Starting phenix.real_space_refine
on Thu Dec  7 23:08:20 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/12_2023/7td6_25824.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/12_2023/7td6_25824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/12_2023/7td6_25824.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/12_2023/7td6_25824.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/12_2023/7td6_25824.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/12_2023/7td6_25824.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      45      5.16       5
     C    3460      2.51       5
     N    1010      2.21       5
     O    1060      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 5575
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "1"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "A"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
  Time building chain proxies: 3.38, per 1000 atoms: 0.61
  Number of scatterers: 5575
  At special positions: 0
  Unit cell: (105.73, 112.27, 53.41, 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      45     16.00
     O    1060      8.00
     N    1010      7.00
     C    3460      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS 1 178 " - pdb=" SG  CYS 1 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 178 " - pdb=" SG  CYS A 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 178 " - pdb=" SG  CYS B 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 178 " - pdb=" SG  CYS C 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 178 " - pdb=" SG  CYS D 213 " distance=2.03

  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: 1.80
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1270

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 13 sheets defined
      0.0% alpha, 40.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 94 through 99
      removed outlier: 6.507A  pdb=" N   THR 1  94 " --> pdb=" O   HIS B  95 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   GLN B  97 " --> pdb=" O   THR 1  94 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ASN 1  96 " --> pdb=" O   GLN B  97 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   ASN B  99 " --> pdb=" O   ASN 1  96 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP 1  98 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   HIS 1  95 " --> pdb=" O   ASN A  96 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   TRP A  98 " --> pdb=" O   HIS 1  95 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   GLN 1  97 " --> pdb=" O   TRP A  98 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   HIS A  95 " --> pdb=" O   ASN C  96 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   TRP C  98 " --> pdb=" O   HIS A  95 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   GLN A  97 " --> pdb=" O   TRP C  98 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   HIS C  95 " --> pdb=" O   ASN D  96 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   TRP D  98 " --> pdb=" O   HIS C  95 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   GLN C  97 " --> pdb=" O   TRP D  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 112
      removed outlier: 7.125A  pdb=" N   HIS B 110 " --> pdb=" O   LYS 1 109 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL 1 111 " --> pdb=" O   HIS B 110 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ALA B 112 " --> pdb=" O   VAL 1 111 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   THR 1 106 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   LYS A 109 " --> pdb=" O   THR 1 106 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   LEU 1 108 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   VAL A 111 " --> pdb=" O   LEU 1 108 " (cutoff:3.500A)
      removed outlier: 8.796A  pdb=" N   HIS 1 110 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR A 106 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   LYS C 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 8.929A  pdb=" N   LEU A 108 " --> pdb=" O   LYS C 109 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   VAL C 111 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   HIS A 110 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   THR C 106 " --> pdb=" O   ASN D 107 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   LYS D 109 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 8.938A  pdb=" N   LEU C 108 " --> pdb=" O   LYS D 109 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   VAL D 111 " --> pdb=" O   LEU C 108 " (cutoff:3.500A)
      removed outlier: 8.797A  pdb=" N   HIS C 110 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain '1' and resid 120 through 121
    Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 134
      removed outlier: 6.336A  pdb=" N   MET 1 128 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   SER B 131 " --> pdb=" O   MET 1 128 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   GLY 1 130 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      removed outlier: 10.502A  pdb=" N   MET B 133 " --> pdb=" O   GLY 1 130 " (cutoff:3.500A)
      removed outlier: 8.958A  pdb=" N   ALA 1 132 " --> pdb=" O   MET B 133 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   SER 1 131 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ALA A 132 " --> pdb=" O   SER 1 131 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   MET 1 133 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   SER A 134 " --> pdb=" O   MET 1 133 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   SER A 131 " --> pdb=" O   GLY C 130 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ALA C 132 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   MET A 133 " --> pdb=" O   ALA C 132 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   SER C 134 " --> pdb=" O   MET A 133 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER C 131 " --> pdb=" O   GLY D 130 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ALA D 132 " --> pdb=" O   SER C 131 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   MET C 133 " --> pdb=" O   ALA D 132 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   SER D 134 " --> pdb=" O   MET C 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 139
      removed outlier: 6.333A  pdb=" N   MET 1 137 " --> pdb=" O   ILE B 138 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 143 through 144
      removed outlier: 6.516A  pdb=" N   ASP 1 143 " --> pdb=" O   TRP B 144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 154 through 155
      removed outlier: 6.812A  pdb=" N   TYR 1 154 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 162
      removed outlier: 6.448A  pdb=" N   GLN 1 159 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   TYR A 162 " --> pdb=" O   GLN 1 159 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   TYR 1 161 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLN A 159 " --> pdb=" O   VAL C 160 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   TYR C 162 " --> pdb=" O   GLN A 159 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   TYR A 161 " --> pdb=" O   TYR C 162 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLN C 159 " --> pdb=" O   VAL D 160 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   TYR D 162 " --> pdb=" O   GLN C 159 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   TYR C 161 " --> pdb=" O   TYR D 162 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 172
      removed outlier: 6.465A  pdb=" N   GLN 1 167 " --> pdb=" O   TYR B 168 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   ASN B 170 " --> pdb=" O   GLN 1 167 " (cutoff:3.500A)
      removed outlier: 9.008A  pdb=" N   SER 1 169 " --> pdb=" O   ASN B 170 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASN B 172 " --> pdb=" O   SER 1 169 " (cutoff:3.500A)
      removed outlier: 9.198A  pdb=" N   GLN 1 171 " --> pdb=" O   ASN B 172 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   GLN A 171 " --> pdb=" O   ASN 1 170 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASN 1 172 " --> pdb=" O   GLN A 171 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   GLN C 171 " --> pdb=" O   ASN A 170 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ASN A 172 " --> pdb=" O   GLN C 171 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   GLN D 171 " --> pdb=" O   ASN C 170 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   ASN C 172 " --> pdb=" O   GLN D 171 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 189
      removed outlier: 6.899A  pdb=" N   ASN 1 180 " --> pdb=" O   VAL B 179 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL 1 179 " --> pdb=" O   ASN A 180 " (cutoff:3.500A)
      removed outlier: 9.015A  pdb=" N   THR A 182 " --> pdb=" O   VAL 1 179 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE 1 181 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   LYS A 184 " --> pdb=" O   ILE 1 181 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ILE 1 183 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   HIS A 186 " --> pdb=" O   ILE 1 183 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   GLN 1 185 " --> pdb=" O   HIS A 186 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   VAL A 188 " --> pdb=" O   GLN 1 185 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   THR 1 187 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 179 " --> pdb=" O   ASN C 180 " (cutoff:3.500A)
      removed outlier: 9.034A  pdb=" N   THR C 182 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE A 181 " --> pdb=" O   THR C 182 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   LYS C 184 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ILE A 183 " --> pdb=" O   LYS C 184 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   HIS C 186 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   GLN A 185 " --> pdb=" O   HIS C 186 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   VAL C 188 " --> pdb=" O   GLN A 185 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   THR A 187 " --> pdb=" O   VAL C 188 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL C 179 " --> pdb=" O   ASN D 180 " (cutoff:3.500A)
      removed outlier: 9.043A  pdb=" N   THR D 182 " --> pdb=" O   VAL C 179 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ILE C 181 " --> pdb=" O   THR D 182 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   LYS D 184 " --> pdb=" O   ILE C 181 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ILE C 183 " --> pdb=" O   LYS D 184 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   HIS D 186 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   GLN C 185 " --> pdb=" O   HIS D 186 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   VAL D 188 " --> pdb=" O   GLN C 185 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   THR C 187 " --> pdb=" O   VAL D 188 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 206
      removed outlier: 6.238A  pdb=" N   GLU 1 199 " --> pdb=" O   THR A 200 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   VAL A 202 " --> pdb=" O   GLU 1 199 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ASP 1 201 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   MET A 204 " --> pdb=" O   ASP 1 201 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LYS 1 203 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   GLU A 206 " --> pdb=" O   LYS 1 203 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   MET 1 205 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   GLU A 199 " --> pdb=" O   THR C 200 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   VAL C 202 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ASP A 201 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   MET C 204 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LYS A 203 " --> pdb=" O   MET C 204 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   GLU C 206 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   MET A 205 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   GLU C 199 " --> pdb=" O   THR D 200 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   VAL D 202 " --> pdb=" O   GLU C 199 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ASP C 201 " --> pdb=" O   VAL D 202 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 218 through 219
      removed outlier: 6.374A  pdb=" N   GLN 1 218 " --> pdb=" O   LYS A 219 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLN A 218 " --> pdb=" O   LYS C 219 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   GLN C 218 " --> pdb=" O   LYS D 219 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 222 through 225
      removed outlier: 6.275A  pdb=" N   ALA 1 223 " --> pdb=" O   TYR A 224 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ALA A 223 " --> pdb=" O   TYR C 224 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ALA C 223 " --> pdb=" O   TYR D 224 " (cutoff:3.500A)

    65 hydrogen bonds defined for protein.
    195 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: 1.42

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1875
        1.34 -     1.46: 1337
        1.46 -     1.58: 2418
        1.58 -     1.70: 0
        1.70 -     1.81: 80
  Bond restraints: 5710
  Sorted by residual:
  bond pdb=" C   ASP B 166 "
       pdb=" N   GLN B 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.40e-02 5.10e+03 7.22e-01
  bond pdb=" C   ASP D 166 "
       pdb=" N   GLN D 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.40e-02 5.10e+03 7.19e-01
  bond pdb=" C   ASP C 166 "
       pdb=" N   GLN C 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.40e-02 5.10e+03 6.90e-01
  bond pdb=" C   ASP 1 166 "
       pdb=" N   GLN 1 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.341 -0.011 1.40e-02 5.10e+03 6.26e-01
  bond pdb=" C   ASP A 166 "
       pdb=" N   GLN A 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.341 -0.011 1.40e-02 5.10e+03 6.03e-01
  ... (remaining 5705 not shown)

  Histogram of bond angle deviations from ideal:
      100.76 -   107.40: 262
      107.40 -   114.04: 2967
      114.04 -   120.68: 2144
      120.68 -   127.31: 2277
      127.31 -   133.95: 70
  Bond angle restraints: 7720
  Sorted by residual:
  angle pdb=" N   ASN B 180 "
        pdb=" CA  ASN B 180 "
        pdb=" C   ASN B 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.08   -4.80 1.35e+00 5.49e-01 1.26e+01
  angle pdb=" N   ASN A 180 "
        pdb=" CA  ASN A 180 "
        pdb=" C   ASN A 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.07   -4.79 1.35e+00 5.49e-01 1.26e+01
  angle pdb=" N   ASN 1 180 "
        pdb=" CA  ASN 1 180 "
        pdb=" C   ASN 1 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.04   -4.76 1.35e+00 5.49e-01 1.24e+01
  angle pdb=" N   ASN D 180 "
        pdb=" CA  ASN D 180 "
        pdb=" C   ASN D 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.04   -4.76 1.35e+00 5.49e-01 1.24e+01
  angle pdb=" N   ASN C 180 "
        pdb=" CA  ASN C 180 "
        pdb=" C   ASN C 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.01   -4.73 1.35e+00 5.49e-01 1.23e+01
  ... (remaining 7715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.38: 2946
       15.38 -    30.77: 279
       30.77 -    46.15: 110
       46.15 -    61.53: 40
       61.53 -    76.92: 25
  Dihedral angle restraints: 3400
    sinusoidal: 1390
      harmonic: 2010
  Sorted by residual:
  dihedral pdb=" CA  ASP A 201 "
           pdb=" CB  ASP A 201 "
           pdb=" CG  ASP A 201 "
           pdb=" OD1 ASP A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.89   51.89     1      2.00e+01 2.50e-03 9.19e+00
  dihedral pdb=" CA  ASP C 201 "
           pdb=" CB  ASP C 201 "
           pdb=" CG  ASP C 201 "
           pdb=" OD1 ASP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.87   51.87     1      2.00e+01 2.50e-03 9.18e+00
  dihedral pdb=" CA  ASP 1 201 "
           pdb=" CB  ASP 1 201 "
           pdb=" CG  ASP 1 201 "
           pdb=" OD1 ASP 1 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.87   51.87     1      2.00e+01 2.50e-03 9.18e+00
  ... (remaining 3397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 516
       0.036 -    0.072: 147
       0.072 -    0.108: 86
       0.108 -    0.145: 26
       0.145 -    0.181: 5
  Chirality restraints: 780
  Sorted by residual:
  chirality pdb=" CA  ASN B 180 "
            pdb=" N   ASN B 180 "
            pdb=" C   ASN B 180 "
            pdb=" CB  ASN B 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.16e-01
  chirality pdb=" CA  ASN A 180 "
            pdb=" N   ASN A 180 "
            pdb=" C   ASN A 180 "
            pdb=" CB  ASN A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.88e-01
  chirality pdb=" CA  ASN 1 180 "
            pdb=" N   ASN 1 180 "
            pdb=" C   ASN 1 180 "
            pdb=" CB  ASN 1 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.77e-01
  ... (remaining 777 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 217 "   -0.005 2.00e-02 2.50e+03   4.37e-03 3.82e-01
        pdb=" CG  TYR D 217 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 217 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 217 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 217 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 217 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 217 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D 217 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 217 "   -0.006 2.00e-02 2.50e+03   4.33e-03 3.75e-01
        pdb=" CG  TYR B 217 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 217 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 217 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 217 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 217 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 217 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 217 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR 1 217 "   -0.006 2.00e-02 2.50e+03   4.31e-03 3.71e-01
        pdb=" CG  TYR 1 217 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR 1 217 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR 1 217 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR 1 217 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR 1 217 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR 1 217 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR 1 217 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 2165
        2.94 -     3.43: 5104
        3.43 -     3.92: 9900
        3.92 -     4.41: 10113
        4.41 -     4.90: 18108
  Nonbonded interactions: 45390
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 145 "
            pdb=" NH2 ARG B 150 "
     model   vdw
     2.449 2.520
  nonbonded pdb=" OE1 GLU C 145 "
            pdb=" NH2 ARG C 150 "
     model   vdw
     2.449 2.520
  nonbonded pdb=" OE1 GLU 1 145 "
            pdb=" NH2 ARG 1 150 "
     model   vdw
     2.449 2.520
  nonbonded pdb=" OE1 GLU A 145 "
            pdb=" NH2 ARG A 150 "
     model   vdw
     2.449 2.520
  nonbonded pdb=" OE1 GLU D 145 "
            pdb=" NH2 ARG D 150 "
     model   vdw
     2.450 2.520
  ... (remaining 45385 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 '1'
  selection = chain 'A'
  selection = chain 'B'
  selection = 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          10.570
  Check model and map are aligned:         0.080
  Set scattering table:                    0.050
  Process input model:                     19.120
  Find NCS groups from input model:        0.390
  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:12.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5710  Z= 0.126
  Angle     :  0.570   5.341   7720  Z= 0.350
  Chirality :  0.049   0.181    780
  Planarity :  0.001   0.012   1020
  Dihedral  : 16.473  76.917   2115
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  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: -3.11 (0.27), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.20), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.002   0.001   TRP C 144 
   HIS   0.001   0.000   HIS A 110 
   PHE   0.009   0.001   PHE B 174 
   TYR   0.010   0.001   TYR B 217 
   ARG   0.001   0.000   ARG C 155 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.635 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 1.5554
  time to fit residues: 321.0107
Evaluate side-chains
  153 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.670 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9003
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
1 172 ASN
1 185 GLN
1 211 GLN
A 172 ASN
A 185 GLN
A 211 GLN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 GLN
B 211 GLN
C 172 ASN
C 185 GLN
C 211 GLN
** D  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 172 ASN
** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 185 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.073   5710  Z= 0.655
  Angle     :  0.863   6.769   7720  Z= 0.478
  Chirality :  0.056   0.205    780
  Planarity :  0.005   0.074   1020
  Dihedral  :  6.235  26.208    780
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 16.81 %
    Favored  : 77.98 %
  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: -3.70 (0.24), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.002   TRP C 144 
   HIS   0.009   0.002   HIS 1 110 
   PHE   0.020   0.004   PHE B 174 
   TYR   0.039   0.004   TYR B 156 
   ARG   0.006   0.001   ARG A 135 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 0.654 
Fit side-chains
  outliers start: 31
  outliers final: 7
  residues processed: 164
  average time/residue: 1.5735
  time to fit residues: 266.2523
Evaluate side-chains
  136 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.668 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 2
  residues processed: 5
  average time/residue: 0.4888
  time to fit residues: 3.4552
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0060
   chunk 52 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
1 211 GLN
A 158 ASN
A 211 GLN
B 158 ASN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.4489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5710  Z= 0.174
  Angle     :  0.648   6.566   7720  Z= 0.354
  Chirality :  0.050   0.179    780
  Planarity :  0.003   0.024   1020
  Dihedral  :  5.389  19.573    780
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.67 %
    Favored  : 76.64 %
  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: -3.63 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP B  98 
   HIS   0.002   0.001   HIS 1 139 
   PHE   0.021   0.003   PHE 1 197 
   TYR   0.026   0.002   TYR 1 217 
   ARG   0.004   0.000   ARG B 207 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.713 
Fit side-chains
  outliers start: 16
  outliers final: 5
  residues processed: 154
  average time/residue: 1.5808
  time to fit residues: 251.1484
Evaluate side-chains
  141 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 0.662 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 5
  residues processed: 1
  average time/residue: 0.1894
  time to fit residues: 1.0751
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0570
   chunk 56 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    4.2104

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

Flipped N/Q/H residues before XYZ refinement:
1 196 ASN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   5710  Z= 0.429
  Angle     :  0.735   8.236   7720  Z= 0.403
  Chirality :  0.051   0.178    780
  Planarity :  0.004   0.029   1020
  Dihedral  :  5.904  21.768    780
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 20.34 %
    Favored  : 75.13 %
  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: -3.77 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP B  98 
   HIS   0.006   0.001   HIS 1 110 
   PHE   0.024   0.003   PHE 1 197 
   TYR   0.028   0.003   TYR C 217 
   ARG   0.004   0.000   ARG B 135 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.697 
Fit side-chains
  outliers start: 27
  outliers final: 5
  residues processed: 152
  average time/residue: 1.6439
  time to fit residues: 257.8525
Evaluate side-chains
  134 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.683 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 2
  average time/residue: 0.2166
  time to fit residues: 1.4319
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0470
   chunk 32 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    3.4086

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

Flipped N/Q/H residues before XYZ refinement:
** 1 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 196 ASN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.5020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5710  Z= 0.349
  Angle     :  0.727   7.866   7720  Z= 0.395
  Chirality :  0.051   0.152    780
  Planarity :  0.003   0.027   1020
  Dihedral  :  5.910  20.668    780
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 21.01 %
    Favored  : 75.13 %
  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: -3.85 (0.24), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP B  98 
   HIS   0.005   0.001   HIS 1 110 
   PHE   0.017   0.003   PHE 1 197 
   TYR   0.028   0.002   TYR C 217 
   ARG   0.004   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.684 
Fit side-chains
  outliers start: 23
  outliers final: 11
  residues processed: 148
  average time/residue: 1.6019
  time to fit residues: 244.7654
Evaluate side-chains
  137 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.771 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 7
  residues processed: 5
  average time/residue: 0.6238
  time to fit residues: 4.2943
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 62 optimal weight:   20.0000
   chunk 52 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 60 optimal weight:   20.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** 1 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 196 ASN
** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 ASN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.5454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.058   5710  Z= 0.638
  Angle     :  0.865   8.243   7720  Z= 0.474
  Chirality :  0.055   0.164    780
  Planarity :  0.005   0.047   1020
  Dihedral  :  6.522  23.386    780
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.35 %
    Favored  : 87.65 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 21.18 %
    Favored  : 73.78 %
  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: -4.07 (0.24), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.18), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.002   TRP B  98 
   HIS   0.008   0.002   HIS 1 110 
   PHE   0.019   0.004   PHE B 197 
   TYR   0.032   0.003   TYR C 217 
   ARG   0.004   0.001   ARG B 135 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.721 
Fit side-chains
  outliers start: 30
  outliers final: 14
  residues processed: 142
  average time/residue: 1.5452
  time to fit residues: 226.6418
Evaluate side-chains
  131 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.678 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 12
  residues processed: 3
  average time/residue: 0.1992
  time to fit residues: 1.6319
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** 1 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.5277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5710  Z= 0.227
  Angle     :  0.757   7.684   7720  Z= 0.405
  Chirality :  0.051   0.190    780
  Planarity :  0.003   0.023   1020
  Dihedral  :  5.924  21.631    780
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 22.69 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.99 (0.24), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.18), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP D 144 
   HIS   0.002   0.001   HIS 1 110 
   PHE   0.012   0.002   PHE B 174 
   TYR   0.025   0.002   TYR C 217 
   ARG   0.004   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.655 
Fit side-chains
  outliers start: 23
  outliers final: 16
  residues processed: 161
  average time/residue: 1.5103
  time to fit residues: 251.1553
Evaluate side-chains
  140 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.706 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 13
  residues processed: 4
  average time/residue: 0.4199
  time to fit residues: 2.8292
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
** 1 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 196 ASN
** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 ASN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.5460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   5710  Z= 0.416
  Angle     :  0.818   8.205   7720  Z= 0.440
  Chirality :  0.052   0.206    780
  Planarity :  0.004   0.044   1020
  Dihedral  :  6.151  23.518    780
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 25.04 %
    Favored  : 71.43 %
  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: -4.03 (0.24), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP D 144 
   HIS   0.005   0.001   HIS 1 110 
   PHE   0.024   0.003   PHE B 197 
   TYR   0.032   0.003   TYR C 217 
   ARG   0.006   0.001   ARG 1 207 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.684 
Fit side-chains
  outliers start: 21
  outliers final: 14
  residues processed: 144
  average time/residue: 1.6218
  time to fit residues: 241.0551
Evaluate side-chains
  139 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.713 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 13
  residues processed: 2
  average time/residue: 0.1985
  time to fit residues: 1.4236
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** 1 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 196 ASN
** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.5408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5710  Z= 0.264
  Angle     :  0.799   8.178   7720  Z= 0.426
  Chirality :  0.052   0.234    780
  Planarity :  0.003   0.037   1020
  Dihedral  :  5.977  22.742    780
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 26.72 %
    Favored  : 70.76 %
  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: -4.00 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP D 144 
   HIS   0.002   0.001   HIS 1 110 
   PHE   0.028   0.003   PHE 1 197 
   TYR   0.030   0.002   TYR C 217 
   ARG   0.006   0.000   ARG 1 207 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.671 
Fit side-chains
  outliers start: 15
  outliers final: 12
  residues processed: 157
  average time/residue: 1.4814
  time to fit residues: 240.5949
Evaluate side-chains
  147 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.645 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 12
  residues processed: 1
  average time/residue: 0.2046
  time to fit residues: 1.1755
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** 1 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 196 ASN
** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 211 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5710  Z= 0.262
  Angle     :  0.805   8.340   7720  Z= 0.429
  Chirality :  0.051   0.237    780
  Planarity :  0.003   0.040   1020
  Dihedral  :  5.884  23.734    780
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 27.39 %
    Favored  : 69.92 %
  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: -3.99 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP D 144 
   HIS   0.003   0.001   HIS 1 110 
   PHE   0.033   0.003   PHE B 197 
   TYR   0.032   0.002   TYR C 217 
   ARG   0.007   0.000   ARG 1 207 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.634 
Fit side-chains
  outliers start: 16
  outliers final: 13
  residues processed: 150
  average time/residue: 1.4655
  time to fit residues: 227.3076
Evaluate side-chains
  142 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.621 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 12
  residues processed: 2
  average time/residue: 0.6254
  time to fit residues: 2.1589
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 2 optimal weight:    0.0020
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    2.3592

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

Flipped N/Q/H residues before XYZ refinement:
** 1 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.113846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.098449 restraints weight = 10731.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 2.79
r_work: 0.3955 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3851 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.5488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5710  Z= 0.299
  Angle     :  0.826   8.788   7720  Z= 0.437
  Chirality :  0.052   0.187    780
  Planarity :  0.003   0.040   1020
  Dihedral  :  5.977  23.377    780
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 26.89 %
    Favored  : 69.92 %
  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: -4.01 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP D 144 
   HIS   0.003   0.001   HIS 1 110 
   PHE   0.025   0.003   PHE 1 197 
   TYR   0.031   0.002   TYR C 217 
   ARG   0.006   0.000   ARG 1 207 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3963.66 seconds
wall clock time: 69 minutes 59.62 seconds (4199.62 seconds total)