Starting phenix.real_space_refine
on Fri Mar 15 04:36:54 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/03_2024/7rpo_24618_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/03_2024/7rpo_24618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/03_2024/7rpo_24618.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/03_2024/7rpo_24618.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/03_2024/7rpo_24618_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/03_2024/7rpo_24618_updated.pdb"
  }
  resolution = 4.16
  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=   0.001 sd=   0.026
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: 6
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      63      5.49       5
     S      25      5.16       5
     C    6571      2.51       5
     N    1753      2.21       5
     O    2186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  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: 10602
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1953
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 8, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 1922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1922
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "C"
      Number of atoms: 1941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1941
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 5, 'TRANS': 239}
    Chain: "X"
      Number of atoms: 408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 408
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "Y"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 229
          Classifications: {'DNA': 11}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 10}
    Chain: "Z"
      Number of atoms: 634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 634
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "E"
      Number of atoms: 3489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3489
          Classifications: {'peptide': 439}
          Link IDs: {'PTRANS': 13, 'TRANS': 425}
    Chain: "X"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 24
          Unusual residues: {' MN': 2}
          Classifications: {'RNA': 1, 'undetermined': 2}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 5.85, per 1000 atoms: 0.55
  Number of scatterers: 10602
  At special positions: 0
  Unit cell: (118.5, 109.5, 124.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      4     24.99
     S      25     16.00
     P      63     15.00
     O    2186      8.00
     N    1753      7.00
     C    6571      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.34
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2218

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      35 helices and 12 sheets defined
      24.3% alpha, 21.0% beta
      30 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 4.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 20
      removed outlier: 4.138A  pdb=" N   SER A  14 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 3.679A  pdb=" N   SER A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 150
      removed outlier: 3.599A  pdb=" N   VAL A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 164
      No H-bonds generated for 'chain 'A' and resid 162 through 164'
    Processing helix  chain 'A' and resid 202 through 211
      removed outlier: 3.538A  pdb=" N   GLY A 211 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 21
      removed outlier: 3.909A  pdb=" N   ASP B  21 " --> pdb=" O   ARG B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 80
      removed outlier: 3.572A  pdb=" N   ASN B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 144
    Processing helix  chain 'B' and resid 148 through 150
      No H-bonds generated for 'chain 'B' and resid 148 through 150'
    Processing helix  chain 'B' and resid 200 through 206
      removed outlier: 3.801A  pdb=" N   THR B 205 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   THR B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 18
      removed outlier: 3.851A  pdb=" N   ILE C  14 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   ILE C  15 " --> pdb=" O   LEU C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 77
    Processing helix  chain 'C' and resid 137 through 148
      removed outlier: 3.662A  pdb=" N   SER C 141 " --> pdb=" O   ASP C 137 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR C 148 " --> pdb=" O   SER C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 204
      No H-bonds generated for 'chain 'C' and resid 202 through 204'
    Processing helix  chain 'E' and resid 4 through 13
      removed outlier: 3.889A  pdb=" N   LYS E  12 " --> pdb=" O   GLU E   8 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LEU E  13 " --> pdb=" O   TYR E   9 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 19 through 32
      removed outlier: 3.778A  pdb=" N   THR E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ALA E  24 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ALA E  27 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ASP E  28 " --> pdb=" O   ALA E  24 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   LEU E  29 " --> pdb=" O   LEU E  25 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU E  30 " --> pdb=" O   LEU E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 38 through 46
      removed outlier: 3.893A  pdb=" N   GLN E  46 " --> pdb=" O   VAL E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 74
      removed outlier: 4.117A  pdb=" N   ILE E  67 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS E  68 " --> pdb=" O   LYS E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 87
      removed outlier: 3.727A  pdb=" N   THR E  87 " --> pdb=" O   ASN E  83 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 91 through 94
      No H-bonds generated for 'chain 'E' and resid 91 through 94'
    Processing helix  chain 'E' and resid 97 through 99
      No H-bonds generated for 'chain 'E' and resid 97 through 99'
    Processing helix  chain 'E' and resid 121 through 133
      removed outlier: 3.583A  pdb=" N   LEU E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 139 through 153
      removed outlier: 3.530A  pdb=" N   ARG E 145 " --> pdb=" O   ASP E 141 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU E 146 " --> pdb=" O   LEU E 142 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY E 149 " --> pdb=" O   ARG E 145 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   LEU E 150 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU E 151 " --> pdb=" O   LEU E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 158 through 167
      removed outlier: 3.628A  pdb=" N   PHE E 161 " --> pdb=" O   GLU E 158 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LEU E 162 " --> pdb=" O   ALA E 159 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   VAL E 163 " --> pdb=" O   LYS E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 177 through 188
    Processing helix  chain 'E' and resid 191 through 203
      removed outlier: 4.039A  pdb=" N   GLU E 195 " --> pdb=" O   SER E 192 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ILE E 196 " --> pdb=" O   ALA E 193 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 216
    Processing helix  chain 'E' and resid 247 through 251
    Processing helix  chain 'E' and resid 287 through 289
      No H-bonds generated for 'chain 'E' and resid 287 through 289'
    Processing helix  chain 'E' and resid 291 through 293
      No H-bonds generated for 'chain 'E' and resid 291 through 293'
    Processing helix  chain 'E' and resid 295 through 298
      No H-bonds generated for 'chain 'E' and resid 295 through 298'
    Processing helix  chain 'E' and resid 324 through 329
      removed outlier: 3.835A  pdb=" N   HIS E 329 " --> pdb=" O   GLN E 325 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 340 through 342
      No H-bonds generated for 'chain 'E' and resid 340 through 342'
    Processing helix  chain 'E' and resid 367 through 372
    Processing helix  chain 'E' and resid 393 through 405
      removed outlier: 3.582A  pdb=" N   LYS E 397 " --> pdb=" O   VAL E 393 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   SER E 398 " --> pdb=" O   GLU E 394 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG E 402 " --> pdb=" O   SER E 398 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.520A  pdb=" N   ILE A 101 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 100 " --> pdb=" O   ILE A 113 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 66 through 71
      removed outlier: 3.816A  pdb=" N   THR A  66 " --> pdb=" O   PHE A  30 " (cutoff:3.500A)
      removed outlier: 10.054A  pdb=" N   SER A  25 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   LEU A  40 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   ILE A  27 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ARG A  38 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN A  29 " --> pdb=" O   PHE A  36 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   PHE A  36 " --> pdb=" O   ASN A  29 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A  31 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ILE A  35 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   MET A  50 " --> pdb=" O   SER A  37 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS A  39 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A  48 " --> pdb=" O   HIS A  39 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A  51 " --> pdb=" O   HIS A 240 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 241 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A 233 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A 231 " --> pdb=" O   PHE A 243 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A 135 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   SER A 191 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A 137 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLU A 189 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 157 through 160
      removed outlier: 3.653A  pdb=" N   ARG A 158 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU A 169 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE A 166 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A 168 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA A 170 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   TYR A 177 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.652A  pdb=" N   SER B  92 " --> pdb=" O   THR B  99 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR B  99 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 68 through 72
      removed outlier: 3.948A  pdb=" N   PHE B  71 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ALA B  26 " --> pdb=" O   PHE B  71 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   GLU B  25 " --> pdb=" O   ILE B  40 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE B  40 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   ASN B  27 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   SER B  38 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B  36 " --> pdb=" O   ILE B  29 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE B  35 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B  48 " --> pdb=" O   GLY B  39 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP B  49 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   TYR B 236 " --> pdb=" O   PHE B  51 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG B 228 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   SER B 214 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 194 through 197
      removed outlier: 3.839A  pdb=" N   LEU B 163 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU B 178 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 2 through 5
      removed outlier: 4.161A  pdb=" N   ALA C  86 " --> pdb=" O   ILE C 102 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ILE C 102 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'C' and resid 24 through 28
      removed outlier: 4.225A  pdb=" N   ALA C  25 " --> pdb=" O   PHE C  69 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE C  69 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   PHE C  67 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'C' and resid 33 through 39
      removed outlier: 3.671A  pdb=" N   ALA C  38 " --> pdb=" O   ILE C  47 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ILE C  47 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU C  46 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER C  48 " --> pdb=" O   THR C 237 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS C 235 " --> pdb=" O   ASN C  50 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   VAL C 236 " --> pdb=" O   PHE C 228 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE C 228 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   TYR C 238 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU C 226 " --> pdb=" O   TYR C 238 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'C' and resid 193 through 197
    Processing sheet with id=  K, first strand: chain 'E' and resid 257 through 260
      removed outlier: 3.956A  pdb=" N   GLY E 410 " --> pdb=" O   LYS E 260 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL E 411 " --> pdb=" O   LEU E 434 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU E 434 " --> pdb=" O   VAL E 411 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ILE E 432 " --> pdb=" O   VAL E 413 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'E' and resid 275 through 278
      removed outlier: 3.626A  pdb=" N   GLY E 309 " --> pdb=" O   ALA E 266 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS E 270 " --> pdb=" O   PHE E 305 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASP E 351 " --> pdb=" O   GLU E 308 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   GLU E 310 " --> pdb=" O   LEU E 349 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   LEU E 349 " --> pdb=" O   GLU E 310 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   VAL E 312 " --> pdb=" O   VAL E 347 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   VAL E 347 " --> pdb=" O   VAL E 312 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   ILE E 314 " --> pdb=" O   VAL E 345 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL E 345 " --> pdb=" O   ILE E 314 " (cutoff:3.500A)

    264 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      77 hydrogen bonds
      154 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 3.13

  Time building geometry restraints manager: 4.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2890
        1.33 -     1.45: 1884
        1.45 -     1.57: 5953
        1.57 -     1.69: 122
        1.69 -     1.80: 50
  Bond restraints: 10899
  Sorted by residual:
  bond pdb=" C4' AMP E 701 "
       pdb=" O4' AMP E 701 "
    ideal  model  delta    sigma   weight residual
    1.454  1.429  0.025 1.50e-02 4.44e+03 2.72e+00
  bond pdb=" CA  LYS C 178 "
       pdb=" C   LYS C 178 "
    ideal  model  delta    sigma   weight residual
    1.522  1.545 -0.023 1.72e-02 3.38e+03 1.77e+00
  bond pdb=" N   GLY E 309 "
       pdb=" CA  GLY E 309 "
    ideal  model  delta    sigma   weight residual
    1.453  1.442  0.011 8.60e-03 1.35e+04 1.65e+00
  bond pdb=" C3'  DA Z  22 "
       pdb=" O3'  DA Z  22 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.53e+00
  bond pdb=" C3'  DT Z  30 "
       pdb=" O3'  DT Z  30 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.45e+00
  ... (remaining 10894 not shown)

  Histogram of bond angle deviations from ideal:
       98.82 -   106.23: 545
      106.23 -   113.64: 6114
      113.64 -   121.06: 5141
      121.06 -   128.47: 3090
      128.47 -   135.88: 73
  Bond angle restraints: 14963
  Sorted by residual:
  angle pdb=" C   LEU A 249 "
        pdb=" CA  LEU A 249 "
        pdb=" CB  LEU A 249 "
      ideal   model   delta    sigma   weight residual
     117.23  109.96    7.27 1.36e+00 5.41e-01 2.86e+01
  angle pdb=" C1' AMP E 701 "
        pdb=" C2' AMP E 701 "
        pdb=" C3' AMP E 701 "
      ideal   model   delta    sigma   weight residual
     101.50  105.65   -4.15 1.00e+00 1.00e+00 1.73e+01
  angle pdb=" CA  LEU A 249 "
        pdb=" C   LEU A 249 "
        pdb=" N   LEU A 250 "
      ideal   model   delta    sigma   weight residual
     119.98  116.82    3.16 8.50e-01 1.38e+00 1.38e+01
  angle pdb=" C2' AMP E 701 "
        pdb=" C3' AMP E 701 "
        pdb=" C4' AMP E 701 "
      ideal   model   delta    sigma   weight residual
     102.60  106.06   -3.46 1.00e+00 1.00e+00 1.20e+01
  angle pdb=" C3' AMP E 701 "
        pdb=" C4' AMP E 701 "
        pdb=" C5' AMP E 701 "
      ideal   model   delta    sigma   weight residual
     115.20  110.34    4.86 1.50e+00 4.44e-01 1.05e+01
  ... (remaining 14958 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.40: 6078
       30.40 -    60.80: 380
       60.80 -    91.19: 4
       91.19 -   121.59: 0
      121.59 -   151.99: 5
  Dihedral angle restraints: 6467
    sinusoidal: 3035
      harmonic: 3432
  Sorted by residual:
  dihedral pdb=" C4'  DT Z  30 "
           pdb=" C3'  DT Z  30 "
           pdb=" O3'  DT Z  30 "
           pdb=" P    DC Z  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   68.01  151.99     1      3.50e+01 8.16e-04 1.48e+01
  dihedral pdb=" C4'  DA Z  22 "
           pdb=" C3'  DA Z  22 "
           pdb=" O3'  DA Z  22 "
           pdb=" P    DC Z  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.14  149.86     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" C4'  DC Z  26 "
           pdb=" C3'  DC Z  26 "
           pdb=" O3'  DC Z  26 "
           pdb=" P    DG Z  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   71.90  148.10     1      3.50e+01 8.16e-04 1.45e+01
  ... (remaining 6464 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1111
       0.030 -    0.060: 401
       0.060 -    0.089: 100
       0.089 -    0.119: 96
       0.119 -    0.149: 15
  Chirality restraints: 1723
  Sorted by residual:
  chirality pdb=" C3' AMP E 701 "
            pdb=" C2' AMP E 701 "
            pdb=" C4' AMP E 701 "
            pdb=" O3' AMP E 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.60   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  ILE E 306 "
            pdb=" N   ILE E 306 "
            pdb=" C   ILE E 306 "
            pdb=" CB  ILE E 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.18e-01
  chirality pdb=" CA  ILE B  68 "
            pdb=" N   ILE B  68 "
            pdb=" C   ILE B  68 "
            pdb=" CB  ILE B  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 1720 not shown)

  Planarity restraints: 1683
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  93 "    0.022 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO C  94 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C  94 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  94 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 121 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO C 122 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C 122 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 122 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 227 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO A 228 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 228 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 228 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1680 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 28
        2.39 -     3.02: 5717
        3.02 -     3.64: 15002
        3.64 -     4.27: 21396
        4.27 -     4.90: 35089
  Nonbonded interactions: 77232
  Sorted by model distance:
  nonbonded pdb=" O1P AMP E 701 "
            pdb="MN    MN E 703 "
     model   vdw
     1.759 2.320
  nonbonded pdb=" O   GLY E  60 "
            pdb="MN    MN X 101 "
     model   vdw
     1.776 2.320
  nonbonded pdb=" OE2 GLU E 409 "
            pdb="MN    MN E 703 "
     model   vdw
     1.815 2.320
  nonbonded pdb=" O3'  DG X  20 "
            pdb="MN    MN X 101 "
     model   vdw
     2.187 2.320
  nonbonded pdb=" OG  SER C 211 "
            pdb=" O   ASN C 229 "
     model   vdw
     2.192 2.440
  ... (remaining 77227 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.310
  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:         0.150
  Set scattering table:                    0.090
  Process input model:                     33.510
  Find NCS groups from input model:        0.290
  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:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10899  Z= 0.155
  Angle     :  0.505   7.267  14963  Z= 0.288
  Chirality :  0.040   0.149   1723
  Planarity :  0.003   0.034   1683
  Dihedral  : 16.976 151.990   4249
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.76 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.25), residues: 1171
  helix: -0.03 (0.33), residues: 294
  sheet: -0.27 (0.32), residues: 303
  loop : -2.74 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  50 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.010   0.001   PHE C 228 
 TYR   0.008   0.001   TYR A 177 
 ARG   0.002   0.000   ARG E 330 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 397
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 VAL cc_start: 0.7540 (t) cc_final: 0.7181 (m)
REVERT: A   24 ASP cc_start: 0.5986 (t70) cc_final: 0.5304 (t0)
REVERT: A   28 LEU cc_start: 0.7221 (mt) cc_final: 0.6808 (mp)
REVERT: A   39 HIS cc_start: 0.7684 (t-90) cc_final: 0.7404 (t-90)
REVERT: A   47 MET cc_start: 0.7688 (ttt) cc_final: 0.7285 (ttt)
REVERT: A   57 LEU cc_start: 0.8144 (mt) cc_final: 0.7881 (mt)
REVERT: A   59 GLU cc_start: 0.8294 (tp30) cc_final: 0.7918 (tp30)
REVERT: A   77 LYS cc_start: 0.8708 (pttt) cc_final: 0.8505 (ptpt)
REVERT: A   79 LEU cc_start: 0.7529 (mt) cc_final: 0.6939 (mt)
REVERT: A   99 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8157 (mtpp)
REVERT: A  101 ILE cc_start: 0.7816 (mt) cc_final: 0.7476 (mp)
REVERT: A  110 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7137 (ttmm)
REVERT: A  136 PHE cc_start: 0.7173 (p90) cc_final: 0.6649 (p90)
REVERT: A  156 GLU cc_start: 0.8103 (mp0) cc_final: 0.7807 (mp0)
REVERT: A  159 ILE cc_start: 0.8047 (mt) cc_final: 0.7839 (mm)
REVERT: A  190 LEU cc_start: 0.7604 (tp) cc_final: 0.7360 (mt)
REVERT: A  212 LEU cc_start: 0.7787 (mt) cc_final: 0.7577 (tp)
REVERT: A  213 ARG cc_start: 0.7061 (mtt90) cc_final: 0.6718 (mtt90)
REVERT: A  221 VAL cc_start: 0.8086 (t) cc_final: 0.7727 (p)
REVERT: A  231 ILE cc_start: 0.8109 (mt) cc_final: 0.7564 (tt)
REVERT: A  233 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7489 (p)
REVERT: B   30 VAL cc_start: 0.8305 (t) cc_final: 0.8098 (t)
REVERT: B   78 ASP cc_start: 0.6720 (m-30) cc_final: 0.6407 (m-30)
REVERT: B   81 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7663 (ttpp)
REVERT: B  156 ILE cc_start: 0.8086 (mm) cc_final: 0.7777 (mt)
REVERT: B  162 LYS cc_start: 0.8349 (mttp) cc_final: 0.7958 (mmmt)
REVERT: B  168 ILE cc_start: 0.8419 (tt) cc_final: 0.8152 (tt)
REVERT: B  184 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.6388 (p)
REVERT: B  200 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6910 (tm-30)
REVERT: C    2 LYS cc_start: 0.7911 (mttt) cc_final: 0.7638 (tppt)
REVERT: C    3 VAL cc_start: 0.8648 (t) cc_final: 0.8389 (p)
REVERT: C    6 ASP cc_start: 0.7991 (t0) cc_final: 0.7649 (t0)
REVERT: C    7 ASP cc_start: 0.7609 (t70) cc_final: 0.7132 (t0)
REVERT: C   23 ASP cc_start: 0.8016 (m-30) cc_final: 0.7815 (m-30)
REVERT: C   30 LYS cc_start: 0.8021 (mptt) cc_final: 0.7562 (mmmm)
REVERT: C   31 GLN cc_start: 0.8039 (mp10) cc_final: 0.7804 (mt0)
REVERT: C   75 MET cc_start: 0.6836 (tmm) cc_final: 0.6633 (tpp)
REVERT: C  139 PHE cc_start: 0.8027 (t80) cc_final: 0.7575 (t80)
REVERT: C  140 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7502 (tttm)
REVERT: C  167 GLU cc_start: 0.7801 (pp20) cc_final: 0.7390 (pp20)
REVERT: C  191 GLU cc_start: 0.7005 (mp0) cc_final: 0.6749 (mp0)
REVERT: C  205 LEU cc_start: 0.8461 (mt) cc_final: 0.7855 (tp)
REVERT: C  229 ASN cc_start: 0.7470 (t0) cc_final: 0.7201 (t0)
REVERT: E    1 MET cc_start: 0.7067 (mmm) cc_final: 0.6704 (mmm)
REVERT: E    2 GLU cc_start: 0.7234 (pm20) cc_final: 0.7029 (pm20)
REVERT: E   11 ASP cc_start: 0.6648 (t70) cc_final: 0.6334 (t0)
REVERT: E   13 LEU cc_start: 0.7464 (tp) cc_final: 0.7235 (tp)
REVERT: E   36 THR cc_start: 0.7292 (p) cc_final: 0.6691 (p)
REVERT: E   46 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: E   48 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7854 (mmmm)
REVERT: E   49 LEU cc_start: 0.7264 (mp) cc_final: 0.7025 (mt)
REVERT: E   67 ILE cc_start: 0.8020 (mt) cc_final: 0.7668 (pt)
REVERT: E   86 LYS cc_start: 0.7898 (tptp) cc_final: 0.7462 (mmmm)
REVERT: E  101 LYS cc_start: 0.8699 (pttm) cc_final: 0.8184 (pttm)
REVERT: E  111 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6243 (pp)
REVERT: E  126 SER cc_start: 0.8510 (t) cc_final: 0.7909 (p)
REVERT: E  169 ARG cc_start: 0.7185 (ptt180) cc_final: 0.6933 (ptt90)
REVERT: E  174 ILE cc_start: 0.7888 (mm) cc_final: 0.7595 (tt)
REVERT: E  197 ILE cc_start: 0.7992 (mm) cc_final: 0.7692 (tp)
REVERT: E  203 LEU cc_start: 0.7947 (mt) cc_final: 0.7669 (mt)
REVERT: E  206 ASP cc_start: 0.7730 (p0) cc_final: 0.7526 (p0)
REVERT: E  212 LYS cc_start: 0.7262 (pttm) cc_final: 0.6989 (pttp)
REVERT: E  236 MET cc_start: 0.7580 (ptp) cc_final: 0.7362 (ptp)
REVERT: E  239 GLU cc_start: 0.7244 (tp30) cc_final: 0.6136 (mp0)
REVERT: E  291 ASP cc_start: 0.7755 (p0) cc_final: 0.7513 (p0)
REVERT: E  321 MET cc_start: 0.6543 (mmm) cc_final: 0.5649 (mmm)
REVERT: E  325 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6995 (tp-100)
REVERT: E  326 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7434 (tp30)
REVERT: E  328 MET cc_start: 0.7739 (mtm) cc_final: 0.7095 (mtm)
REVERT: E  336 ILE cc_start: 0.7362 (mt) cc_final: 0.6787 (mm)
REVERT: E  360 TYR cc_start: 0.7426 (m-80) cc_final: 0.6726 (m-80)
REVERT: E  373 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7817 (mm-30)
REVERT: E  397 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7605 (mmtp)
REVERT: E  434 LEU cc_start: 0.8334 (tp) cc_final: 0.7901 (pt)
  outliers start: 17
  outliers final: 4
  residues processed: 410
  average time/residue: 0.2729
  time to fit residues: 146.7418
Evaluate side-chains
  350 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 343
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
B 116 GLN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  10899  Z= 0.290
  Angle     :  0.642   7.902  14963  Z= 0.352
  Chirality :  0.046   0.177   1723
  Planarity :  0.005   0.052   1683
  Dihedral  : 20.958 154.780   1931
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.76 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.48 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.24), residues: 1171
  helix: -0.33 (0.32), residues: 278
  sheet:  0.03 (0.33), residues: 293
  loop : -2.98 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP E  50 
 HIS   0.005   0.001   HIS A 240 
 PHE   0.026   0.002   PHE C 228 
 TYR   0.015   0.002   TYR A 177 
 ARG   0.004   0.001   ARG E 199 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 355
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7844 (mmmt)
REVERT: A   24 ASP cc_start: 0.5564 (t70) cc_final: 0.5359 (t0)
REVERT: A   39 HIS cc_start: 0.7598 (t-90) cc_final: 0.7235 (t-90)
REVERT: A   57 LEU cc_start: 0.8280 (mt) cc_final: 0.7991 (mt)
REVERT: A   59 GLU cc_start: 0.8413 (tp30) cc_final: 0.8116 (tp30)
REVERT: A   70 LEU cc_start: 0.7447 (mt) cc_final: 0.7222 (mt)
REVERT: A   99 LYS cc_start: 0.8249 (ttmt) cc_final: 0.8017 (mtpp)
REVERT: A  105 GLU cc_start: 0.6040 (tm-30) cc_final: 0.5795 (tm-30)
REVERT: A  116 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7690 (tptt)
REVERT: A  213 ARG cc_start: 0.6943 (mtt90) cc_final: 0.6655 (mtt90)
REVERT: A  229 MET cc_start: 0.6485 (ttt) cc_final: 0.6036 (ttt)
REVERT: A  231 ILE cc_start: 0.7984 (mt) cc_final: 0.7602 (tt)
REVERT: B    8 ASP cc_start: 0.6650 (t70) cc_final: 0.6415 (t0)
REVERT: B   21 ASP cc_start: 0.7418 (t0) cc_final: 0.6663 (t0)
REVERT: B   35 ILE cc_start: 0.8589 (mm) cc_final: 0.8305 (tp)
REVERT: B   40 ILE cc_start: 0.8884 (tp) cc_final: 0.8438 (tp)
REVERT: B   73 LEU cc_start: 0.7177 (tp) cc_final: 0.6839 (tp)
REVERT: B  132 LYS cc_start: 0.8428 (ttmt) cc_final: 0.7972 (ttmm)
REVERT: B  159 LYS cc_start: 0.7907 (ttpp) cc_final: 0.7646 (ttmm)
REVERT: C    3 VAL cc_start: 0.8592 (t) cc_final: 0.8174 (p)
REVERT: C    6 ASP cc_start: 0.7471 (t0) cc_final: 0.7217 (t0)
REVERT: C    7 ASP cc_start: 0.7772 (t70) cc_final: 0.7273 (t0)
REVERT: C   31 GLN cc_start: 0.8033 (mp10) cc_final: 0.7820 (mt0)
REVERT: C   75 MET cc_start: 0.7088 (tmm) cc_final: 0.6783 (tpp)
REVERT: C   76 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8018 (ttpt)
REVERT: C  100 ASN cc_start: 0.7632 (m-40) cc_final: 0.6852 (m-40)
REVERT: C  108 GLU cc_start: 0.6912 (pp20) cc_final: 0.6617 (tm-30)
REVERT: C  140 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7834 (tttm)
REVERT: C  165 LYS cc_start: 0.7833 (pttp) cc_final: 0.7198 (ptpt)
REVERT: C  205 LEU cc_start: 0.8450 (mt) cc_final: 0.8224 (tp)
REVERT: C  209 LYS cc_start: 0.8212 (ptmm) cc_final: 0.7753 (ptmm)
REVERT: C  215 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7809 (ttmm)
REVERT: C  218 PHE cc_start: 0.8575 (p90) cc_final: 0.8371 (p90)
REVERT: C  229 ASN cc_start: 0.7479 (t0) cc_final: 0.7259 (t0)
REVERT: C  230 MET cc_start: 0.5483 (mtm) cc_final: 0.4959 (mtm)
REVERT: E    8 GLU cc_start: 0.6528 (pt0) cc_final: 0.6269 (pt0)
REVERT: E   46 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7433 (tm-30)
REVERT: E   48 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7679 (mmmm)
REVERT: E   52 ASP cc_start: 0.7462 (m-30) cc_final: 0.7196 (t70)
REVERT: E   86 LYS cc_start: 0.7775 (tppt) cc_final: 0.7550 (mmmm)
REVERT: E  101 LYS cc_start: 0.8631 (pttm) cc_final: 0.8068 (pttm)
REVERT: E  117 GLU cc_start: 0.5146 (mp0) cc_final: 0.4749 (mp0)
REVERT: E  126 SER cc_start: 0.8373 (t) cc_final: 0.7860 (p)
REVERT: E  127 THR cc_start: 0.8109 (m) cc_final: 0.7813 (m)
REVERT: E  135 THR cc_start: 0.8062 (m) cc_final: 0.7773 (p)
REVERT: E  174 ILE cc_start: 0.7901 (mm) cc_final: 0.7645 (tt)
REVERT: E  194 SER cc_start: 0.8120 (p) cc_final: 0.7752 (p)
REVERT: E  202 ASN cc_start: 0.7998 (m110) cc_final: 0.7759 (m110)
REVERT: E  203 LEU cc_start: 0.7720 (mt) cc_final: 0.7502 (mt)
REVERT: E  206 ASP cc_start: 0.8007 (p0) cc_final: 0.7734 (p0)
REVERT: E  216 GLU cc_start: 0.6840 (tp30) cc_final: 0.6572 (mm-30)
REVERT: E  239 GLU cc_start: 0.7432 (tp30) cc_final: 0.6249 (mp0)
REVERT: E  248 LEU cc_start: 0.6776 (mp) cc_final: 0.6566 (mp)
REVERT: E  265 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7262 (mtm180)
REVERT: E  274 LYS cc_start: 0.7004 (mppt) cc_final: 0.6458 (mppt)
REVERT: E  290 PRO cc_start: 0.8051 (Cg_endo) cc_final: 0.7689 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7386 (mm-40) cc_final: 0.7050 (tp-100)
REVERT: E  326 GLU cc_start: 0.7390 (tp30) cc_final: 0.6622 (tp30)
REVERT: E  328 MET cc_start: 0.7760 (mtm) cc_final: 0.6766 (mtm)
REVERT: E  329 HIS cc_start: 0.7206 (m90) cc_final: 0.5972 (m-70)
REVERT: E  336 ILE cc_start: 0.7356 (mt) cc_final: 0.7099 (mm)
REVERT: E  360 TYR cc_start: 0.7643 (m-80) cc_final: 0.6763 (m-80)
REVERT: E  363 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8227 (mmtp)
REVERT: E  397 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7686 (mmtp)
REVERT: E  434 LEU cc_start: 0.8407 (tp) cc_final: 0.8011 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 356
  average time/residue: 0.2980
  time to fit residues: 139.1772
Evaluate side-chains
  316 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 110 optimal weight:    4.9990
   chunk 119 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0270
   chunk 37 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 109 optimal weight:    0.4980
   overall best weight:    1.4842

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

Flipped N/Q/H residues before XYZ refinement:
B 116 GLN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 386 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  10899  Z= 0.293
  Angle     :  0.651  10.436  14963  Z= 0.353
  Chirality :  0.046   0.171   1723
  Planarity :  0.005   0.060   1683
  Dihedral  : 21.100 154.832   1931
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.25 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.86 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.24), residues: 1171
  helix: -0.63 (0.31), residues: 278
  sheet: -0.09 (0.32), residues: 304
  loop : -3.01 (0.22), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E  50 
 HIS   0.004   0.001   HIS A  39 
 PHE   0.028   0.002   PHE A  30 
 TYR   0.033   0.002   TYR C  59 
 ARG   0.012   0.001   ARG E 234 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 350
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.7936 (t80) cc_final: 0.7690 (t80)
REVERT: A   24 ASP cc_start: 0.5658 (t70) cc_final: 0.5380 (t0)
REVERT: A   39 HIS cc_start: 0.7590 (t-90) cc_final: 0.7169 (t-90)
REVERT: A   57 LEU cc_start: 0.8202 (mt) cc_final: 0.7987 (mt)
REVERT: A   59 GLU cc_start: 0.8422 (tp30) cc_final: 0.8100 (tp30)
REVERT: A   99 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7856 (mtpp)
REVERT: A  116 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7633 (tptt)
REVERT: A  119 LYS cc_start: 0.7212 (mppt) cc_final: 0.6904 (mppt)
REVERT: A  136 PHE cc_start: 0.7396 (p90) cc_final: 0.7132 (p90)
REVERT: A  206 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7709 (ttmm)
REVERT: A  213 ARG cc_start: 0.6989 (mtt90) cc_final: 0.6720 (mtt90)
REVERT: A  220 MET cc_start: 0.7421 (tmm) cc_final: 0.7175 (ttp)
REVERT: A  229 MET cc_start: 0.6366 (ttt) cc_final: 0.6148 (ttt)
REVERT: B   21 ASP cc_start: 0.7440 (t0) cc_final: 0.6632 (t0)
REVERT: B   35 ILE cc_start: 0.8527 (mm) cc_final: 0.8312 (tp)
REVERT: B  132 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8009 (ttmm)
REVERT: B  155 ASN cc_start: 0.7497 (t0) cc_final: 0.7275 (t0)
REVERT: B  201 TYR cc_start: 0.8425 (m-80) cc_final: 0.8109 (m-80)
REVERT: C    6 ASP cc_start: 0.7524 (t0) cc_final: 0.7255 (t0)
REVERT: C    7 ASP cc_start: 0.7761 (t70) cc_final: 0.7353 (t0)
REVERT: C   30 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7557 (mmmm)
REVERT: C   72 GLN cc_start: 0.7660 (tt0) cc_final: 0.7285 (mt0)
REVERT: C   75 MET cc_start: 0.7192 (tmm) cc_final: 0.6883 (tpp)
REVERT: C   76 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7965 (ttpt)
REVERT: C   85 GLU cc_start: 0.7321 (mp0) cc_final: 0.6836 (mp0)
REVERT: C   92 GLU cc_start: 0.7389 (tp30) cc_final: 0.7159 (tp30)
REVERT: C  108 GLU cc_start: 0.7069 (pp20) cc_final: 0.6846 (tm-30)
REVERT: C  165 LYS cc_start: 0.8074 (pttp) cc_final: 0.7444 (ptpt)
REVERT: C  171 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6959 (mm-30)
REVERT: C  205 LEU cc_start: 0.8528 (mt) cc_final: 0.8041 (tp)
REVERT: C  209 LYS cc_start: 0.8222 (ptmm) cc_final: 0.7757 (ptmm)
REVERT: C  215 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7794 (ttmm)
REVERT: C  218 PHE cc_start: 0.8605 (p90) cc_final: 0.8372 (p90)
REVERT: C  229 ASN cc_start: 0.7461 (t0) cc_final: 0.7222 (t0)
REVERT: C  230 MET cc_start: 0.5703 (mtm) cc_final: 0.5345 (mtm)
REVERT: E    1 MET cc_start: 0.7197 (mtm) cc_final: 0.6949 (mtm)
REVERT: E   11 ASP cc_start: 0.7024 (t0) cc_final: 0.6695 (t70)
REVERT: E   13 LEU cc_start: 0.7326 (tp) cc_final: 0.6965 (tp)
REVERT: E   46 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7363 (tm-30)
REVERT: E   48 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7715 (mmmm)
REVERT: E   77 ASP cc_start: 0.7979 (t70) cc_final: 0.7736 (t70)
REVERT: E   86 LYS cc_start: 0.7823 (tppt) cc_final: 0.7545 (mmmm)
REVERT: E  101 LYS cc_start: 0.8675 (pttm) cc_final: 0.8030 (pttm)
REVERT: E  117 GLU cc_start: 0.5044 (mp0) cc_final: 0.4697 (mp0)
REVERT: E  126 SER cc_start: 0.8354 (t) cc_final: 0.7858 (p)
REVERT: E  135 THR cc_start: 0.8008 (m) cc_final: 0.7666 (p)
REVERT: E  174 ILE cc_start: 0.7954 (mm) cc_final: 0.7685 (tp)
REVERT: E  203 LEU cc_start: 0.7784 (mt) cc_final: 0.7544 (mt)
REVERT: E  206 ASP cc_start: 0.7947 (p0) cc_final: 0.7656 (p0)
REVERT: E  216 GLU cc_start: 0.6957 (tp30) cc_final: 0.6503 (tp30)
REVERT: E  224 THR cc_start: 0.7104 (p) cc_final: 0.6879 (p)
REVERT: E  236 MET cc_start: 0.7529 (ptp) cc_final: 0.7297 (ptp)
REVERT: E  239 GLU cc_start: 0.7418 (tp30) cc_final: 0.6564 (mp0)
REVERT: E  248 LEU cc_start: 0.6691 (mp) cc_final: 0.6455 (mp)
REVERT: E  265 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7500 (mtp85)
REVERT: E  270 LYS cc_start: 0.7370 (tttt) cc_final: 0.7099 (tttt)
REVERT: E  274 LYS cc_start: 0.7188 (mppt) cc_final: 0.6733 (mppt)
REVERT: E  290 PRO cc_start: 0.8054 (Cg_endo) cc_final: 0.7618 (Cg_exo)
REVERT: E  294 ASP cc_start: 0.8554 (p0) cc_final: 0.7993 (p0)
REVERT: E  325 GLN cc_start: 0.7322 (mm-40) cc_final: 0.7028 (tp-100)
REVERT: E  326 GLU cc_start: 0.7495 (tp30) cc_final: 0.6675 (tp30)
REVERT: E  328 MET cc_start: 0.7837 (mtm) cc_final: 0.6885 (mtm)
REVERT: E  329 HIS cc_start: 0.7159 (m90) cc_final: 0.5890 (m-70)
REVERT: E  363 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8279 (mmtp)
REVERT: E  397 LYS cc_start: 0.7963 (mmmt) cc_final: 0.7632 (mmtp)
REVERT: E  434 LEU cc_start: 0.8434 (tp) cc_final: 0.8000 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 350
  average time/residue: 0.2922
  time to fit residues: 133.3379
Evaluate side-chains
  324 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 323
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 116 GLN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.103  10899  Z= 0.380
  Angle     :  0.720  10.638  14963  Z= 0.391
  Chirality :  0.048   0.203   1723
  Planarity :  0.005   0.067   1683
  Dihedral  : 21.318 158.550   1931
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.64 %
    Favored  : 87.28 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.48 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.23), residues: 1171
  helix: -1.24 (0.30), residues: 284
  sheet: -0.44 (0.31), residues: 302
  loop : -3.01 (0.22), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.004   TRP E  50 
 HIS   0.005   0.001   HIS E 386 
 PHE   0.022   0.003   PHE C 228 
 TYR   0.030   0.002   TYR C  59 
 ARG   0.006   0.001   ARG E 234 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 350
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5649 (t70) cc_final: 0.5371 (t0)
REVERT: A   39 HIS cc_start: 0.7644 (t-90) cc_final: 0.7070 (t-90)
REVERT: A   55 ASP cc_start: 0.7804 (t0) cc_final: 0.7578 (t0)
REVERT: A   57 LEU cc_start: 0.8192 (mt) cc_final: 0.7886 (mt)
REVERT: A   59 GLU cc_start: 0.8485 (tp30) cc_final: 0.8133 (tp30)
REVERT: A   99 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7889 (mtpp)
REVERT: A  113 ILE cc_start: 0.8134 (mt) cc_final: 0.7677 (mm)
REVERT: A  116 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7488 (tptt)
REVERT: A  119 LYS cc_start: 0.7219 (mppt) cc_final: 0.6921 (mppt)
REVERT: A  136 PHE cc_start: 0.7409 (p90) cc_final: 0.7167 (p90)
REVERT: A  169 GLU cc_start: 0.6228 (tp30) cc_final: 0.5877 (mm-30)
REVERT: A  213 ARG cc_start: 0.7015 (mtt90) cc_final: 0.6772 (mtt90)
REVERT: A  220 MET cc_start: 0.7501 (tmm) cc_final: 0.7269 (ttp)
REVERT: A  229 MET cc_start: 0.6372 (ttt) cc_final: 0.6090 (ttt)
REVERT: B   11 SER cc_start: 0.8316 (m) cc_final: 0.7891 (p)
REVERT: B   21 ASP cc_start: 0.7251 (t0) cc_final: 0.6332 (t0)
REVERT: B   22 PHE cc_start: 0.7761 (m-80) cc_final: 0.7363 (m-10)
REVERT: B   67 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6256 (mt-10)
REVERT: B  107 THR cc_start: 0.8024 (p) cc_final: 0.7726 (t)
REVERT: B  132 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8177 (ttmm)
REVERT: B  155 ASN cc_start: 0.7500 (t0) cc_final: 0.7228 (t0)
REVERT: B  162 LYS cc_start: 0.8277 (mttp) cc_final: 0.8025 (mmmt)
REVERT: C    6 ASP cc_start: 0.7697 (t0) cc_final: 0.7452 (t0)
REVERT: C    7 ASP cc_start: 0.7894 (t70) cc_final: 0.7509 (t0)
REVERT: C   28 LYS cc_start: 0.8668 (mttp) cc_final: 0.8045 (mttp)
REVERT: C   30 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7358 (tppp)
REVERT: C   35 GLU cc_start: 0.6976 (mp0) cc_final: 0.6645 (pm20)
REVERT: C   72 GLN cc_start: 0.7690 (tt0) cc_final: 0.7411 (mt0)
REVERT: C   75 MET cc_start: 0.7057 (tmm) cc_final: 0.6812 (tpp)
REVERT: C   76 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7967 (ttmt)
REVERT: C   92 GLU cc_start: 0.7428 (tp30) cc_final: 0.7211 (tp30)
REVERT: C   95 ASP cc_start: 0.8486 (t70) cc_final: 0.8137 (t70)
REVERT: C  108 GLU cc_start: 0.7011 (pp20) cc_final: 0.6515 (tm-30)
REVERT: C  165 LYS cc_start: 0.7959 (pttp) cc_final: 0.7402 (ptpt)
REVERT: C  171 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6959 (mm-30)
REVERT: C  215 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7756 (ttmm)
REVERT: C  218 PHE cc_start: 0.8564 (p90) cc_final: 0.8291 (p90)
REVERT: C  229 ASN cc_start: 0.7332 (t0) cc_final: 0.7011 (t0)
REVERT: C  230 MET cc_start: 0.5925 (mtm) cc_final: 0.5344 (mtm)
REVERT: E    1 MET cc_start: 0.7280 (mtm) cc_final: 0.7036 (mtm)
REVERT: E   13 LEU cc_start: 0.7581 (tp) cc_final: 0.7354 (tp)
REVERT: E   15 LYS cc_start: 0.8554 (mtmt) cc_final: 0.8077 (mmtt)
REVERT: E   46 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: E   48 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7702 (mmmm)
REVERT: E   49 LEU cc_start: 0.7298 (mt) cc_final: 0.6965 (mt)
REVERT: E   58 GLU cc_start: 0.6941 (pt0) cc_final: 0.6510 (pt0)
REVERT: E   78 GLU cc_start: 0.7694 (pp20) cc_final: 0.7469 (pp20)
REVERT: E   86 LYS cc_start: 0.7897 (tppt) cc_final: 0.7576 (mmmm)
REVERT: E  101 LYS cc_start: 0.8640 (pttm) cc_final: 0.8001 (pttm)
REVERT: E  117 GLU cc_start: 0.5147 (mp0) cc_final: 0.4774 (mp0)
REVERT: E  126 SER cc_start: 0.8405 (t) cc_final: 0.7886 (p)
REVERT: E  127 THR cc_start: 0.8050 (m) cc_final: 0.7820 (m)
REVERT: E  135 THR cc_start: 0.8083 (m) cc_final: 0.7830 (p)
REVERT: E  137 GLU cc_start: 0.7261 (tp30) cc_final: 0.7059 (tp30)
REVERT: E  174 ILE cc_start: 0.7934 (mm) cc_final: 0.7667 (tp)
REVERT: E  194 SER cc_start: 0.8161 (p) cc_final: 0.7958 (p)
REVERT: E  202 ASN cc_start: 0.8170 (m110) cc_final: 0.7928 (m110)
REVERT: E  206 ASP cc_start: 0.8049 (p0) cc_final: 0.7777 (p0)
REVERT: E  216 GLU cc_start: 0.7191 (tp30) cc_final: 0.6758 (tp30)
REVERT: E  224 THR cc_start: 0.7269 (p) cc_final: 0.7051 (p)
REVERT: E  239 GLU cc_start: 0.6970 (tp30) cc_final: 0.6397 (mp0)
REVERT: E  248 LEU cc_start: 0.6798 (mp) cc_final: 0.6552 (mp)
REVERT: E  265 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7453 (mtm180)
REVERT: E  274 LYS cc_start: 0.7207 (mppt) cc_final: 0.6666 (mppt)
REVERT: E  285 ILE cc_start: 0.8789 (pt) cc_final: 0.8319 (mm)
REVERT: E  290 PRO cc_start: 0.7954 (Cg_endo) cc_final: 0.7460 (Cg_exo)
REVERT: E  294 ASP cc_start: 0.8597 (p0) cc_final: 0.8051 (p0)
REVERT: E  325 GLN cc_start: 0.7359 (mm-40) cc_final: 0.7050 (tp-100)
REVERT: E  326 GLU cc_start: 0.7850 (tp30) cc_final: 0.7577 (tp30)
REVERT: E  328 MET cc_start: 0.7695 (mtm) cc_final: 0.6458 (mtm)
REVERT: E  353 MET cc_start: 0.6579 (tpp) cc_final: 0.6275 (tpp)
REVERT: E  360 TYR cc_start: 0.8028 (m-80) cc_final: 0.7782 (m-10)
REVERT: E  373 GLU cc_start: 0.7887 (tp30) cc_final: 0.7557 (mm-30)
REVERT: E  397 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7676 (mmtp)
  outliers start: 1
  outliers final: 1
  residues processed: 351
  average time/residue: 0.2934
  time to fit residues: 134.6192
Evaluate side-chains
  316 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 315
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0270
   chunk 100 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
E  75 ASN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10899  Z= 0.187
  Angle     :  0.600  10.331  14963  Z= 0.325
  Chirality :  0.044   0.169   1723
  Planarity :  0.004   0.061   1683
  Dihedral  : 21.111 154.355   1931
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.24), residues: 1171
  helix: -0.75 (0.32), residues: 276
  sheet: -0.00 (0.32), residues: 309
  loop : -2.96 (0.23), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  50 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.021   0.002   PHE E  10 
 TYR   0.016   0.001   TYR B 218 
 ARG   0.006   0.000   ARG C 112 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 347
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5613 (t70) cc_final: 0.5300 (t0)
REVERT: A   38 ARG cc_start: 0.7648 (ttt-90) cc_final: 0.7361 (ttt90)
REVERT: A   39 HIS cc_start: 0.7683 (t-90) cc_final: 0.7113 (t-90)
REVERT: A   55 ASP cc_start: 0.7772 (t0) cc_final: 0.7560 (t0)
REVERT: A   57 LEU cc_start: 0.8162 (mt) cc_final: 0.7908 (mt)
REVERT: A   99 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7848 (mtpp)
REVERT: A  113 ILE cc_start: 0.7943 (mt) cc_final: 0.7581 (mm)
REVERT: A  116 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7628 (tptt)
REVERT: A  136 PHE cc_start: 0.7388 (p90) cc_final: 0.7078 (p90)
REVERT: A  169 GLU cc_start: 0.6116 (tp30) cc_final: 0.5777 (mm-30)
REVERT: A  190 LEU cc_start: 0.7677 (tp) cc_final: 0.7461 (mt)
REVERT: A  213 ARG cc_start: 0.6989 (mtt90) cc_final: 0.6615 (mtt90)
REVERT: A  229 MET cc_start: 0.6319 (ttt) cc_final: 0.6049 (ttt)
REVERT: B   21 ASP cc_start: 0.7460 (t0) cc_final: 0.6550 (t0)
REVERT: B   22 PHE cc_start: 0.7597 (m-80) cc_final: 0.7241 (m-10)
REVERT: B   73 LEU cc_start: 0.7142 (tp) cc_final: 0.6823 (tp)
REVERT: B  132 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8084 (ttmm)
REVERT: B  155 ASN cc_start: 0.7555 (t0) cc_final: 0.7150 (t0)
REVERT: B  159 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7705 (ttmm)
REVERT: B  162 LYS cc_start: 0.8179 (mttp) cc_final: 0.7951 (mmmt)
REVERT: C    2 LYS cc_start: 0.7609 (tppt) cc_final: 0.7212 (tppt)
REVERT: C    3 VAL cc_start: 0.8678 (t) cc_final: 0.8145 (p)
REVERT: C    6 ASP cc_start: 0.7542 (t0) cc_final: 0.7287 (t0)
REVERT: C    7 ASP cc_start: 0.7867 (t70) cc_final: 0.7543 (t0)
REVERT: C   28 LYS cc_start: 0.8665 (mttp) cc_final: 0.8011 (mttp)
REVERT: C   30 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7312 (tppp)
REVERT: C   35 GLU cc_start: 0.6914 (mp0) cc_final: 0.6601 (pm20)
REVERT: C   75 MET cc_start: 0.6914 (tmm) cc_final: 0.6670 (tpp)
REVERT: C   76 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7954 (ttpt)
REVERT: C   77 ILE cc_start: 0.8221 (pt) cc_final: 0.7941 (tt)
REVERT: C   85 GLU cc_start: 0.7434 (mp0) cc_final: 0.6994 (mp0)
REVERT: C  140 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7534 (tptp)
REVERT: C  159 GLU cc_start: 0.7167 (tp30) cc_final: 0.6956 (tp30)
REVERT: C  165 LYS cc_start: 0.8057 (pttp) cc_final: 0.7358 (ptpt)
REVERT: C  171 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7008 (mm-30)
REVERT: C  189 SER cc_start: 0.8175 (t) cc_final: 0.7727 (p)
REVERT: C  205 LEU cc_start: 0.8432 (mt) cc_final: 0.7978 (tp)
REVERT: C  215 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7706 (ttmm)
REVERT: C  218 PHE cc_start: 0.8532 (p90) cc_final: 0.8251 (p90)
REVERT: C  229 ASN cc_start: 0.7431 (t0) cc_final: 0.7149 (t0)
REVERT: C  230 MET cc_start: 0.5850 (mtm) cc_final: 0.5281 (mtm)
REVERT: E    1 MET cc_start: 0.7309 (mtm) cc_final: 0.6982 (mtm)
REVERT: E    6 ILE cc_start: 0.6776 (tp) cc_final: 0.6398 (tp)
REVERT: E   15 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7963 (mmtt)
REVERT: E   46 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7599 (tm-30)
REVERT: E   48 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7804 (mmmm)
REVERT: E   58 GLU cc_start: 0.7009 (pt0) cc_final: 0.6599 (pt0)
REVERT: E   78 GLU cc_start: 0.7730 (pp20) cc_final: 0.7492 (pp20)
REVERT: E   86 LYS cc_start: 0.7739 (tppt) cc_final: 0.7477 (mmmm)
REVERT: E  101 LYS cc_start: 0.8763 (pttm) cc_final: 0.8165 (pttm)
REVERT: E  126 SER cc_start: 0.8393 (t) cc_final: 0.7828 (p)
REVERT: E  127 THR cc_start: 0.8115 (m) cc_final: 0.7898 (m)
REVERT: E  135 THR cc_start: 0.7837 (m) cc_final: 0.7474 (p)
REVERT: E  174 ILE cc_start: 0.8032 (mm) cc_final: 0.7679 (tp)
REVERT: E  194 SER cc_start: 0.8155 (p) cc_final: 0.7947 (p)
REVERT: E  202 ASN cc_start: 0.8168 (m110) cc_final: 0.7934 (m110)
REVERT: E  216 GLU cc_start: 0.6912 (tp30) cc_final: 0.6507 (tp30)
REVERT: E  223 LYS cc_start: 0.7572 (mmtp) cc_final: 0.7287 (mmtm)
REVERT: E  239 GLU cc_start: 0.6953 (tp30) cc_final: 0.6473 (mp0)
REVERT: E  248 LEU cc_start: 0.6684 (mp) cc_final: 0.6431 (mp)
REVERT: E  265 ARG cc_start: 0.7731 (mtp180) cc_final: 0.7423 (mtm180)
REVERT: E  274 LYS cc_start: 0.7197 (mppt) cc_final: 0.6735 (mppt)
REVERT: E  285 ILE cc_start: 0.8785 (pt) cc_final: 0.8398 (tt)
REVERT: E  290 PRO cc_start: 0.7950 (Cg_endo) cc_final: 0.7489 (Cg_exo)
REVERT: E  294 ASP cc_start: 0.8460 (p0) cc_final: 0.7812 (p0)
REVERT: E  326 GLU cc_start: 0.7688 (tp30) cc_final: 0.7420 (tp30)
REVERT: E  328 MET cc_start: 0.7640 (mtm) cc_final: 0.6508 (mtm)
REVERT: E  397 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7625 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 347
  average time/residue: 0.2856
  time to fit residues: 128.8170
Evaluate side-chains
  329 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 329
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 23 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 118 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10899  Z= 0.203
  Angle     :  0.604  10.097  14963  Z= 0.325
  Chirality :  0.044   0.163   1723
  Planarity :  0.004   0.057   1683
  Dihedral  : 21.119 153.713   1931
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.24), residues: 1171
  helix: -0.62 (0.32), residues: 271
  sheet:  0.06 (0.31), residues: 311
  loop : -2.93 (0.23), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E  50 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.020   0.002   PHE E  10 
 TYR   0.022   0.001   TYR B 197 
 ARG   0.012   0.000   ARG E 234 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 343
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7567 (ttpp)
REVERT: A   24 ASP cc_start: 0.5619 (t70) cc_final: 0.5302 (t0)
REVERT: A   39 HIS cc_start: 0.7632 (t-90) cc_final: 0.7091 (t-90)
REVERT: A   55 ASP cc_start: 0.7786 (t0) cc_final: 0.7537 (t0)
REVERT: A   57 LEU cc_start: 0.8140 (mt) cc_final: 0.7866 (mt)
REVERT: A   65 PRO cc_start: 0.6646 (Cg_exo) cc_final: 0.6327 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7405 (mppt) cc_final: 0.7089 (mmtp)
REVERT: A   90 GLU cc_start: 0.6279 (tm-30) cc_final: 0.6063 (tm-30)
REVERT: A   99 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7834 (mtpp)
REVERT: A  112 THR cc_start: 0.7220 (p) cc_final: 0.6475 (p)
REVERT: A  113 ILE cc_start: 0.7933 (mt) cc_final: 0.7602 (mm)
REVERT: A  116 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7626 (tptt)
REVERT: A  119 LYS cc_start: 0.7125 (mppt) cc_final: 0.6854 (mppt)
REVERT: A  136 PHE cc_start: 0.7498 (p90) cc_final: 0.7104 (p90)
REVERT: A  169 GLU cc_start: 0.6102 (tp30) cc_final: 0.5782 (mm-30)
REVERT: A  229 MET cc_start: 0.6358 (ttt) cc_final: 0.6035 (ttt)
REVERT: B   21 ASP cc_start: 0.7543 (t0) cc_final: 0.6616 (t0)
REVERT: B   22 PHE cc_start: 0.7684 (m-80) cc_final: 0.7318 (m-10)
REVERT: B   73 LEU cc_start: 0.7101 (tp) cc_final: 0.6792 (tp)
REVERT: B  107 THR cc_start: 0.8032 (p) cc_final: 0.7706 (t)
REVERT: B  132 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8152 (ttmm)
REVERT: B  155 ASN cc_start: 0.7450 (t0) cc_final: 0.7027 (t0)
REVERT: B  162 LYS cc_start: 0.7901 (mttp) cc_final: 0.7616 (mmmt)
REVERT: C    6 ASP cc_start: 0.7503 (t0) cc_final: 0.7224 (t0)
REVERT: C    7 ASP cc_start: 0.7837 (t70) cc_final: 0.7495 (t0)
REVERT: C   30 LYS cc_start: 0.7883 (mmtm) cc_final: 0.7174 (tppp)
REVERT: C   35 GLU cc_start: 0.6910 (mp0) cc_final: 0.6569 (pm20)
REVERT: C   55 MET cc_start: 0.7057 (ttm) cc_final: 0.6851 (ttm)
REVERT: C   72 GLN cc_start: 0.7663 (tt0) cc_final: 0.7114 (mt0)
REVERT: C   75 MET cc_start: 0.7001 (tmm) cc_final: 0.6772 (tpp)
REVERT: C   77 ILE cc_start: 0.8268 (pt) cc_final: 0.7930 (tt)
REVERT: C   85 GLU cc_start: 0.7457 (mp0) cc_final: 0.6923 (mp0)
REVERT: C  154 VAL cc_start: 0.8000 (t) cc_final: 0.7610 (p)
REVERT: C  165 LYS cc_start: 0.7998 (pttp) cc_final: 0.7223 (ptpt)
REVERT: C  171 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6885 (mm-30)
REVERT: C  189 SER cc_start: 0.8166 (t) cc_final: 0.7736 (p)
REVERT: C  205 LEU cc_start: 0.8562 (mt) cc_final: 0.8150 (tp)
REVERT: C  218 PHE cc_start: 0.8520 (p90) cc_final: 0.8238 (p90)
REVERT: C  220 ASN cc_start: 0.6491 (t0) cc_final: 0.6279 (t0)
REVERT: C  229 ASN cc_start: 0.7427 (t0) cc_final: 0.7141 (t0)
REVERT: C  230 MET cc_start: 0.5737 (mtm) cc_final: 0.5196 (mtm)
REVERT: E    6 ILE cc_start: 0.6743 (tp) cc_final: 0.6383 (tp)
REVERT: E   15 LYS cc_start: 0.8444 (mtmt) cc_final: 0.7951 (mmtt)
REVERT: E   46 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7403 (tm-30)
REVERT: E   58 GLU cc_start: 0.7016 (pt0) cc_final: 0.6570 (pt0)
REVERT: E   78 GLU cc_start: 0.7752 (pp20) cc_final: 0.7440 (pp20)
REVERT: E   86 LYS cc_start: 0.7719 (tppt) cc_final: 0.7467 (mmmm)
REVERT: E  101 LYS cc_start: 0.8794 (pttm) cc_final: 0.8174 (pttm)
REVERT: E  126 SER cc_start: 0.8349 (t) cc_final: 0.7909 (p)
REVERT: E  174 ILE cc_start: 0.7987 (mm) cc_final: 0.7670 (tp)
REVERT: E  194 SER cc_start: 0.8197 (p) cc_final: 0.7988 (p)
REVERT: E  216 GLU cc_start: 0.6986 (tp30) cc_final: 0.6518 (tp30)
REVERT: E  239 GLU cc_start: 0.6981 (tp30) cc_final: 0.6491 (mp0)
REVERT: E  274 LYS cc_start: 0.7174 (mppt) cc_final: 0.6906 (mppt)
REVERT: E  285 ILE cc_start: 0.8772 (pt) cc_final: 0.8395 (tt)
REVERT: E  290 PRO cc_start: 0.8006 (Cg_endo) cc_final: 0.7582 (Cg_exo)
REVERT: E  294 ASP cc_start: 0.8471 (p0) cc_final: 0.7938 (p0)
REVERT: E  325 GLN cc_start: 0.7346 (tp-100) cc_final: 0.7035 (tp-100)
REVERT: E  326 GLU cc_start: 0.7849 (tp30) cc_final: 0.6687 (tp30)
REVERT: E  329 HIS cc_start: 0.7128 (m90) cc_final: 0.5892 (m-70)
REVERT: E  352 LEU cc_start: 0.7543 (tp) cc_final: 0.7333 (tp)
REVERT: E  360 TYR cc_start: 0.7410 (m-10) cc_final: 0.6948 (m-80)
REVERT: E  397 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7615 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 343
  average time/residue: 0.2918
  time to fit residues: 130.0549
Evaluate side-chains
  322 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 157 HIS
C 110 ASN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  10899  Z= 0.272
  Angle     :  0.656  10.623  14963  Z= 0.354
  Chirality :  0.045   0.157   1723
  Planarity :  0.005   0.059   1683
  Dihedral  : 21.249 156.356   1931
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.76 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.24), residues: 1171
  helix: -0.90 (0.31), residues: 280
  sheet: -0.08 (0.31), residues: 311
  loop : -2.98 (0.23), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP E  50 
 HIS   0.008   0.001   HIS B 157 
 PHE   0.023   0.002   PHE E  10 
 TYR   0.018   0.002   TYR C  59 
 ARG   0.006   0.001   ARG A 103 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 335
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5612 (t70) cc_final: 0.5288 (t0)
REVERT: A   55 ASP cc_start: 0.7847 (t0) cc_final: 0.7594 (t0)
REVERT: A   57 LEU cc_start: 0.8144 (mt) cc_final: 0.7843 (mt)
REVERT: A   65 PRO cc_start: 0.6655 (Cg_exo) cc_final: 0.6353 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7302 (mppt) cc_final: 0.7044 (mmtp)
REVERT: A   90 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6321 (tm-30)
REVERT: A   99 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7808 (mtpp)
REVERT: A  101 ILE cc_start: 0.8160 (tp) cc_final: 0.7933 (tp)
REVERT: A  112 THR cc_start: 0.7247 (p) cc_final: 0.6928 (p)
REVERT: A  113 ILE cc_start: 0.7982 (mt) cc_final: 0.7590 (mm)
REVERT: A  116 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7590 (tptt)
REVERT: A  119 LYS cc_start: 0.7148 (mppt) cc_final: 0.6894 (mppt)
REVERT: A  144 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7359 (t0)
REVERT: A  203 GLU cc_start: 0.7165 (tp30) cc_final: 0.6784 (tp30)
REVERT: A  229 MET cc_start: 0.6281 (ttt) cc_final: 0.6029 (ttt)
REVERT: B   21 ASP cc_start: 0.7514 (t0) cc_final: 0.6603 (t0)
REVERT: B   22 PHE cc_start: 0.7658 (m-80) cc_final: 0.7304 (m-10)
REVERT: B   36 ARG cc_start: 0.7076 (mtt-85) cc_final: 0.6857 (mtp85)
REVERT: B   66 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7984 (mmmt)
REVERT: B  107 THR cc_start: 0.8047 (p) cc_final: 0.7692 (t)
REVERT: B  132 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8001 (ttmm)
REVERT: B  155 ASN cc_start: 0.7440 (t0) cc_final: 0.6924 (t0)
REVERT: B  159 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7647 (ttmm)
REVERT: B  162 LYS cc_start: 0.7879 (mttp) cc_final: 0.7613 (mmmt)
REVERT: B  177 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6635 (tm-30)
REVERT: C    2 LYS cc_start: 0.7705 (tppt) cc_final: 0.7341 (tppt)
REVERT: C    6 ASP cc_start: 0.7697 (t0) cc_final: 0.7334 (t0)
REVERT: C    7 ASP cc_start: 0.7886 (t70) cc_final: 0.7537 (t0)
REVERT: C   30 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7140 (tppp)
REVERT: C   35 GLU cc_start: 0.6975 (mp0) cc_final: 0.6613 (pm20)
REVERT: C   55 MET cc_start: 0.7035 (ttm) cc_final: 0.6773 (ttm)
REVERT: C   72 GLN cc_start: 0.7708 (tt0) cc_final: 0.7453 (mt0)
REVERT: C   75 MET cc_start: 0.7055 (tmm) cc_final: 0.6787 (tpp)
REVERT: C   76 LYS cc_start: 0.8314 (ttmt) cc_final: 0.8079 (ttpt)
REVERT: C   88 GLU cc_start: 0.7433 (pp20) cc_final: 0.6631 (pm20)
REVERT: C  165 LYS cc_start: 0.8044 (pttp) cc_final: 0.7531 (ptpt)
REVERT: C  171 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7046 (mm-30)
REVERT: C  189 SER cc_start: 0.8148 (t) cc_final: 0.7719 (p)
REVERT: C  205 LEU cc_start: 0.8424 (mt) cc_final: 0.8166 (tp)
REVERT: C  218 PHE cc_start: 0.8538 (p90) cc_final: 0.8226 (p90)
REVERT: C  220 ASN cc_start: 0.6482 (t0) cc_final: 0.6263 (t0)
REVERT: C  229 ASN cc_start: 0.7431 (t0) cc_final: 0.7151 (t0)
REVERT: C  230 MET cc_start: 0.5804 (mtm) cc_final: 0.5246 (mtm)
REVERT: E    6 ILE cc_start: 0.6819 (tp) cc_final: 0.6495 (tp)
REVERT: E   12 LYS cc_start: 0.7234 (ptmt) cc_final: 0.6928 (ptmt)
REVERT: E   15 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7980 (mmtm)
REVERT: E   46 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: E   49 LEU cc_start: 0.7326 (mt) cc_final: 0.7107 (mt)
REVERT: E   58 GLU cc_start: 0.7052 (pt0) cc_final: 0.6569 (pt0)
REVERT: E   78 GLU cc_start: 0.7768 (pp20) cc_final: 0.7445 (pp20)
REVERT: E   86 LYS cc_start: 0.7819 (tppt) cc_final: 0.7548 (mmmm)
REVERT: E  101 LYS cc_start: 0.8675 (pttm) cc_final: 0.8468 (pttm)
REVERT: E  126 SER cc_start: 0.8341 (t) cc_final: 0.7798 (p)
REVERT: E  127 THR cc_start: 0.7888 (m) cc_final: 0.7629 (m)
REVERT: E  174 ILE cc_start: 0.7968 (mm) cc_final: 0.7564 (tp)
REVERT: E  202 ASN cc_start: 0.8013 (m110) cc_final: 0.7787 (m110)
REVERT: E  216 GLU cc_start: 0.6986 (tp30) cc_final: 0.6530 (tp30)
REVERT: E  239 GLU cc_start: 0.6938 (tp30) cc_final: 0.6497 (mp0)
REVERT: E  265 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7035 (mtm180)
REVERT: E  270 LYS cc_start: 0.7516 (tttt) cc_final: 0.7305 (ttmt)
REVERT: E  274 LYS cc_start: 0.7159 (mppt) cc_final: 0.6703 (mppt)
REVERT: E  285 ILE cc_start: 0.8869 (pt) cc_final: 0.8435 (tt)
REVERT: E  290 PRO cc_start: 0.8023 (Cg_endo) cc_final: 0.7581 (Cg_exo)
REVERT: E  294 ASP cc_start: 0.8573 (p0) cc_final: 0.7987 (p0)
REVERT: E  397 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7616 (mmtp)
  outliers start: 1
  outliers final: 0
  residues processed: 335
  average time/residue: 0.2994
  time to fit residues: 130.3531
Evaluate side-chains
  322 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 321
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0050
   chunk 10 optimal weight:    0.5980
   chunk 92 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
E  75 ASN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10899  Z= 0.193
  Angle     :  0.627  10.665  14963  Z= 0.333
  Chirality :  0.044   0.179   1723
  Planarity :  0.004   0.059   1683
  Dihedral  : 21.156 153.698   1931
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.24), residues: 1171
  helix: -0.79 (0.31), residues: 286
  sheet:  0.04 (0.31), residues: 309
  loop : -2.98 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E  50 
 HIS   0.002   0.000   HIS A  39 
 PHE   0.023   0.002   PHE E  10 
 TYR   0.015   0.001   TYR E 354 
 ARG   0.006   0.000   ARG A 103 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 351
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.7620 (t-90) cc_final: 0.7166 (t-90)
REVERT: A   55 ASP cc_start: 0.7809 (t0) cc_final: 0.7522 (t0)
REVERT: A   57 LEU cc_start: 0.8134 (mt) cc_final: 0.7930 (mt)
REVERT: A   65 PRO cc_start: 0.6664 (Cg_exo) cc_final: 0.6326 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7427 (mppt) cc_final: 0.7193 (mmtp)
REVERT: A  112 THR cc_start: 0.7180 (p) cc_final: 0.6794 (p)
REVERT: A  116 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7603 (tptt)
REVERT: A  210 LYS cc_start: 0.8122 (mttp) cc_final: 0.7916 (mtmt)
REVERT: A  227 LEU cc_start: 0.7659 (tp) cc_final: 0.7292 (tt)
REVERT: A  234 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6203 (mp0)
REVERT: B   21 ASP cc_start: 0.7361 (t0) cc_final: 0.6422 (t0)
REVERT: B   22 PHE cc_start: 0.7602 (m-80) cc_final: 0.7275 (m-10)
REVERT: B   97 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7639 (ptmm)
REVERT: B  107 THR cc_start: 0.8051 (p) cc_final: 0.7717 (t)
REVERT: B  132 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8169 (ttmm)
REVERT: B  159 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7540 (ttmm)
REVERT: B  166 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6426 (mm-30)
REVERT: B  200 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6700 (tm-30)
REVERT: C    7 ASP cc_start: 0.7833 (t70) cc_final: 0.7533 (t0)
REVERT: C   30 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7132 (tppp)
REVERT: C   35 GLU cc_start: 0.6954 (mp0) cc_final: 0.6547 (pm20)
REVERT: C   55 MET cc_start: 0.7102 (ttm) cc_final: 0.6731 (ttm)
REVERT: C   60 ASP cc_start: 0.6251 (p0) cc_final: 0.5819 (p0)
REVERT: C   72 GLN cc_start: 0.7639 (tt0) cc_final: 0.7271 (mt0)
REVERT: C   75 MET cc_start: 0.7022 (tmm) cc_final: 0.6821 (tpp)
REVERT: C   85 GLU cc_start: 0.7511 (mp0) cc_final: 0.7132 (mp0)
REVERT: C   88 GLU cc_start: 0.7386 (pp20) cc_final: 0.6885 (pp20)
REVERT: C  165 LYS cc_start: 0.8009 (pttp) cc_final: 0.7495 (ptpt)
REVERT: C  171 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6949 (mm-30)
REVERT: C  189 SER cc_start: 0.8141 (t) cc_final: 0.7708 (p)
REVERT: C  195 SER cc_start: 0.8445 (m) cc_final: 0.8239 (p)
REVERT: C  205 LEU cc_start: 0.8361 (mt) cc_final: 0.7990 (tp)
REVERT: C  218 PHE cc_start: 0.8514 (p90) cc_final: 0.8191 (p90)
REVERT: C  220 ASN cc_start: 0.6504 (t0) cc_final: 0.6292 (t0)
REVERT: C  229 ASN cc_start: 0.7387 (t0) cc_final: 0.7102 (t0)
REVERT: C  230 MET cc_start: 0.5802 (mtm) cc_final: 0.5315 (mtm)
REVERT: E    6 ILE cc_start: 0.6799 (tp) cc_final: 0.6494 (tp)
REVERT: E   12 LYS cc_start: 0.7274 (ptmt) cc_final: 0.7015 (ptmt)
REVERT: E   15 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8092 (mmtm)
REVERT: E   46 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7452 (tm-30)
REVERT: E   49 LEU cc_start: 0.7361 (mt) cc_final: 0.7153 (mt)
REVERT: E   58 GLU cc_start: 0.7046 (pt0) cc_final: 0.6772 (pt0)
REVERT: E   78 GLU cc_start: 0.7756 (pp20) cc_final: 0.7424 (pp20)
REVERT: E   86 LYS cc_start: 0.7780 (tppt) cc_final: 0.7515 (mmmm)
REVERT: E  126 SER cc_start: 0.8328 (t) cc_final: 0.7780 (p)
REVERT: E  127 THR cc_start: 0.7862 (m) cc_final: 0.7582 (m)
REVERT: E  174 ILE cc_start: 0.7971 (mm) cc_final: 0.7678 (tp)
REVERT: E  198 GLU cc_start: 0.6907 (mp0) cc_final: 0.6587 (mp0)
REVERT: E  202 ASN cc_start: 0.8074 (m110) cc_final: 0.7827 (m110)
REVERT: E  203 LEU cc_start: 0.7760 (mt) cc_final: 0.7467 (mt)
REVERT: E  216 GLU cc_start: 0.6927 (tp30) cc_final: 0.6726 (mm-30)
REVERT: E  239 GLU cc_start: 0.6988 (tp30) cc_final: 0.6512 (mp0)
REVERT: E  270 LYS cc_start: 0.7258 (tttt) cc_final: 0.7051 (ttmt)
REVERT: E  274 LYS cc_start: 0.7214 (mppt) cc_final: 0.6908 (mppt)
REVERT: E  285 ILE cc_start: 0.8738 (pt) cc_final: 0.8361 (tt)
REVERT: E  290 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7635 (Cg_exo)
REVERT: E  294 ASP cc_start: 0.8485 (p0) cc_final: 0.7935 (p0)
REVERT: E  325 GLN cc_start: 0.7416 (tp-100) cc_final: 0.7128 (tp-100)
REVERT: E  397 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7569 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 351
  average time/residue: 0.2845
  time to fit residues: 130.8661
Evaluate side-chains
  316 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 112 optimal weight:    0.5980
   chunk 102 optimal weight:    0.7980
   chunk 109 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0070
   chunk 71 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0870
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
E  75 ASN
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10899  Z= 0.175
  Angle     :  0.615   9.911  14963  Z= 0.327
  Chirality :  0.044   0.164   1723
  Planarity :  0.004   0.057   1683
  Dihedral  : 21.120 151.402   1931
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.24), residues: 1171
  helix: -0.61 (0.32), residues: 271
  sheet:  0.18 (0.31), residues: 307
  loop : -2.80 (0.23), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E  50 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.032   0.002   PHE C  65 
 TYR   0.014   0.001   TYR B 218 
 ARG   0.006   0.000   ARG A 103 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 340
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7688 (tmtt)
REVERT: A    8 ASN cc_start: 0.6984 (t0) cc_final: 0.6428 (t0)
REVERT: A   39 HIS cc_start: 0.7691 (t-90) cc_final: 0.7051 (t-90)
REVERT: A   55 ASP cc_start: 0.7784 (t0) cc_final: 0.7470 (t0)
REVERT: A   65 PRO cc_start: 0.6748 (Cg_exo) cc_final: 0.6512 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7472 (mppt) cc_final: 0.7178 (mmtp)
REVERT: A   93 GLU cc_start: 0.8608 (pp20) cc_final: 0.8274 (pp20)
REVERT: A  112 THR cc_start: 0.6253 (p) cc_final: 0.5809 (p)
REVERT: A  116 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7706 (tptt)
REVERT: A  164 ASP cc_start: 0.6446 (t70) cc_final: 0.6072 (t70)
REVERT: B   21 ASP cc_start: 0.7492 (t0) cc_final: 0.6599 (t0)
REVERT: B   22 PHE cc_start: 0.7616 (m-80) cc_final: 0.7274 (m-10)
REVERT: B   94 ASN cc_start: 0.6939 (t0) cc_final: 0.6704 (t0)
REVERT: B  132 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8062 (ttmm)
REVERT: B  159 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7576 (ttmm)
REVERT: B  162 LYS cc_start: 0.8003 (mmmt) cc_final: 0.7706 (mmmt)
REVERT: C    6 ASP cc_start: 0.7588 (t0) cc_final: 0.7324 (t0)
REVERT: C    7 ASP cc_start: 0.7831 (t70) cc_final: 0.7500 (t0)
REVERT: C   24 GLU cc_start: 0.7365 (mp0) cc_final: 0.7162 (mp0)
REVERT: C   28 LYS cc_start: 0.8693 (mttp) cc_final: 0.8155 (mttp)
REVERT: C   30 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7175 (tppp)
REVERT: C   35 GLU cc_start: 0.6925 (mp0) cc_final: 0.6570 (pm20)
REVERT: C   55 MET cc_start: 0.7199 (ttm) cc_final: 0.6821 (ttm)
REVERT: C   60 ASP cc_start: 0.6043 (p0) cc_final: 0.5679 (p0)
REVERT: C   76 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7833 (ttmt)
REVERT: C   85 GLU cc_start: 0.7495 (mp0) cc_final: 0.7174 (mp0)
REVERT: C  165 LYS cc_start: 0.8006 (pttp) cc_final: 0.7588 (ptpt)
REVERT: C  171 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6864 (mm-30)
REVERT: C  189 SER cc_start: 0.8162 (t) cc_final: 0.7738 (p)
REVERT: C  195 SER cc_start: 0.8378 (m) cc_final: 0.8117 (p)
REVERT: C  205 LEU cc_start: 0.8524 (mt) cc_final: 0.8155 (tp)
REVERT: C  218 PHE cc_start: 0.8548 (p90) cc_final: 0.8212 (p90)
REVERT: C  220 ASN cc_start: 0.6450 (t0) cc_final: 0.6164 (t0)
REVERT: C  229 ASN cc_start: 0.7392 (t0) cc_final: 0.7114 (t0)
REVERT: C  230 MET cc_start: 0.5809 (mtm) cc_final: 0.5322 (mtm)
REVERT: E   12 LYS cc_start: 0.7249 (ptmt) cc_final: 0.6998 (ptmt)
REVERT: E   15 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8039 (mmtm)
REVERT: E   46 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7525 (tm-30)
REVERT: E   49 LEU cc_start: 0.7351 (mt) cc_final: 0.6961 (mt)
REVERT: E   58 GLU cc_start: 0.7049 (pt0) cc_final: 0.6788 (pt0)
REVERT: E   78 GLU cc_start: 0.7770 (pp20) cc_final: 0.7407 (pp20)
REVERT: E   86 LYS cc_start: 0.7785 (tppt) cc_final: 0.7511 (mmmm)
REVERT: E  126 SER cc_start: 0.8333 (t) cc_final: 0.7757 (p)
REVERT: E  127 THR cc_start: 0.7858 (m) cc_final: 0.7583 (m)
REVERT: E  174 ILE cc_start: 0.7935 (mm) cc_final: 0.7634 (tp)
REVERT: E  198 GLU cc_start: 0.6880 (mp0) cc_final: 0.6540 (mp0)
REVERT: E  202 ASN cc_start: 0.8090 (m110) cc_final: 0.7832 (m110)
REVERT: E  203 LEU cc_start: 0.7727 (mt) cc_final: 0.7454 (mt)
REVERT: E  216 GLU cc_start: 0.6927 (tp30) cc_final: 0.6384 (tp30)
REVERT: E  239 GLU cc_start: 0.6974 (tp30) cc_final: 0.6511 (mp0)
REVERT: E  274 LYS cc_start: 0.7171 (mppt) cc_final: 0.6908 (mppt)
REVERT: E  285 ILE cc_start: 0.8687 (pt) cc_final: 0.8415 (tt)
REVERT: E  290 PRO cc_start: 0.7914 (Cg_endo) cc_final: 0.7437 (Cg_exo)
REVERT: E  294 ASP cc_start: 0.8496 (p0) cc_final: 0.7791 (p0)
REVERT: E  325 GLN cc_start: 0.7370 (tp-100) cc_final: 0.6890 (tp-100)
REVERT: E  326 GLU cc_start: 0.7815 (tp30) cc_final: 0.6729 (tp30)
REVERT: E  329 HIS cc_start: 0.7156 (m90) cc_final: 0.5852 (m-70)
REVERT: E  397 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7508 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 340
  average time/residue: 0.2853
  time to fit residues: 126.7589
Evaluate side-chains
  313 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 121 optimal weight:    0.0270
   chunk 111 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 103 optimal weight:    0.4980
   overall best weight:    1.0842

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

Flipped N/Q/H residues before XYZ refinement:
B 116 GLN
B 157 HIS
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.4270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10899  Z= 0.246
  Angle     :  0.669  11.041  14963  Z= 0.353
  Chirality :  0.045   0.157   1723
  Planarity :  0.004   0.058   1683
  Dihedral  : 21.221 154.379   1931
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.27 %
    Favored  : 88.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.24), residues: 1171
  helix: -0.81 (0.31), residues: 281
  sheet:  0.02 (0.32), residues: 305
  loop : -2.85 (0.23), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP E  50 
 HIS   0.007   0.001   HIS B 157 
 PHE   0.024   0.002   PHE A  30 
 TYR   0.024   0.002   TYR C  59 
 ARG   0.007   0.000   ARG A 103 

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 334
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.7597 (ttpt) cc_final: 0.7104 (tmmt)
REVERT: A   55 ASP cc_start: 0.7795 (t0) cc_final: 0.7508 (t0)
REVERT: A   57 LEU cc_start: 0.8154 (mt) cc_final: 0.7938 (mt)
REVERT: A   59 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6869 (tm-30)
REVERT: A   65 PRO cc_start: 0.6722 (Cg_exo) cc_final: 0.6391 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7482 (mppt) cc_final: 0.7264 (mmtp)
REVERT: A   93 GLU cc_start: 0.8686 (pp20) cc_final: 0.8230 (pp20)
REVERT: A  112 THR cc_start: 0.6923 (p) cc_final: 0.6376 (p)
REVERT: A  113 ILE cc_start: 0.7957 (mt) cc_final: 0.7700 (mm)
REVERT: A  116 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7775 (tptt)
REVERT: A  190 LEU cc_start: 0.8637 (mm) cc_final: 0.8433 (mt)
REVERT: B   21 ASP cc_start: 0.7207 (t0) cc_final: 0.6300 (t0)
REVERT: B   22 PHE cc_start: 0.7668 (m-80) cc_final: 0.7334 (m-10)
REVERT: B   66 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8066 (mmmt)
REVERT: B  132 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8219 (ttmm)
REVERT: B  162 LYS cc_start: 0.7829 (mmmt) cc_final: 0.7482 (mmmt)
REVERT: B  166 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7032 (tp30)
REVERT: B  168 ILE cc_start: 0.8622 (tp) cc_final: 0.7892 (tp)
REVERT: C    2 LYS cc_start: 0.7849 (tppt) cc_final: 0.7351 (tppt)
REVERT: C    7 ASP cc_start: 0.7900 (t70) cc_final: 0.7563 (t0)
REVERT: C   30 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7150 (tppp)
REVERT: C   35 GLU cc_start: 0.6952 (mp0) cc_final: 0.6578 (pm20)
REVERT: C   55 MET cc_start: 0.7085 (ttm) cc_final: 0.6684 (ttm)
REVERT: C   60 ASP cc_start: 0.6067 (p0) cc_final: 0.5712 (p0)
REVERT: C   75 MET cc_start: 0.7609 (tpp) cc_final: 0.7233 (tpp)
REVERT: C   76 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7788 (ttmm)
REVERT: C   85 GLU cc_start: 0.7436 (mp0) cc_final: 0.7130 (mp0)
REVERT: C  165 LYS cc_start: 0.8010 (pttp) cc_final: 0.7579 (ptpt)
REVERT: C  171 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6993 (mm-30)
REVERT: C  189 SER cc_start: 0.8146 (t) cc_final: 0.7721 (p)
REVERT: C  195 SER cc_start: 0.8520 (m) cc_final: 0.8171 (p)
REVERT: C  205 LEU cc_start: 0.8450 (mt) cc_final: 0.8161 (tp)
REVERT: C  218 PHE cc_start: 0.8541 (p90) cc_final: 0.8184 (p90)
REVERT: C  220 ASN cc_start: 0.6436 (t0) cc_final: 0.6213 (t0)
REVERT: C  229 ASN cc_start: 0.7441 (t0) cc_final: 0.7148 (t0)
REVERT: C  230 MET cc_start: 0.5721 (mtm) cc_final: 0.5183 (mtm)
REVERT: E   12 LYS cc_start: 0.7312 (ptmt) cc_final: 0.7025 (ptmt)
REVERT: E   15 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8122 (mmtm)
REVERT: E   46 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7488 (tm-30)
REVERT: E   49 LEU cc_start: 0.7296 (mt) cc_final: 0.7083 (mt)
REVERT: E   58 GLU cc_start: 0.7042 (pt0) cc_final: 0.6752 (pt0)
REVERT: E   78 GLU cc_start: 0.7796 (pp20) cc_final: 0.7447 (pp20)
REVERT: E   86 LYS cc_start: 0.7837 (tppt) cc_final: 0.7540 (mmmm)
REVERT: E  126 SER cc_start: 0.8325 (t) cc_final: 0.7789 (p)
REVERT: E  127 THR cc_start: 0.7903 (m) cc_final: 0.7653 (m)
REVERT: E  137 GLU cc_start: 0.7260 (tp30) cc_final: 0.6992 (tp30)
REVERT: E  140 ARG cc_start: 0.6669 (ttp-170) cc_final: 0.6341 (ttp-110)
REVERT: E  174 ILE cc_start: 0.7944 (mm) cc_final: 0.7643 (tp)
REVERT: E  198 GLU cc_start: 0.6954 (mp0) cc_final: 0.6629 (mp0)
REVERT: E  202 ASN cc_start: 0.8086 (m110) cc_final: 0.7780 (m110)
REVERT: E  203 LEU cc_start: 0.7827 (mt) cc_final: 0.7591 (mt)
REVERT: E  216 GLU cc_start: 0.6915 (tp30) cc_final: 0.6585 (tp30)
REVERT: E  239 GLU cc_start: 0.6961 (tp30) cc_final: 0.6554 (mp0)
REVERT: E  274 LYS cc_start: 0.7214 (mppt) cc_final: 0.6968 (mppt)
REVERT: E  285 ILE cc_start: 0.8701 (pt) cc_final: 0.8404 (tt)
REVERT: E  290 PRO cc_start: 0.7956 (Cg_endo) cc_final: 0.7488 (Cg_exo)
REVERT: E  294 ASP cc_start: 0.8528 (p0) cc_final: 0.7981 (p0)
REVERT: E  304 GLU cc_start: 0.7456 (mp0) cc_final: 0.7226 (mp0)
REVERT: E  325 GLN cc_start: 0.7416 (tp-100) cc_final: 0.7157 (tp-100)
REVERT: E  373 GLU cc_start: 0.8041 (tp30) cc_final: 0.7721 (mm-30)
REVERT: E  397 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7562 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 334
  average time/residue: 0.2786
  time to fit residues: 121.3691
Evaluate side-chains
  315 residues out of total 1035 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 315
  time to evaluate  : 1.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 99 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 116 GLN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.137461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114887 restraints weight = 19076.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.117679 restraints weight = 12105.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.119579 restraints weight = 8609.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10899  Z= 0.210
  Angle     :  0.644  10.997  14963  Z= 0.341
  Chirality :  0.044   0.154   1723
  Planarity :  0.004   0.059   1683
  Dihedral  : 21.187 153.320   1931
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.48 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.48 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.24), residues: 1171
  helix: -0.80 (0.31), residues: 281
  sheet: -0.01 (0.31), residues: 309
  loop : -2.83 (0.23), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E  50 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.024   0.002   PHE A  30 
 TYR   0.022   0.001   TYR C  59 
 ARG   0.004   0.000   ARG E 199 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2888.87 seconds
wall clock time: 52 minutes 22.49 seconds (3142.49 seconds total)