Starting phenix.real_space_refine
on Fri Dec  8 14:39:53 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/12_2023/6jbh_9790.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/12_2023/6jbh_9790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/12_2023/6jbh_9790.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/12_2023/6jbh_9790.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/12_2023/6jbh_9790.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbh_9790/12_2023/6jbh_9790.pdb"
  }
  resolution = 3.94
  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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    5654      2.51       5
     N    1408      2.21       5
     O    1486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   23": "NH1" <-> "NH2"
    Residue "A ARG   41": "NH1" <-> "NH2"
    Residue "A ARG  103": "NH1" <-> "NH2"
    Residue "A ARG  121": "NH1" <-> "NH2"
    Residue "A ARG  192": "NH1" <-> "NH2"
    Residue "A ARG  222": "NH1" <-> "NH2"
    Residue "A ARG  258": "NH1" <-> "NH2"
    Residue "B ARG   23": "NH1" <-> "NH2"
    Residue "B ARG   41": "NH1" <-> "NH2"
    Residue "B ARG  103": "NH1" <-> "NH2"
    Residue "B ARG  121": "NH1" <-> "NH2"
    Residue "B ARG  192": "NH1" <-> "NH2"
    Residue "B ARG  222": "NH1" <-> "NH2"
    Residue "B ARG  258": "NH1" <-> "NH2"
    Residue "C TYR   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   60": "NH1" <-> "NH2"
    Residue "C ARG  175": "NH1" <-> "NH2"
    Residue "C ARG  186": "NH1" <-> "NH2"
    Residue "C ARG  222": "NH1" <-> "NH2"
    Residue "C ARG  261": "NH1" <-> "NH2"
    Residue "D TYR   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG   60": "NH1" <-> "NH2"
    Residue "D ARG  175": "NH1" <-> "NH2"
    Residue "D ARG  186": "NH1" <-> "NH2"
    Residue "D ARG  222": "NH1" <-> "NH2"
    Residue "D ARG  261": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8592
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2075
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 7, 'TRANS': 256}
    Chain: "B"
      Number of atoms: 2075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2075
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 7, 'TRANS': 256}
    Chain: "C"
      Number of atoms: 2221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2221
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 11, 'TRANS': 255}
    Chain: "D"
      Number of atoms: 2221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2221
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 11, 'TRANS': 255}
  Time building chain proxies: 4.71, per 1000 atoms: 0.55
  Number of scatterers: 8592
  At special positions: 0
  Unit cell: (93.84, 88.4, 107.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1486      8.00
     N    1408      7.00
     C    5654      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=0, symmetry=0
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      57.4% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 62
    Processing helix  chain 'A' and resid 64 through 71
      removed outlier: 3.667A  pdb=" N   ILE A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 114
      removed outlier: 3.670A  pdb=" N   GLU A 107 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 123 through 132
      removed outlier: 4.060A  pdb=" N   ILE A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE A 128 " --> pdb=" O   GLU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 139
      removed outlier: 3.575A  pdb=" N   ILE A 137 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASP A 138 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 144
    Processing helix  chain 'A' and resid 145 through 157
      removed outlier: 3.871A  pdb=" N   SER A 150 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA A 155 " --> pdb=" O   ARG A 151 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 3.535A  pdb=" N   ASP A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLU A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   PHE A 189 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 210
    Processing helix  chain 'A' and resid 229 through 244
      removed outlier: 3.530A  pdb=" N   ALA A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   MET A 244 " --> pdb=" O   GLU A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 261
    Processing helix  chain 'A' and resid 262 through 264
      No H-bonds generated for 'chain 'A' and resid 262 through 264'
    Processing helix  chain 'B' and resid 58 through 62
    Processing helix  chain 'B' and resid 64 through 71
      removed outlier: 3.667A  pdb=" N   ILE B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 114
      removed outlier: 3.670A  pdb=" N   GLU B 107 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 123 through 132
      removed outlier: 4.060A  pdb=" N   ILE B 127 " --> pdb=" O   MET B 123 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE B 128 " --> pdb=" O   GLU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 139
      removed outlier: 3.575A  pdb=" N   ILE B 137 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASP B 138 " --> pdb=" O   LYS B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 144
    Processing helix  chain 'B' and resid 145 through 157
      removed outlier: 3.871A  pdb=" N   SER B 150 " --> pdb=" O   SER B 146 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA B 155 " --> pdb=" O   ARG B 151 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER B 157 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 193
      removed outlier: 3.535A  pdb=" N   ASP B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   PHE B 189 " --> pdb=" O   LYS B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 210
    Processing helix  chain 'B' and resid 229 through 244
      removed outlier: 3.530A  pdb=" N   ALA B 243 " --> pdb=" O   LYS B 239 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   MET B 244 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 261
    Processing helix  chain 'B' and resid 262 through 264
      No H-bonds generated for 'chain 'B' and resid 262 through 264'
    Processing helix  chain 'C' and resid 3 through 14
      removed outlier: 3.826A  pdb=" N   VAL C   7 " --> pdb=" O   SER C   3 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU C  10 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 21
    Processing helix  chain 'C' and resid 21 through 30
      removed outlier: 4.530A  pdb=" N   GLU C  25 " --> pdb=" O   LEU C  21 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU C  26 " --> pdb=" O   SER C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 56
      removed outlier: 3.993A  pdb=" N   ILE C  42 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      Proline residue:  C  44  - end of helix
      removed outlier: 3.707A  pdb=" N   ALA C  49 " --> pdb=" O   MET C  45 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE C  50 " --> pdb=" O   ILE C  46 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   TYR C  51 " --> pdb=" O   GLN C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 76
      removed outlier: 3.745A  pdb=" N   ALA C  76 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 86
      removed outlier: 4.204A  pdb=" N   TRP C  81 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   PHE C  82 " --> pdb=" O   MET C  78 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE C  83 " --> pdb=" O   THR C  79 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL C  84 " --> pdb=" O   VAL C  80 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   GLN C  86 " --> pdb=" O   PHE C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 93
    Processing helix  chain 'C' and resid 99 through 104
      removed outlier: 4.003A  pdb=" N   GLN C 104 " --> pdb=" O   ARG C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 112
      removed outlier: 3.534A  pdb=" N   VAL C 111 " --> pdb=" O   PRO C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 120
      removed outlier: 3.672A  pdb=" N   ILE C 117 " --> pdb=" O   PRO C 113 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR C 118 " --> pdb=" O   THR C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 128
    Processing helix  chain 'C' and resid 131 through 136
    Processing helix  chain 'C' and resid 149 through 167
      removed outlier: 4.070A  pdb=" N   LEU C 156 " --> pdb=" O   TYR C 152 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU C 157 " --> pdb=" O   MET C 153 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   LEU C 165 " --> pdb=" O   VAL C 161 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE C 166 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 175
      removed outlier: 3.592A  pdb=" N   THR C 172 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL C 173 " --> pdb=" O   THR C 169 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL C 174 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 188
      removed outlier: 3.653A  pdb=" N   SER C 183 " --> pdb=" O   MET C 179 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ARG C 186 " --> pdb=" O   GLN C 182 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU C 188 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 223
      removed outlier: 3.909A  pdb=" N   ILE C 217 " --> pdb=" O   PRO C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 234
      No H-bonds generated for 'chain 'C' and resid 232 through 234'
    Processing helix  chain 'C' and resid 235 through 259
      removed outlier: 4.050A  pdb=" N   VAL C 240 " --> pdb=" O   ALA C 236 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   TYR C 241 " --> pdb=" O   SER C 237 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE C 247 " --> pdb=" O   TRP C 243 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 14
      removed outlier: 3.826A  pdb=" N   VAL D   7 " --> pdb=" O   SER D   3 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU D  10 " --> pdb=" O   THR D   6 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 21
    Processing helix  chain 'D' and resid 21 through 30
      removed outlier: 4.530A  pdb=" N   GLU D  25 " --> pdb=" O   LEU D  21 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU D  26 " --> pdb=" O   SER D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 56
      removed outlier: 3.993A  pdb=" N   ILE D  42 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      Proline residue:  D  44  - end of helix
      removed outlier: 3.707A  pdb=" N   ALA D  49 " --> pdb=" O   MET D  45 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE D  50 " --> pdb=" O   ILE D  46 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TYR D  51 " --> pdb=" O   GLN D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 70 through 76
      removed outlier: 3.745A  pdb=" N   ALA D  76 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 86
      removed outlier: 4.205A  pdb=" N   TRP D  81 " --> pdb=" O   GLY D  77 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   PHE D  82 " --> pdb=" O   MET D  78 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE D  83 " --> pdb=" O   THR D  79 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL D  84 " --> pdb=" O   VAL D  80 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   GLN D  86 " --> pdb=" O   PHE D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 93
    Processing helix  chain 'D' and resid 99 through 104
      removed outlier: 4.011A  pdb=" N   GLN D 104 " --> pdb=" O   ARG D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 112
      removed outlier: 3.534A  pdb=" N   VAL D 111 " --> pdb=" O   PRO D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 120
      removed outlier: 3.672A  pdb=" N   ILE D 117 " --> pdb=" O   PRO D 113 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR D 118 " --> pdb=" O   THR D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 128
    Processing helix  chain 'D' and resid 131 through 136
    Processing helix  chain 'D' and resid 149 through 167
      removed outlier: 4.070A  pdb=" N   LEU D 156 " --> pdb=" O   TYR D 152 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU D 157 " --> pdb=" O   MET D 153 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   LEU D 165 " --> pdb=" O   VAL D 161 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE D 166 " --> pdb=" O   SER D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 175
      removed outlier: 3.592A  pdb=" N   THR D 172 " --> pdb=" O   SER D 168 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL D 173 " --> pdb=" O   THR D 169 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL D 174 " --> pdb=" O   LEU D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 176 through 188
      removed outlier: 3.653A  pdb=" N   SER D 183 " --> pdb=" O   MET D 179 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ARG D 186 " --> pdb=" O   GLN D 182 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 223
      removed outlier: 3.908A  pdb=" N   ILE D 217 " --> pdb=" O   PRO D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 234
      No H-bonds generated for 'chain 'D' and resid 232 through 234'
    Processing helix  chain 'D' and resid 235 through 259
      removed outlier: 4.050A  pdb=" N   VAL D 240 " --> pdb=" O   ALA D 236 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   TYR D 241 " --> pdb=" O   SER D 237 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE D 247 " --> pdb=" O   TRP D 243 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 45
      removed outlier: 5.746A  pdb=" N   ARG A  41 " --> pdb=" O   LYS A  12 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   LYS A  12 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   PHE A  45 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   GLU A   8 " --> pdb=" O   PHE A  45 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   ASN A   9 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   THR A  80 " --> pdb=" O   ASN A   9 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER A  78 " --> pdb=" O   THR A  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167
      removed outlier: 6.270A  pdb=" N   VAL A  52 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU A 214 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   GLY A  54 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LEU A 216 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ALA A 213 " --> pdb=" O   TYR A 224 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   TYR A 224 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   TRP A 215 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 40 through 45
      removed outlier: 5.746A  pdb=" N   ARG B  41 " --> pdb=" O   LYS B  12 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   LYS B  12 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   PHE B  45 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   GLU B   8 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASN B   9 " --> pdb=" O   THR B  80 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   THR B  80 " --> pdb=" O   ASN B   9 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER B  78 " --> pdb=" O   THR B  11 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167
      removed outlier: 6.271A  pdb=" N   VAL B  52 " --> pdb=" O   LYS B 212 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU B 214 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   GLY B  54 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   LEU B 216 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ALA B 213 " --> pdb=" O   TYR B 224 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   TYR B 224 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   TRP B 215 " --> pdb=" O   ARG B 222 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    852 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 3.17 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: 2459
        1.33 -     1.45: 1542
        1.45 -     1.57: 4719
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 8802
  Sorted by residual:
  bond pdb=" C   ILE C  68 "
       pdb=" N   PRO C  69 "
    ideal  model  delta    sigma   weight residual
    1.331  1.410 -0.079 1.20e-02 6.94e+03 4.29e+01
  bond pdb=" C   ILE D  68 "
       pdb=" N   PRO D  69 "
    ideal  model  delta    sigma   weight residual
    1.331  1.410 -0.078 1.20e-02 6.94e+03 4.28e+01
  bond pdb=" N   ARG C 186 "
       pdb=" CA  ARG C 186 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.024 1.26e-02 6.30e+03 3.73e+00
  bond pdb=" N   ARG C 175 "
       pdb=" CA  ARG C 175 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 1.48e-02 4.57e+03 3.69e+00
  bond pdb=" N   ARG D 175 "
       pdb=" CA  ARG D 175 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 1.48e-02 4.57e+03 3.63e+00
  ... (remaining 8797 not shown)

  Histogram of bond angle deviations from ideal:
       98.73 -   105.78: 182
      105.78 -   112.83: 4509
      112.83 -   119.88: 3243
      119.88 -   126.93: 3868
      126.93 -   133.98: 116
  Bond angle restraints: 11918
  Sorted by residual:
  angle pdb=" C   ASP A  48 "
        pdb=" N   LYS A  49 "
        pdb=" CA  LYS A  49 "
      ideal   model   delta    sigma   weight residual
     121.54  130.80   -9.26 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   ASP B  48 "
        pdb=" N   LYS B  49 "
        pdb=" CA  LYS B  49 "
      ideal   model   delta    sigma   weight residual
     121.54  130.79   -9.25 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   ALA A  47 "
        pdb=" N   ASP A  48 "
        pdb=" CA  ASP A  48 "
      ideal   model   delta    sigma   weight residual
     121.54  130.05   -8.51 1.91e+00 2.74e-01 1.99e+01
  angle pdb=" C   ALA B  47 "
        pdb=" N   ASP B  48 "
        pdb=" CA  ASP B  48 "
      ideal   model   delta    sigma   weight residual
     121.54  130.02   -8.48 1.91e+00 2.74e-01 1.97e+01
  angle pdb=" C   ALA B 170 "
        pdb=" N   LEU B 171 "
        pdb=" CA  LEU B 171 "
      ideal   model   delta    sigma   weight residual
     121.54  129.91   -8.37 1.91e+00 2.74e-01 1.92e+01
  ... (remaining 11913 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.32: 4674
       15.32 -    30.65: 394
       30.65 -    45.97: 110
       45.97 -    61.30: 11
       61.30 -    76.62: 3
  Dihedral angle restraints: 5192
    sinusoidal: 2090
      harmonic: 3102
  Sorted by residual:
  dihedral pdb=" CD  ARG C 175 "
           pdb=" NE  ARG C 175 "
           pdb=" CZ  ARG C 175 "
           pdb=" NH1 ARG C 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   76.62  -76.62     1      1.00e+01 1.00e-02 7.38e+01
  dihedral pdb=" CA  ALA B  87 "
           pdb=" C   ALA B  87 "
           pdb=" N   SER B  88 "
           pdb=" CA  SER B  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.60   37.40     0      5.00e+00 4.00e-02 5.60e+01
  dihedral pdb=" CA  ALA A  87 "
           pdb=" C   ALA A  87 "
           pdb=" N   SER A  88 "
           pdb=" CA  SER A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.63   37.37     0      5.00e+00 4.00e-02 5.59e+01
  ... (remaining 5189 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 759
       0.048 -    0.095: 413
       0.095 -    0.143: 126
       0.143 -    0.191: 42
       0.191 -    0.238: 10
  Chirality restraints: 1350
  Sorted by residual:
  chirality pdb=" CB  ILE C  59 "
            pdb=" CA  ILE C  59 "
            pdb=" CG1 ILE C  59 "
            pdb=" CG2 ILE C  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  ILE D  59 "
            pdb=" CA  ILE D  59 "
            pdb=" CG1 ILE D  59 "
            pdb=" CG2 ILE D  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  VAL A   5 "
            pdb=" CA  VAL A   5 "
            pdb=" CG1 VAL A   5 "
            pdb=" CG2 VAL A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1347 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 175 "   -1.068 9.50e-02 1.11e+02   4.79e-01 1.38e+02
        pdb=" NE  ARG C 175 "    0.064 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 175 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 175 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 175 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 175 "    0.986 9.50e-02 1.11e+02   4.42e-01 1.18e+02
        pdb=" NE  ARG D 175 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 175 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 175 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 175 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 100 "   -0.920 9.50e-02 1.11e+02   4.12e-01 1.03e+02
        pdb=" NE  ARG D 100 "    0.055 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 100 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 100 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2191
        2.79 -     3.32: 8165
        3.32 -     3.84: 13283
        3.84 -     4.37: 15766
        4.37 -     4.90: 25436
  Nonbonded interactions: 64841
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 138 "
            pdb=" O   TYR D 140 "
     model   vdw
     2.260 2.440
  nonbonded pdb=" OG1 THR C 138 "
            pdb=" O   TYR C 140 "
     model   vdw
     2.261 2.440
  nonbonded pdb=" OE1 GLU D 219 "
            pdb=" OH  TYR D 231 "
     model   vdw
     2.267 2.440
  nonbonded pdb=" OE1 GLU C 219 "
            pdb=" OH  TYR C 231 "
     model   vdw
     2.267 2.440
  nonbonded pdb=" OG  SER A  21 "
            pdb=" OE1 GLU A  22 "
     model   vdw
     2.318 2.440
  ... (remaining 64836 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.520
  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:          2.250
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     23.450
  Find NCS groups from input model:        0.410
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
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      :  0.007   0.079   8802  Z= 0.442
  Angle     :  1.225  12.267  11918  Z= 0.636
  Chirality :  0.066   0.238   1350
  Planarity :  0.028   0.479   1468
  Dihedral  : 12.504  76.622   3204
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 14.33 %
    Favored  : 85.48 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  8.19 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

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: -5.84 (0.18), residues: 1054
  helix: -3.92 (0.13), residues: 498
  sheet: -3.55 (0.55), residues: 46
  loop : -3.87 (0.23), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.030   0.004   TRP A 215 
   HIS   0.011   0.002   HIS C 124 
   PHE   0.038   0.003   PHE C 264 
   TYR   0.027   0.003   TYR B  14 
   ARG   0.007   0.001   ARG B  41 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 392
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 394
  average time/residue: 0.2396
  time to fit residues: 122.6925
Evaluate side-chains
  203 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 1.052 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.5515
  time to fit residues: 2.6776
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0370
   chunk 81 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 ASN
A 251 GLN
B 187 ASN
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  14 ASN
C  32 ASN
C 104 GLN
C 136 GLN
C 200 HIS
C 257 HIS
D  14 ASN
D  32 ASN
D 136 GLN
D 200 HIS
D 257 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8802  Z= 0.223
  Angle     :  0.890  10.285  11918  Z= 0.449
  Chirality :  0.049   0.256   1350
  Planarity :  0.005   0.043   1468
  Dihedral  :  7.388  29.910   1164
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 14.33 %
    Favored  : 85.48 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.23 %
    Favored  : 79.79 %
  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: -4.62 (0.21), residues: 1054
  helix: -2.63 (0.18), residues: 512
  sheet: -2.67 (0.68), residues: 44
  loop : -3.60 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.027   0.002   TRP C  52 
   HIS   0.007   0.001   HIS D 257 
   PHE   0.046   0.002   PHE C  70 
   TYR   0.040   0.002   TYR C 215 
   ARG   0.007   0.001   ARG D 186 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 255
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 20
  residues processed: 273
  average time/residue: 0.1707
  time to fit residues: 67.0818
Evaluate side-chains
  231 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 211
  time to evaluate  : 1.079 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0795
  time to fit residues: 4.4028
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 94 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0370
   chunk 93 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.3664

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

Flipped N/Q/H residues before XYZ refinement:
B 251 GLN
C 200 HIS
D  47 GLN
D 200 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8802  Z= 0.234
  Angle     :  0.850   8.956  11918  Z= 0.425
  Chirality :  0.049   0.272   1350
  Planarity :  0.004   0.031   1468
  Dihedral  :  6.891  28.299   1164
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.33 %
    Favored  : 85.67 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 19.79 %
    Favored  : 75.74 %
  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: -3.85 (0.23), residues: 1054
  helix: -1.82 (0.20), residues: 512
  sheet: -2.63 (0.68), residues: 46
  loop : -3.40 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP C  81 
   HIS   0.004   0.001   HIS C 124 
   PHE   0.042   0.002   PHE C  70 
   TYR   0.026   0.002   TYR D 215 
   ARG   0.005   0.001   ARG D 175 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 224
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
  outliers start: 42
  outliers final: 15
  residues processed: 255
  average time/residue: 0.1589
  time to fit residues: 60.0550
Evaluate side-chains
  225 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 210
  time to evaluate  : 1.023 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0802
  time to fit residues: 3.4997
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 89 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 260 GLN
C 200 HIS
** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
D 200 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8802  Z= 0.208
  Angle     :  0.832  11.502  11918  Z= 0.409
  Chirality :  0.049   0.261   1350
  Planarity :  0.004   0.033   1468
  Dihedral  :  6.577  26.796   1164
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.99 %
    Favored  : 85.01 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.49 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.37 (0.24), residues: 1054
  helix: -1.31 (0.22), residues: 514
  sheet: -2.35 (0.70), residues: 46
  loop : -3.31 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP D  52 
   HIS   0.003   0.001   HIS C 124 
   PHE   0.033   0.001   PHE C  70 
   TYR   0.023   0.002   TYR D 215 
   ARG   0.004   0.000   ARG D 175 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 232
  time to evaluate  : 0.928 
Fit side-chains
  outliers start: 23
  outliers final: 12
  residues processed: 246
  average time/residue: 0.1548
  time to fit residues: 55.5920
Evaluate side-chains
  222 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 210
  time to evaluate  : 0.912 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0814
  time to fit residues: 3.0770
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    0.6980
   chunk 90 optimal weight:    0.4980
   chunk 25 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.4846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8802  Z= 0.209
  Angle     :  0.840  11.565  11918  Z= 0.409
  Chirality :  0.048   0.225   1350
  Planarity :  0.004   0.030   1468
  Dihedral  :  6.438  28.984   1164
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.90 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 22.77 %
    Favored  : 75.11 %
  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: -2.95 (0.25), residues: 1054
  helix: -1.07 (0.22), residues: 524
  sheet: -1.89 (0.70), residues: 46
  loop : -3.01 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP D  52 
   HIS   0.006   0.001   HIS C 235 
   PHE   0.028   0.001   PHE D  70 
   TYR   0.021   0.002   TYR D  51 
   ARG   0.003   0.000   ARG A  41 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 240
  time to evaluate  : 1.121 
Fit side-chains
  outliers start: 20
  outliers final: 8
  residues processed: 254
  average time/residue: 0.1631
  time to fit residues: 60.6594
Evaluate side-chains
  219 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 211
  time to evaluate  : 0.941 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0898
  time to fit residues: 2.5663
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 100 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0670
   chunk 52 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    2.1324

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 GLN
B 260 GLN
C 200 HIS
** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 HIS
** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.5066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083   8802  Z= 0.314
  Angle     :  0.856  12.476  11918  Z= 0.425
  Chirality :  0.050   0.387   1350
  Planarity :  0.004   0.032   1468
  Dihedral  :  6.425  27.936   1164
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.70 %
    Favored  : 83.30 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.51 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.25), residues: 1054
  helix: -1.08 (0.21), residues: 550
  sheet: -1.29 (0.76), residues: 46
  loop : -3.07 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP C  81 
   HIS   0.005   0.001   HIS C 124 
   PHE   0.010   0.001   PHE C 264 
   TYR   0.022   0.002   TYR B  14 
   ARG   0.007   0.001   ARG A 250 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 217
  time to evaluate  : 1.026 
Fit side-chains
  outliers start: 29
  outliers final: 19
  residues processed: 237
  average time/residue: 0.1691
  time to fit residues: 58.2018
Evaluate side-chains
  224 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 205
  time to evaluate  : 1.035 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0793
  time to fit residues: 4.1586
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 62 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 HIS
D 200 HIS
** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.5251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089   8802  Z= 0.239
  Angle     :  0.853  12.851  11918  Z= 0.416
  Chirality :  0.049   0.272   1350
  Planarity :  0.004   0.031   1468
  Dihedral  :  6.379  26.933   1164
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.03 %
    Favored  : 83.97 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 26.06 %
    Favored  : 72.77 %
  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: -2.68 (0.26), residues: 1054
  helix: -0.87 (0.22), residues: 546
  sheet: -0.81 (0.80), residues: 46
  loop : -3.06 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP D  52 
   HIS   0.004   0.001   HIS C 124 
   PHE   0.017   0.001   PHE C 242 
   TYR   0.021   0.002   TYR C  96 
   ARG   0.006   0.000   ARG A 250 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 227
  time to evaluate  : 1.076 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 234
  average time/residue: 0.1649
  time to fit residues: 56.4053
Evaluate side-chains
  218 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 211
  time to evaluate  : 0.920 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0875
  time to fit residues: 2.5076
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0040
   chunk 96 optimal weight:    0.0570
   chunk 87 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.7912

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 HIS
** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.5423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8802  Z= 0.194
  Angle     :  0.840  13.023  11918  Z= 0.407
  Chirality :  0.047   0.211   1350
  Planarity :  0.004   0.029   1468
  Dihedral  :  6.248  27.557   1164
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.75 %
    Favored  : 84.25 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 27.45 %
    Favored  : 71.28 %
  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: -2.48 (0.26), residues: 1054
  helix: -0.74 (0.22), residues: 548
  sheet: -0.46 (0.82), residues: 46
  loop : -2.95 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP C  52 
   HIS   0.004   0.001   HIS D 124 
   PHE   0.024   0.001   PHE B 264 
   TYR   0.024   0.002   TYR C 151 
   ARG   0.006   0.000   ARG A 250 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 224
  time to evaluate  : 1.044 
Fit side-chains
  outliers start: 12
  outliers final: 6
  residues processed: 233
  average time/residue: 0.1615
  time to fit residues: 55.2797
Evaluate side-chains
  214 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 208
  time to evaluate  : 0.918 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0778
  time to fit residues: 2.1278
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    0.0980
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0070
   chunk 88 optimal weight:    0.5980
   chunk 93 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.5647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8802  Z= 0.184
  Angle     :  0.869  13.345  11918  Z= 0.414
  Chirality :  0.047   0.200   1350
  Planarity :  0.004   0.040   1468
  Dihedral  :  6.129  26.584   1164
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.09 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 28.51 %
    Favored  : 70.96 %
  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: -2.27 (0.27), residues: 1054
  helix: -0.52 (0.23), residues: 534
  sheet:  0.23 (0.87), residues: 46
  loop : -2.93 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP C  81 
   HIS   0.004   0.001   HIS D 124 
   PHE   0.021   0.001   PHE C 242 
   TYR   0.023   0.002   TYR C 151 
   ARG   0.005   0.000   ARG A 250 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 235
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 238
  average time/residue: 0.2070
  time to fit residues: 70.1633
Evaluate side-chains
  218 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 216
  time to evaluate  : 1.013 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1007
  time to fit residues: 1.7194
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 87 optimal weight:    0.2980
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 ASN
D 200 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.5765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8802  Z= 0.199
  Angle     :  0.867  13.532  11918  Z= 0.413
  Chirality :  0.048   0.187   1350
  Planarity :  0.004   0.028   1468
  Dihedral  :  6.012  27.535   1164
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.03 %
    Favored  : 83.97 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 28.62 %
    Favored  : 70.96 %
  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: -2.13 (0.27), residues: 1054
  helix: -0.33 (0.23), residues: 516
  sheet:  0.41 (0.90), residues: 46
  loop : -2.89 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP C  81 
   HIS   0.005   0.001   HIS D 124 
   PHE   0.019   0.001   PHE B 264 
   TYR   0.022   0.002   TYR C 151 
   ARG   0.002   0.000   ARG B 255 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 224
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 225
  average time/residue: 0.1765
  time to fit residues: 57.6607
Evaluate side-chains
  214 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 211
  time to evaluate  : 1.043 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0872
  time to fit residues: 1.9798
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   chunk 84 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.103413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.084807 restraints weight = 22816.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.087097 restraints weight = 13774.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.088721 restraints weight = 9739.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.5887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8802  Z= 0.213
  Angle     :  0.876  11.448  11918  Z= 0.421
  Chirality :  0.048   0.193   1350
  Planarity :  0.004   0.027   1468
  Dihedral  :  5.976  25.748   1164
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.37 %
    Favored  : 84.63 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 29.79 %
    Favored  : 69.57 %
  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: -2.08 (0.27), residues: 1054
  helix: -0.26 (0.24), residues: 506
  sheet:  0.47 (0.91), residues: 46
  loop : -2.85 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP C  52 
   HIS   0.005   0.001   HIS D 124 
   PHE   0.022   0.001   PHE A 264 
   TYR   0.037   0.002   TYR C  96 
   ARG   0.008   0.001   ARG A  41 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1970.24 seconds
wall clock time: 36 minutes 35.25 seconds (2195.25 seconds total)