Starting phenix.real_space_refine
on Thu Mar 14 14:55:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/03_2024/7w2z_32268_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/03_2024/7w2z_32268.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/03_2024/7w2z_32268.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/03_2024/7w2z_32268.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/03_2024/7w2z_32268_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2z_32268/03_2024/7w2z_32268_updated.pdb"
  }
  resolution = 2.8
  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=  -0.000 sd=   0.008
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      61      5.16       5
     C    5812      2.51       5
     N    1544      2.21       5
     O    1663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   20": "OE1" <-> "OE2"
    Residue "A PHE  251": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  277": "OE1" <-> "OE2"
    Residue "A ARG  313": "NH1" <-> "NH2"
    Residue "A GLU  318": "OE1" <-> "OE2"
    Residue "R ARG   70": "NH1" <-> "NH2"
    Residue "R ARG   75": "NH1" <-> "NH2"
    Residue "R ARG  102": "NH1" <-> "NH2"
    Residue "R ARG  107": "NH1" <-> "NH2"
    Residue "R ARG  141": "NH1" <-> "NH2"
    Residue "R GLU  185": "OE1" <-> "OE2"
    Residue "R ARG  243": "NH1" <-> "NH2"
    Residue "R ARG  244": "NH1" <-> "NH2"
    Residue "R GLU  291": "OE1" <-> "OE2"
    Residue "R ARG  336": "NH1" <-> "NH2"
    Residue "G GLU   58": "OE1" <-> "OE2"
    Residue "S ARG   98": "NH1" <-> "NH2"
    Residue "S ARG  148": "NH1" <-> "NH2"
    Residue "S ARG  206": "NH1" <-> "NH2"
    Residue "B ARG   42": "NH1" <-> "NH2"
    Residue "B ARG   48": "NH1" <-> "NH2"
    Residue "B ARG  129": "NH1" <-> "NH2"
    Residue "B ARG  137": "NH1" <-> "NH2"
    Residue "B PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  197": "NH1" <-> "NH2"
    Residue "B ARG  219": "NH1" <-> "NH2"
    Residue "B ARG  256": "NH1" <-> "NH2"
    Residue "B ARG  314": "NH1" <-> "NH2"
    Residue "L ARG   15": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9080
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1691
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 208}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2421
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 12, 'TRANS': 288}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 418
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1760
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2593
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "L"
      Number of atoms: 141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 141
          Unusual residues: {'K4Q': 1}
          Classifications: {'peptide': 15, 'undetermined': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 12, None: 2}
            Not linked:
              pdbres="SER L   2 "
              pdbres="K4Q L   3 "
            Not linked:
              pdbres="K4Q L   3 "
              pdbres="PHE L   4 "
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.44, per 1000 atoms: 0.60
  Number of scatterers: 9080
  At special positions: 0
  Unit cell: (109.512, 119.652, 126.75, 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      61     16.00
     O    1663      8.00
     N    1544      7.00
     C    5812      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 198 " distance=2.05
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.39
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      31.9% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 31
      removed outlier: 3.554A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   SER A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      removed outlier: 3.528A  pdb=" N   PHE A 216 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 216'
    Processing helix  chain 'A' and resid 244 through 255
    Processing helix  chain 'A' and resid 272 through 281
      removed outlier: 4.865A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 279 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 311
      removed outlier: 4.050A  pdb=" N   ALA A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   LYS A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.524A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 40 through 70
      removed outlier: 3.947A  pdb=" N   ALA R  44 " --> pdb=" O   ALA R  40 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL R  56 " --> pdb=" O   ALA R  52 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA R  59 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   THR R  64 " --> pdb=" O   GLY R  60 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET R  65 " --> pdb=" O   ASN R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 74
      No H-bonds generated for 'chain 'R' and resid 72 through 74'
    Processing helix  chain 'R' and resid 77 through 94
      removed outlier: 3.937A  pdb=" N   PHE R  93 " --> pdb=" O   ASP R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 96 through 104
      removed outlier: 3.539A  pdb=" N   LEU R 100 " --> pdb=" O   MET R  96 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 115 through 143
      removed outlier: 3.621A  pdb=" N   GLN R 120 " --> pdb=" O   CYS R 116 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR R 128 " --> pdb=" O   GLU R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 160 through 174
      removed outlier: 3.632A  pdb=" N   PHE R 165 " --> pdb=" O   LYS R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 176 through 181
      removed outlier: 3.668A  pdb=" N   VAL R 180 " --> pdb=" O   PRO R 177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 202 through 207
    Processing helix  chain 'R' and resid 209 through 239
      removed outlier: 3.673A  pdb=" N   TRP R 215 " --> pdb=" O   THR R 211 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ILE R 219 " --> pdb=" O   TRP R 215 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   PHE R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   PHE R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU R 223 " --> pdb=" O   ILE R 219 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
      removed outlier: 3.592A  pdb=" N   CYS R 227 " --> pdb=" O   LEU R 223 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL R 230 " --> pdb=" O   PHE R 226 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER R 233 " --> pdb=" O   THR R 229 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG R 237 " --> pdb=" O   SER R 233 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 280
      removed outlier: 3.596A  pdb=" N   VAL R 269 " --> pdb=" O   LEU R 265 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   PHE R 272 " --> pdb=" O   VAL R 268 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   CYS R 275 " --> pdb=" O   ALA R 271 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 282 through 290
      removed outlier: 4.236A  pdb=" N   PHE R 290 " --> pdb=" O   PHE R 286 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 315
      removed outlier: 3.668A  pdb=" N   ASN R 305 " --> pdb=" O   SER R 301 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU R 306 " --> pdb=" O   GLN R 302 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE R 309 " --> pdb=" O   ASN R 305 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL R 310 " --> pdb=" O   LEU R 306 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU R 311 " --> pdb=" O   VAL R 307 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 319 through 322
      No H-bonds generated for 'chain 'R' and resid 319 through 322'
    Processing helix  chain 'R' and resid 328 through 338
      removed outlier: 3.502A  pdb=" N   VAL R 332 " --> pdb=" O   LYS R 328 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 11 through 21
      removed outlier: 4.085A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 43
      removed outlier: 3.542A  pdb=" N   ALA G  43 " --> pdb=" O   ALA G  39 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing helix  chain 'S' and resid 88 through 90
      No H-bonds generated for 'chain 'S' and resid 88 through 90'
    Processing helix  chain 'S' and resid 209 through 211
      No H-bonds generated for 'chain 'S' and resid 209 through 211'
    Processing helix  chain 'B' and resid 4 through 24
      removed outlier: 3.595A  pdb=" N   ILE B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 35
    Processing helix  chain 'L' and resid 9 through 13
    Processing sheet with id=  A, first strand: chain 'A' and resid 319 through 322
      removed outlier: 6.459A  pdb=" N   ILE A 265 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU A 267 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'R' and resid 182 through 185
      removed outlier: 3.647A  pdb=" N   ARG R 199 " --> pdb=" O   GLY R 183 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=  D, first strand: chain 'S' and resid 115 through 117
      removed outlier: 3.593A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.963A  pdb=" N   LYS S 232 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  E
    Processing sheet with id=  F, first strand: chain 'S' and resid 143 through 148
    Processing sheet with id=  G, first strand: chain 'S' and resid 213 through 219
      removed outlier: 3.628A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ARG S 168 " --> pdb=" O   PRO S 173 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.745A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.817A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.545A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.990A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.836A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'B' and resid 294 through 298
      removed outlier: 3.508A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.489A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)

    340 hydrogen bonds defined for protein.
    978 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: 2.39

  Time building geometry restraints manager: 3.67 seconds

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

  Histogram of bond lengths:
        1.06 -     1.21: 2
        1.21 -     1.37: 3077
        1.37 -     1.52: 3750
        1.52 -     1.67: 2359
        1.67 -     1.82: 86
  Bond restraints: 9274
  Sorted by residual:
  bond pdb=" C08 K4Q L   3 "
       pdb=" O10 K4Q L   3 "
    ideal  model  delta    sigma   weight residual
    1.335  1.062  0.273 2.00e-02 2.50e+03 1.87e+02
  bond pdb=" C08 K4Q L   3 "
       pdb=" O09 K4Q L   3 "
    ideal  model  delta    sigma   weight residual
    1.204  1.404 -0.200 2.00e-02 2.50e+03 1.00e+02
  bond pdb=" CB  VAL B  71 "
       pdb=" CG2 VAL B  71 "
    ideal  model  delta    sigma   weight residual
    1.521  1.405  0.116 3.30e-02 9.18e+02 1.24e+01
  bond pdb=" C   VAL S  12 "
       pdb=" N   GLN S  13 "
    ideal  model  delta    sigma   weight residual
    1.329  1.384 -0.055 1.60e-02 3.91e+03 1.19e+01
  bond pdb=" C   MET R  96 "
       pdb=" N   PRO R  97 "
    ideal  model  delta    sigma   weight residual
    1.335  1.377 -0.042 1.36e-02 5.41e+03 9.51e+00
  ... (remaining 9269 not shown)

  Histogram of bond angle deviations from ideal:
       84.12 -    97.51: 1
       97.51 -   110.90: 3282
      110.90 -   124.30: 9061
      124.30 -   137.69: 225
      137.69 -   151.08: 1
  Bond angle restraints: 12570
  Sorted by residual:
  angle pdb=" C07 K4Q L   3 "
        pdb=" C08 K4Q L   3 "
        pdb=" O10 K4Q L   3 "
      ideal   model   delta    sigma   weight residual
     118.23   84.12   34.11 3.00e+00 1.11e-01 1.29e+02
  angle pdb=" O09 K4Q L   3 "
        pdb=" C08 K4Q L   3 "
        pdb=" O10 K4Q L   3 "
      ideal   model   delta    sigma   weight residual
     117.69  151.08  -33.39 3.00e+00 1.11e-01 1.24e+02
  angle pdb=" N   VAL R 212 "
        pdb=" CA  VAL R 212 "
        pdb=" C   VAL R 212 "
      ideal   model   delta    sigma   weight residual
     111.00  103.44    7.56 1.09e+00 8.42e-01 4.81e+01
  angle pdb=" N   LYS R 117 "
        pdb=" CA  LYS R 117 "
        pdb=" C   LYS R 117 "
      ideal   model   delta    sigma   weight residual
     111.69  104.40    7.29 1.23e+00 6.61e-01 3.51e+01
  angle pdb=" N   ASN S 182 "
        pdb=" CA  ASN S 182 "
        pdb=" C   ASN S 182 "
      ideal   model   delta    sigma   weight residual
     109.15  117.61   -8.46 1.44e+00 4.82e-01 3.45e+01
  ... (remaining 12565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.02: 5455
       33.02 -    66.05: 127
       66.05 -    99.07: 11
       99.07 -   132.09: 1
      132.09 -   165.11: 2
  Dihedral angle restraints: 5596
    sinusoidal: 2259
      harmonic: 3337
  Sorted by residual:
  dihedral pdb=" CA  LEU A 353 "
           pdb=" C   LEU A 353 "
           pdb=" N   TYR A 354 "
           pdb=" CA  TYR A 354 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.08  -24.92     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" C11 K4Q L   3 "
           pdb=" C08 K4Q L   3 "
           pdb=" O10 K4Q L   3 "
           pdb=" O09 K4Q L   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.48   14.37  165.11     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C04 K4Q L   3 "
           pdb=" C05 K4Q L   3 "
           pdb=" C06 K4Q L   3 "
           pdb=" C07 K4Q L   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     182.71   25.83  156.88     1      3.00e+01 1.11e-03 2.05e+01
  ... (remaining 5593 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1285
       0.097 -    0.194: 130
       0.194 -    0.290: 17
       0.290 -    0.387: 2
       0.387 -    0.484: 1
  Chirality restraints: 1435
  Sorted by residual:
  chirality pdb=" CA  MET S 180 "
            pdb=" N   MET S 180 "
            pdb=" C   MET S 180 "
            pdb=" CB  MET S 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.86e+00
  chirality pdb=" CA  LYS A  46 "
            pdb=" N   LYS A  46 "
            pdb=" C   LYS A  46 "
            pdb=" CB  LYS A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.52e+00
  chirality pdb=" CA  ARG S 179 "
            pdb=" N   ARG S 179 "
            pdb=" C   ARG S 179 "
            pdb=" CB  ARG S 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.46e+00
  ... (remaining 1432 not shown)

  Planarity restraints: 1577
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C07 K4Q L   3 "    0.018 2.00e-02 2.50e+03   1.03e-01 1.07e+02
        pdb=" C08 K4Q L   3 "   -0.173 2.00e-02 2.50e+03
        pdb=" O09 K4Q L   3 "    0.069 2.00e-02 2.50e+03
        pdb=" O10 K4Q L   3 "    0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 107 "   -0.100 5.00e-02 4.00e+02   1.50e-01 3.61e+01
        pdb=" N   PRO R 108 "    0.260 5.00e-02 4.00e+02
        pdb=" CA  PRO R 108 "   -0.089 5.00e-02 4.00e+02
        pdb=" CD  PRO R 108 "   -0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 277 "    0.050 5.00e-02 4.00e+02   7.41e-02 8.79e+00
        pdb=" N   PRO R 278 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO R 278 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO R 278 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1574 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 108
        2.64 -     3.21: 7527
        3.21 -     3.77: 13450
        3.77 -     4.34: 19712
        4.34 -     4.90: 32643
  Nonbonded interactions: 73440
  Sorted by model distance:
  nonbonded pdb=" O   ASN A  43 "
            pdb=" ND2 ASN A  43 "
     model   vdw
     2.078 2.520
  nonbonded pdb=" OD2 ASP R  99 "
            pdb=" OH  TYR R 313 "
     model   vdw
     2.196 2.440
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.228 2.440
  nonbonded pdb=" OE2 GLU R 197 "
            pdb=" OG  SER L   6 "
     model   vdw
     2.258 2.440
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.290 2.440
  ... (remaining 73435 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.320
  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:          1.910
  Check model and map are aligned:         0.110
  Set scattering table:                    0.080
  Process input model:                     27.570
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  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:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
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      :  0.009   0.273   9274  Z= 0.600
  Angle     :  1.133  34.107  12570  Z= 0.608
  Chirality :  0.064   0.484   1435
  Planarity :  0.009   0.150   1577
  Dihedral  : 14.810 165.115   3431
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.62 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.53 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -4.01 (0.20), residues: 1132
  helix: -4.36 (0.12), residues: 390
  sheet: -0.81 (0.28), residues: 295
  loop : -2.09 (0.24), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP R 276 
 HIS   0.008   0.002   HIS R 258 
 PHE   0.024   0.003   PHE B 234 
 TYR   0.048   0.003   TYR B 105 
 ARG   0.014   0.001   ARG S  67 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8227 (mtpt)
REVERT: A  209 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7636 (tpp80)
REVERT: A  252 ASP cc_start: 0.7529 (t0) cc_final: 0.7306 (t0)
REVERT: A  271 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7507 (mptp)
REVERT: A  309 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7213 (mt-10)
REVERT: R   65 MET cc_start: 0.6998 (mtp) cc_final: 0.6746 (mtp)
REVERT: R   70 ARG cc_start: 0.6766 (ttt180) cc_final: 0.6444 (ttt90)
REVERT: R  326 MET cc_start: 0.6695 (mmm) cc_final: 0.6355 (mmt)
REVERT: R  328 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7113 (mptp)
REVERT: G   21 MET cc_start: 0.6579 (tpt) cc_final: 0.6049 (pp-130)
REVERT: G   38 MET cc_start: 0.8176 (ttp) cc_final: 0.7920 (ttp)
REVERT: S    3 GLN cc_start: 0.7676 (pt0) cc_final: 0.7438 (pt0)
REVERT: S  147 CYS cc_start: 0.7079 (t) cc_final: 0.6755 (t)
REVERT: B  254 ASP cc_start: 0.8484 (p0) cc_final: 0.8156 (p0)
REVERT: B  258 ASP cc_start: 0.7730 (t0) cc_final: 0.7195 (t70)
  outliers start: 8
  outliers final: 1
  residues processed: 141
  average time/residue: 1.2709
  time to fit residues: 190.6928
Evaluate side-chains
  109 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  119 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0770
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
A 256 ASN
A 312 ASN
A 330 ASN
R  79 ASN
R 196 ASN
R 305 ASN
R 324 ASN
G  11 GLN
S 130 GLN
B  13 GLN
B  32 GLN
B 155 ASN
B 239 ASN
B 340 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9274  Z= 0.171
  Angle     :  0.545   6.125  12570  Z= 0.289
  Chirality :  0.042   0.232   1435
  Planarity :  0.006   0.135   1577
  Dihedral  :  8.303 111.560   1392
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.39 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.94 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.22), residues: 1132
  helix: -2.02 (0.22), residues: 383
  sheet: -0.15 (0.30), residues: 287
  loop : -1.62 (0.25), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.019   0.001   PHE R 119 
 TYR   0.021   0.001   TYR A 297 
 ARG   0.007   0.000   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.057 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8043 (mtpt)
REVERT: A  209 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.6846 (ttp-110)
REVERT: A  252 ASP cc_start: 0.7589 (t0) cc_final: 0.7379 (t0)
REVERT: A  309 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7178 (mt-10)
REVERT: A  323 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7949 (mtm)
REVERT: R   70 ARG cc_start: 0.6812 (ttt180) cc_final: 0.6470 (ttt90)
REVERT: R  209 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.7034 (mp)
REVERT: R  326 MET cc_start: 0.6686 (mmm) cc_final: 0.6321 (mmt)
REVERT: R  328 LYS cc_start: 0.7508 (mmtt) cc_final: 0.7098 (mptp)
REVERT: S    3 GLN cc_start: 0.7572 (pt0) cc_final: 0.7344 (pt0)
REVERT: S   83 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8072 (mtp)
REVERT: B  219 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7208 (mmt90)
REVERT: B  254 ASP cc_start: 0.8252 (p0) cc_final: 0.8032 (p0)
REVERT: B  260 GLU cc_start: 0.7716 (pt0) cc_final: 0.7235 (tt0)
REVERT: B  340 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8099 (t160)
  outliers start: 23
  outliers final: 3
  residues processed: 130
  average time/residue: 1.2235
  time to fit residues: 170.0542
Evaluate side-chains
  102 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 111 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 101 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
L  10 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9274  Z= 0.359
  Angle     :  0.634   9.351  12570  Z= 0.331
  Chirality :  0.046   0.190   1435
  Planarity :  0.006   0.131   1577
  Dihedral  :  8.056  95.276   1390
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.53 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 13.57 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.23), residues: 1132
  helix: -1.03 (0.25), residues: 383
  sheet:  0.02 (0.30), residues: 288
  loop : -1.42 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 109 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.029   0.002   PHE R 119 
 TYR   0.017   0.002   TYR S 178 
 ARG   0.005   0.001   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 103
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8127 (mtpt)
REVERT: A  209 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.6885 (ttp-110)
REVERT: A  252 ASP cc_start: 0.7657 (t0) cc_final: 0.7445 (t0)
REVERT: R   70 ARG cc_start: 0.6736 (ttt180) cc_final: 0.6388 (ttt90)
REVERT: R  209 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7221 (tp)
REVERT: R  264 MET cc_start: 0.6364 (mmm) cc_final: 0.6099 (mmm)
REVERT: R  328 LYS cc_start: 0.7579 (mmtt) cc_final: 0.7241 (mptp)
REVERT: G   42 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6931 (mp0)
REVERT: S   83 MET cc_start: 0.8600 (mtp) cc_final: 0.7888 (mtp)
REVERT: B  219 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7232 (mmt90)
REVERT: B  254 ASP cc_start: 0.8403 (p0) cc_final: 0.8139 (p0)
REVERT: B  260 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7569 (tt0)
REVERT: B  340 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7716 (t160)
  outliers start: 42
  outliers final: 19
  residues processed: 130
  average time/residue: 1.1576
  time to fit residues: 161.3333
Evaluate side-chains
  112 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  308 SER
Chi-restraints excluded: chain R residue  332 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  205 SER
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   chunk 109 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
R 257 ASN
** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9274  Z= 0.220
  Angle     :  0.549   7.212  12570  Z= 0.286
  Chirality :  0.043   0.192   1435
  Planarity :  0.005   0.128   1577
  Dihedral  :  7.494  79.921   1390
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.39 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.51 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.89 (0.24), residues: 1132
  helix: -0.29 (0.26), residues: 385
  sheet:  0.13 (0.30), residues: 292
  loop : -1.24 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 109 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.020   0.001   PHE R 119 
 TYR   0.023   0.002   TYR R 128 
 ARG   0.008   0.000   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 93
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7345 (mttt)
REVERT: A   35 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8075 (mtpt)
REVERT: A  209 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.6839 (ttp-110)
REVERT: R   70 ARG cc_start: 0.6723 (ttt180) cc_final: 0.6404 (ttt90)
REVERT: R  264 MET cc_start: 0.6316 (mmm) cc_final: 0.6063 (mmm)
REVERT: R  328 LYS cc_start: 0.7566 (mmtt) cc_final: 0.7217 (mptp)
REVERT: G   42 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6829 (mp0)
REVERT: S   83 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7963 (mtp)
REVERT: B  219 ARG cc_start: 0.7456 (mtm180) cc_final: 0.7203 (mmt90)
REVERT: B  254 ASP cc_start: 0.8331 (p0) cc_final: 0.8058 (p0)
REVERT: B  260 GLU cc_start: 0.7999 (pt0) cc_final: 0.7586 (tt0)
  outliers start: 33
  outliers final: 14
  residues processed: 114
  average time/residue: 1.2447
  time to fit residues: 151.5992
Evaluate side-chains
  104 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  303 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    0.0870
   chunk 1 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 98 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0030
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.1170

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

Flipped N/Q/H residues before XYZ refinement:
** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9274  Z= 0.168
  Angle     :  0.501   5.889  12570  Z= 0.262
  Chirality :  0.041   0.190   1435
  Planarity :  0.005   0.125   1577
  Dihedral  :  6.628  62.592   1390
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.56 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 15.41 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.51 (0.24), residues: 1132
  helix:  0.09 (0.27), residues: 393
  sheet:  0.33 (0.30), residues: 286
  loop : -1.05 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.014   0.001   PHE R 119 
 TYR   0.014   0.001   TYR A 297 
 ARG   0.008   0.000   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 98
  time to evaluate  : 1.024 
Fit side-chains
REVERT: A    5 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7783 (mm)
REVERT: A   25 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.5888 (mp0)
REVERT: A   35 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8061 (mtpt)
REVERT: A  209 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.6809 (ttp-110)
REVERT: A  318 GLU cc_start: 0.6142 (tp30) cc_final: 0.5870 (tp30)
REVERT: A  323 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8089 (mtm)
REVERT: R   70 ARG cc_start: 0.6749 (ttt180) cc_final: 0.6432 (ttt90)
REVERT: R  264 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.6071 (mmm)
REVERT: R  328 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7066 (mptp)
REVERT: G   42 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6880 (mp0)
REVERT: S   83 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8019 (mtp)
REVERT: B  254 ASP cc_start: 0.8270 (p0) cc_final: 0.8013 (p0)
REVERT: B  260 GLU cc_start: 0.7930 (pt0) cc_final: 0.7615 (tt0)
REVERT: B  291 ASP cc_start: 0.7308 (p0) cc_final: 0.7082 (p0)
  outliers start: 42
  outliers final: 15
  residues processed: 125
  average time/residue: 1.2203
  time to fit residues: 163.3541
Evaluate side-chains
  113 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 21 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 109 optimal weight:    8.9990
   chunk 90 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 305 ASN
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9274  Z= 0.355
  Angle     :  0.612   9.674  12570  Z= 0.319
  Chirality :  0.046   0.173   1435
  Planarity :  0.005   0.124   1577
  Dihedral  :  7.260  62.967   1390
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.80 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 16.73 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.67 (0.24), residues: 1132
  helix: -0.13 (0.26), residues: 393
  sheet:  0.22 (0.30), residues: 289
  loop : -1.05 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 109 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.024   0.002   PHE R 119 
 TYR   0.017   0.002   TYR S 178 
 ARG   0.007   0.001   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 93
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7984 (mm)
REVERT: A  209 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.6867 (ttp-110)
REVERT: A  244 MET cc_start: 0.7318 (tpp) cc_final: 0.7087 (tpp)
REVERT: R   70 ARG cc_start: 0.6687 (ttt180) cc_final: 0.6347 (ttt90)
REVERT: R  240 TRP cc_start: 0.6353 (OUTLIER) cc_final: 0.5945 (t60)
REVERT: R  264 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.6151 (mmm)
REVERT: R  328 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7247 (mptp)
REVERT: G   42 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6886 (mp0)
REVERT: S   83 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8004 (mtp)
REVERT: B  254 ASP cc_start: 0.8412 (p0) cc_final: 0.8124 (p0)
REVERT: B  340 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8081 (t160)
  outliers start: 43
  outliers final: 23
  residues processed: 117
  average time/residue: 1.2642
  time to fit residues: 157.9196
Evaluate side-chains
  118 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  240 TRP
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  308 SER
Chi-restraints excluded: chain R residue  332 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 108 optimal weight:    8.9990
   chunk 68 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9274  Z= 0.239
  Angle     :  0.597  22.433  12570  Z= 0.298
  Chirality :  0.044   0.266   1435
  Planarity :  0.006   0.189   1577
  Dihedral  :  7.005  60.159   1390
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.65 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 17.04 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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: -0.49 (0.24), residues: 1132
  helix:  0.08 (0.27), residues: 393
  sheet:  0.28 (0.30), residues: 292
  loop : -1.00 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 109 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.025   0.001   PHE R 119 
 TYR   0.017   0.001   TYR R 128 
 ARG   0.008   0.000   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 88
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7990 (mm)
REVERT: A   35 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8079 (mtpt)
REVERT: A  209 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.6824 (ttp-110)
REVERT: R   42 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6234 (tt)
REVERT: R   70 ARG cc_start: 0.6685 (ttt180) cc_final: 0.6350 (ttt90)
REVERT: R  240 TRP cc_start: 0.6317 (OUTLIER) cc_final: 0.5839 (t60)
REVERT: R  264 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.6105 (mmm)
REVERT: S   67 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.5407 (ptm-80)
REVERT: S   83 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8060 (mtp)
REVERT: B  234 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8899 (m-80)
REVERT: B  254 ASP cc_start: 0.8346 (p0) cc_final: 0.8082 (p0)
REVERT: B  260 GLU cc_start: 0.8017 (tt0) cc_final: 0.7797 (tt0)
  outliers start: 44
  outliers final: 20
  residues processed: 117
  average time/residue: 1.2675
  time to fit residues: 158.3227
Evaluate side-chains
  112 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  240 TRP
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  332 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 69 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0870
   chunk 104 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    2.5564

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

Flipped N/Q/H residues before XYZ refinement:
** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9274  Z= 0.294
  Angle     :  0.593  10.161  12570  Z= 0.309
  Chirality :  0.045   0.157   1435
  Planarity :  0.005   0.084   1577
  Dihedral  :  7.185  60.578   1390
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 17.14 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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: -0.52 (0.24), residues: 1132
  helix:  0.02 (0.27), residues: 394
  sheet:  0.25 (0.30), residues: 293
  loop : -0.97 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.027   0.002   PHE R 119 
 TYR   0.016   0.002   TYR S 178 
 ARG   0.009   0.000   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 84
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8013 (mm)
REVERT: A   35 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8098 (mtpt)
REVERT: A  209 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.6823 (ttp-110)
REVERT: A  295 ASN cc_start: 0.7140 (t0) cc_final: 0.6849 (m110)
REVERT: R   42 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6266 (tt)
REVERT: R   70 ARG cc_start: 0.6728 (ttt180) cc_final: 0.6353 (ttt90)
REVERT: R  240 TRP cc_start: 0.6324 (OUTLIER) cc_final: 0.5914 (t60)
REVERT: R  264 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.6142 (mmm)
REVERT: R  308 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7386 (m)
REVERT: S   67 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.5435 (ptm-80)
REVERT: S   83 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8051 (mtp)
REVERT: B  234 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8852 (m-80)
REVERT: B  254 ASP cc_start: 0.8394 (p0) cc_final: 0.8119 (p0)
REVERT: B  260 GLU cc_start: 0.8087 (tt0) cc_final: 0.7863 (tt0)
  outliers start: 45
  outliers final: 24
  residues processed: 115
  average time/residue: 1.3233
  time to fit residues: 163.8952
Evaluate side-chains
  113 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  240 TRP
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  308 SER
Chi-restraints excluded: chain R residue  332 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  303 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 95 optimal weight:    0.0270
   chunk 66 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9274  Z= 0.129
  Angle     :  0.497   7.109  12570  Z= 0.259
  Chirality :  0.041   0.153   1435
  Planarity :  0.004   0.081   1577
  Dihedral  :  6.450  59.665   1390
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.18 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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: -0.09 (0.25), residues: 1132
  helix:  0.49 (0.27), residues: 391
  sheet:  0.45 (0.30), residues: 293
  loop : -0.81 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 280 
 PHE   0.021   0.001   PHE R 119 
 TYR   0.020   0.001   TYR R 128 
 ARG   0.009   0.000   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.5880 (mp0)
REVERT: A   35 LYS cc_start: 0.8347 (mtmm) cc_final: 0.7956 (mtpt)
REVERT: A  209 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.6797 (ttp-110)
REVERT: A  323 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7936 (mtm)
REVERT: R   42 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6139 (tt)
REVERT: R   70 ARG cc_start: 0.6732 (ttt180) cc_final: 0.6448 (ttt90)
REVERT: R  264 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.6071 (mmm)
REVERT: S   83 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8067 (mtp)
REVERT: B  254 ASP cc_start: 0.8224 (p0) cc_final: 0.7954 (p0)
REVERT: B  291 ASP cc_start: 0.7272 (p0) cc_final: 0.7016 (p0)
  outliers start: 24
  outliers final: 10
  residues processed: 110
  average time/residue: 1.3175
  time to fit residues: 155.0532
Evaluate side-chains
  101 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 112 optimal weight:    5.9990
   chunk 103 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 95 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9274  Z= 0.270
  Angle     :  0.586   8.442  12570  Z= 0.304
  Chirality :  0.044   0.158   1435
  Planarity :  0.005   0.085   1577
  Dihedral  :  6.849  60.391   1390
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.49 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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: -0.22 (0.25), residues: 1132
  helix:  0.32 (0.27), residues: 390
  sheet:  0.39 (0.30), residues: 287
  loop : -0.80 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 109 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.021   0.001   PHE R 119 
 TYR   0.016   0.001   TYR S 178 
 ARG   0.009   0.000   ARG S  87 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8074 (mtpt)
REVERT: A  209 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.6784 (ttp-110)
REVERT: R   42 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6183 (tt)
REVERT: R   70 ARG cc_start: 0.6728 (ttt180) cc_final: 0.6377 (ttt90)
REVERT: R  240 TRP cc_start: 0.6293 (OUTLIER) cc_final: 0.5906 (t60)
REVERT: R  264 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.6154 (mmm)
REVERT: S   67 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.5279 (ptm-80)
REVERT: S   83 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8022 (mtp)
REVERT: B  254 ASP cc_start: 0.8382 (p0) cc_final: 0.8060 (p0)
  outliers start: 24
  outliers final: 16
  residues processed: 96
  average time/residue: 1.4144
  time to fit residues: 144.2666
Evaluate side-chains
  100 residues out of total 991 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  240 TRP
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0770
   overall best weight:    1.1944

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

Flipped N/Q/H residues before XYZ refinement:
** G  11 GLN ** 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 = 0.3870 r_free = 0.3870 target = 0.165014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.129208 restraints weight = 9838.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.94
r_work: 0.3280 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9274  Z= 0.171
  Angle     :  0.534   6.790  12570  Z= 0.276
  Chirality :  0.042   0.146   1435
  Planarity :  0.004   0.083   1577
  Dihedral  :  6.548  59.860   1390
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.49 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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: -0.05 (0.25), residues: 1132
  helix:  0.49 (0.27), residues: 391
  sheet:  0.45 (0.30), residues: 288
  loop : -0.71 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 109 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.026   0.001   PHE R 119 
 TYR   0.021   0.001   TYR R 128 
 ARG   0.009   0.000   ARG S  87 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3389.88 seconds
wall clock time: 60 minutes 39.30 seconds (3639.30 seconds total)