)
REVERT: D  160 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7655 (t)
REVERT: D  180 MET cc_start: 0.6746 (pmm) cc_final: 0.6031 (pmm)
REVERT: E  161 MET cc_start: 0.7903 (tmm) cc_final: 0.7555 (tmm)
REVERT: E  217 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7770 (m-80)
  outliers start: 15
  outliers final: 11
  residues processed: 131
  average time/residue: 0.2514
  time to fit residues: 47.7681
Evaluate side-chains
  133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TRP
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  197 PHE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain D residue  109 ASP
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain E residue  217 PHE
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   51 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 71 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 100 optimal weight:    8.9990
   chunk 67 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 68 optimal weight:    4.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
E  84 ASN
** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.163745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.126835 restraints weight = 13073.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 3.40
r_work: 0.3493 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   8185  Z= 0.242
  Angle     :  0.683   7.352  11184  Z= 0.372
  Chirality :  0.046   0.160   1327
  Planarity :  0.004   0.060   1417
  Dihedral  :  4.559  23.697   1179
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.47 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.26), residues: 1081
  helix:  1.97 (0.27), residues: 378
  sheet:  0.47 (0.33), residues: 249
  loop : -1.61 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E 108 
 HIS   0.010   0.003   HIS D 220 
 PHE   0.021   0.002   PHE A 222 
 TYR   0.034   0.003   TYR A 105 
 ARG   0.003   0.000   ARG D  72 

Details of bonding type rmsd
  link_TRANS           : bond        0.00089 (    1)
  link_TRANS           : angle       0.87287 (    3)
  hydrogen bonds       : bond        0.06394 (  402)
  hydrogen bonds       : angle       4.39248 ( 1155)
  SS BOND              : bond        0.00645 (    3)
  SS BOND              : angle       1.28819 (    6)
  covalent geometry    : bond        0.00577 ( 8181)
  covalent geometry    : angle       0.68257 (11175)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5233.52 seconds
wall clock time: 93 minutes 45.97 seconds (5625.97 seconds total)