Starting phenix.real_space_refine
on Mon Sep 23 21:48:43 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/09_2024/7td6_25824.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/09_2024/7td6_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_25824/09_2024/7td6_25824.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/09_2024/7td6_25824.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/09_2024/7td6_25824.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/09_2024/7td6_25824.cif"
  }
  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
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.12, per 1000 atoms: 0.74
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 664.0 milliseconds
  

  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: 0.84
  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: 1.47

  Time building geometry restraints manager: 1.48 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:
        0.00 -     1.07: 7320
        1.07 -     2.14: 291
        2.14 -     3.20: 64
        3.20 -     4.27: 30
        4.27 -     5.34: 15
  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 3.120
  nonbonded pdb=" OE1 GLU C 145 "
            pdb=" NH2 ARG C 150 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" OE1 GLU 1 145 "
            pdb=" NH2 ARG 1 150 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" OE1 GLU A 145 "
            pdb=" NH2 ARG A 150 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" OE1 GLU D 145 "
            pdb=" NH2 ARG D 150 "
     model   vdw
     2.450 3.120
  ... (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
Time spend for trying shortcut: 0.00
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:             3.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.110
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.130
-------------------------------------------------------------------------------
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  : 0.682 
Fit side-chains
REVERT: 1  153 MET cc_start: 0.7616 (mmm) cc_final: 0.7408 (mmm)
REVERT: 1  220 GLU cc_start: 0.8457 (mp0) cc_final: 0.7958 (mp0)
REVERT: 1  226 ASP cc_start: 0.7652 (m-30) cc_final: 0.7089 (p0)
REVERT: A  224 TYR cc_start: 0.7614 (m-80) cc_final: 0.7379 (m-80)
REVERT: B  151 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7071 (pm20)
REVERT: B  155 ARG cc_start: 0.7969 (mtt180) cc_final: 0.6605 (mmp-170)
REVERT: B  163 ARG cc_start: 0.8144 (mtt180) cc_final: 0.6928 (mmp-170)
REVERT: B  175 VAL cc_start: 0.8551 (t) cc_final: 0.8148 (m)
REVERT: B  199 GLU cc_start: 0.8007 (mp0) cc_final: 0.7556 (mp0)
REVERT: B  207 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6030 (ppt90)
REVERT: B  212 MET cc_start: 0.8166 (tpp) cc_final: 0.7840 (ttm)
REVERT: B  219 LYS cc_start: 0.8094 (mttt) cc_final: 0.6418 (pmtt)
REVERT: B  220 GLU cc_start: 0.8054 (mp0) cc_final: 0.7338 (pp20)
REVERT: B  221 SER cc_start: 0.8904 (m) cc_final: 0.8403 (m)
REVERT: C  128 MET cc_start: 0.8796 (mtp) cc_final: 0.8456 (mtp)
REVERT: C  155 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7245 (mtp85)
REVERT: C  215 THR cc_start: 0.8787 (m) cc_final: 0.8521 (t)
REVERT: C  220 GLU cc_start: 0.8455 (mp0) cc_final: 0.8002 (mp0)
REVERT: C  226 ASP cc_start: 0.7721 (m-30) cc_final: 0.7145 (p0)
REVERT: D  100 LYS cc_start: 0.7426 (mtmt) cc_final: 0.6745 (mmtt)
REVERT: D  135 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7247 (tpm170)
REVERT: D  140 PHE cc_start: 0.7749 (m-80) cc_final: 0.6770 (p90)
REVERT: D  143 ASP cc_start: 0.8149 (t0) cc_final: 0.7946 (m-30)
REVERT: D  153 MET cc_start: 0.8006 (mmm) cc_final: 0.6871 (ptt)
REVERT: D  155 ARG cc_start: 0.7800 (mtt180) cc_final: 0.6756 (ptt-90)
REVERT: D  163 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7261 (pmt170)
REVERT: D  207 ARG cc_start: 0.7603 (mtt180) cc_final: 0.6783 (mmp-170)
REVERT: D  212 MET cc_start: 0.8244 (tpp) cc_final: 0.6896 (pmt)
REVERT: D  217 TYR cc_start: 0.8499 (p90) cc_final: 0.7999 (p90)
REVERT: D  219 LYS cc_start: 0.8071 (mttt) cc_final: 0.7761 (mmtt)
REVERT: D  222 GLN cc_start: 0.8555 (mp-120) cc_final: 0.8158 (mp10)
REVERT: D  224 TYR cc_start: 0.7638 (m-80) cc_final: 0.7131 (m-80)
REVERT: D  229 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7277 (pmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 1.5062
  time to fit residues: 311.0790
Evaluate side-chains
  155 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0000
   chunk 37 optimal weight:    0.7980
   chunk 59 optimal weight:    8.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
1 158 ASN
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
A 158 ASN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
B 158 ASN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
C 158 ASN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
D 173 ASN
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2450

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= 0.217
  Angle     :  0.596   6.466   7720  Z= 0.322
  Chirality :  0.047   0.131    780
  Planarity :  0.003   0.020   1020
  Dihedral  :  4.599  16.757    780
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.62 %
    Favored  : 83.19 %
  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: -3.29 (0.26), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.20), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 144 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.015   0.003   PHE B 197 
 TYR   0.026   0.002   TYR C 217 
 ARG   0.004   0.000   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
  176 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.677 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8283 (ttm) cc_final: 0.8053 (ttm)
REVERT: 1  219 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7599 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8514 (mp0) cc_final: 0.8034 (mp0)
REVERT: A  135 ARG cc_start: 0.8157 (ptp-110) cc_final: 0.7913 (ptp90)
REVERT: A  145 GLU cc_start: 0.8145 (mp0) cc_final: 0.7918 (mp0)
REVERT: A  197 PHE cc_start: 0.6562 (m-10) cc_final: 0.6134 (m-80)
REVERT: A  229 ARG cc_start: 0.8152 (mmt-90) cc_final: 0.7890 (mmt-90)
REVERT: B  135 ARG cc_start: 0.5919 (OUTLIER) cc_final: 0.4646 (pmt170)
REVERT: B  151 GLU cc_start: 0.8254 (mt-10) cc_final: 0.6941 (pm20)
REVERT: B  155 ARG cc_start: 0.8108 (mtt180) cc_final: 0.6642 (mmp-170)
REVERT: B  175 VAL cc_start: 0.8708 (t) cc_final: 0.8288 (m)
REVERT: B  212 MET cc_start: 0.8124 (tpp) cc_final: 0.7864 (ttm)
REVERT: B  219 LYS cc_start: 0.8075 (mttt) cc_final: 0.6573 (pmtt)
REVERT: B  220 GLU cc_start: 0.8151 (mp0) cc_final: 0.7477 (pp20)
REVERT: B  221 SER cc_start: 0.8876 (m) cc_final: 0.8403 (m)
REVERT: C  128 MET cc_start: 0.8853 (mtp) cc_final: 0.8539 (mtp)
REVERT: C  137 MET cc_start: 0.8114 (ttm) cc_final: 0.7682 (ttm)
REVERT: C  155 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7305 (mtp85)
REVERT: C  204 MET cc_start: 0.6844 (tmt) cc_final: 0.6458 (tmt)
REVERT: C  220 GLU cc_start: 0.8460 (mp0) cc_final: 0.8258 (mp0)
REVERT: D  100 LYS cc_start: 0.7392 (mtmt) cc_final: 0.6743 (mmtt)
REVERT: D  133 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6525 (mpt)
REVERT: D  135 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7296 (tpm170)
REVERT: D  140 PHE cc_start: 0.7789 (m-80) cc_final: 0.6673 (p90)
REVERT: D  143 ASP cc_start: 0.8159 (t0) cc_final: 0.7824 (m-30)
REVERT: D  153 MET cc_start: 0.7895 (mmm) cc_final: 0.6827 (ptt)
REVERT: D  155 ARG cc_start: 0.7778 (mtt180) cc_final: 0.6617 (ptt-90)
REVERT: D  163 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7165 (pmt170)
REVERT: D  177 ASP cc_start: 0.7863 (m-30) cc_final: 0.7467 (m-30)
REVERT: D  204 MET cc_start: 0.6801 (tmm) cc_final: 0.6590 (tmm)
REVERT: D  206 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7283 (tm-30)
REVERT: D  207 ARG cc_start: 0.8019 (mtt180) cc_final: 0.6671 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8336 (mm-40)
REVERT: D  212 MET cc_start: 0.8268 (tpp) cc_final: 0.6933 (pmt)
REVERT: D  222 GLN cc_start: 0.8588 (mp-120) cc_final: 0.8186 (mp10)
REVERT: D  224 TYR cc_start: 0.7793 (m-80) cc_final: 0.7372 (m-80)
REVERT: D  226 ASP cc_start: 0.7327 (p0) cc_final: 0.6942 (p0)
REVERT: D  229 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7185 (pmt170)
  outliers start: 13
  outliers final: 2
  residues processed: 168
  average time/residue: 1.3570
  time to fit residues: 236.2731
Evaluate side-chains
  162 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 157
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
A  96 ASN
A 172 ASN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 172 ASN
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.040   5710  Z= 0.562
  Angle     :  0.786   8.591   7720  Z= 0.429
  Chirality :  0.053   0.157    780
  Planarity :  0.004   0.024   1020
  Dihedral  :  6.146  24.164    780
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 17.14 %
    Favored  : 79.83 %
  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: -3.75 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  98 
 HIS   0.008   0.002   HIS 1 110 
 PHE   0.020   0.003   PHE B 174 
 TYR   0.029   0.003   TYR C 217 
 ARG   0.005   0.001   ARG D 135 

*********************** 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
  171 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.650 
Fit side-chains
REVERT: 1  100 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7762 (mttp)
REVERT: 1  137 MET cc_start: 0.8259 (ttm) cc_final: 0.7806 (ttm)
REVERT: 1  219 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7939 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8664 (mp0) cc_final: 0.8261 (mp0)
REVERT: A  145 GLU cc_start: 0.8318 (mp0) cc_final: 0.7960 (mp0)
REVERT: A  155 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6853 (mpp80)
REVERT: A  197 PHE cc_start: 0.6662 (m-10) cc_final: 0.5991 (m-10)
REVERT: A  211 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8295 (mt0)
REVERT: B  100 LYS cc_start: 0.8334 (mtmt) cc_final: 0.8012 (mttp)
REVERT: B  140 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6881 (m-10)
REVERT: B  145 GLU cc_start: 0.8295 (mp0) cc_final: 0.8062 (mp0)
REVERT: B  155 ARG cc_start: 0.8083 (mtt180) cc_final: 0.6616 (mmt-90)
REVERT: B  207 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6082 (tmm160)
REVERT: B  210 GLU cc_start: 0.4200 (pm20) cc_final: 0.3774 (pm20)
REVERT: B  212 MET cc_start: 0.8008 (tpp) cc_final: 0.7731 (ttm)
REVERT: B  219 LYS cc_start: 0.8249 (mttt) cc_final: 0.6946 (pptt)
REVERT: B  220 GLU cc_start: 0.8217 (mp0) cc_final: 0.7423 (pp20)
REVERT: B  228 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.6242 (pmt-80)
REVERT: C  124 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8733 (mp)
REVERT: C  128 MET cc_start: 0.8977 (mtp) cc_final: 0.8664 (mtp)
REVERT: C  137 MET cc_start: 0.8193 (ttm) cc_final: 0.7804 (ttm)
REVERT: C  155 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7088 (mtp85)
REVERT: C  195 GLU cc_start: 0.5931 (tm-30) cc_final: 0.5067 (tt0)
REVERT: C  220 GLU cc_start: 0.8721 (mp0) cc_final: 0.8318 (mp0)
REVERT: D  100 LYS cc_start: 0.7813 (mtmt) cc_final: 0.6883 (mmmt)
REVERT: D  135 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7469 (tpm170)
REVERT: D  140 PHE cc_start: 0.8092 (m-80) cc_final: 0.6199 (p90)
REVERT: D  155 ARG cc_start: 0.8094 (mtt180) cc_final: 0.6735 (ptt90)
REVERT: D  163 ARG cc_start: 0.8697 (mtt180) cc_final: 0.7137 (pmt170)
REVERT: D  207 ARG cc_start: 0.8064 (mtt180) cc_final: 0.6246 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7610 (mt0)
REVERT: D  212 MET cc_start: 0.8348 (tpp) cc_final: 0.6984 (pmt)
REVERT: D  217 TYR cc_start: 0.8709 (p90) cc_final: 0.8494 (p90)
REVERT: D  224 TYR cc_start: 0.7994 (m-80) cc_final: 0.7638 (m-80)
REVERT: D  229 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7308 (pmt170)
  outliers start: 18
  outliers final: 5
  residues processed: 164
  average time/residue: 1.5224
  time to fit residues: 257.7643
Evaluate side-chains
  145 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    2.7990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5710  Z= 0.297
  Angle     :  0.685   7.864   7720  Z= 0.369
  Chirality :  0.050   0.148    780
  Planarity :  0.003   0.016   1020
  Dihedral  :  5.807  20.466    780
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.99 %
    Favored  : 77.31 %
  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: -3.79 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.020   0.003   PHE B 197 
 TYR   0.028   0.002   TYR 1 217 
 ARG   0.003   0.000   ARG A 229 

*********************** 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
  169 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.783 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8271 (ttm) cc_final: 0.7878 (ttm)
REVERT: A  145 GLU cc_start: 0.8354 (mp0) cc_final: 0.7959 (mp0)
REVERT: A  197 PHE cc_start: 0.6634 (m-10) cc_final: 0.6334 (m-10)
REVERT: A  211 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8017 (mt0)
REVERT: B  100 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8056 (mttp)
REVERT: B  137 MET cc_start: 0.8698 (ttp) cc_final: 0.8448 (ttt)
REVERT: B  140 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6852 (m-10)
REVERT: B  145 GLU cc_start: 0.8313 (mp0) cc_final: 0.8071 (mp0)
REVERT: B  155 ARG cc_start: 0.8049 (mtt180) cc_final: 0.6621 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: B  207 ARG cc_start: 0.7902 (mtt180) cc_final: 0.6260 (ttp80)
REVERT: B  210 GLU cc_start: 0.4473 (pm20) cc_final: 0.4049 (pm20)
REVERT: B  212 MET cc_start: 0.8044 (tpp) cc_final: 0.7746 (ttm)
REVERT: B  219 LYS cc_start: 0.8221 (mttt) cc_final: 0.6726 (pmtt)
REVERT: B  220 GLU cc_start: 0.8191 (mp0) cc_final: 0.7573 (pp20)
REVERT: B  228 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.6249 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8368 (m-40)
REVERT: C  124 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8677 (mp)
REVERT: C  128 MET cc_start: 0.8935 (mtp) cc_final: 0.8595 (mtp)
REVERT: C  137 MET cc_start: 0.8171 (ttm) cc_final: 0.7806 (ttm)
REVERT: C  155 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7221 (mtt90)
REVERT: C  195 GLU cc_start: 0.5966 (tm-30) cc_final: 0.5001 (tt0)
REVERT: C  220 GLU cc_start: 0.8844 (mp0) cc_final: 0.8350 (mp0)
REVERT: D  100 LYS cc_start: 0.7775 (mtmt) cc_final: 0.6904 (mmtt)
REVERT: D  135 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7432 (tpm170)
REVERT: D  140 PHE cc_start: 0.8143 (m-80) cc_final: 0.6191 (p90)
REVERT: D  145 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7900 (mt-10)
REVERT: D  155 ARG cc_start: 0.7923 (mtt180) cc_final: 0.6874 (ptt90)
REVERT: D  158 ASN cc_start: 0.8755 (m110) cc_final: 0.8513 (m-40)
REVERT: D  163 ARG cc_start: 0.8694 (mtt180) cc_final: 0.7079 (pmt170)
REVERT: D  207 ARG cc_start: 0.8278 (mtt180) cc_final: 0.6268 (mmp-170)
REVERT: D  212 MET cc_start: 0.8352 (tpp) cc_final: 0.7040 (pmt)
REVERT: D  224 TYR cc_start: 0.7960 (m-80) cc_final: 0.7604 (m-80)
REVERT: D  229 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7255 (pmt170)
  outliers start: 22
  outliers final: 5
  residues processed: 159
  average time/residue: 1.5843
  time to fit residues: 260.0417
Evaluate side-chains
  146 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   overall best weight:    4.5990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.4203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   5710  Z= 0.458
  Angle     :  0.749   7.956   7720  Z= 0.403
  Chirality :  0.051   0.162    780
  Planarity :  0.003   0.019   1020
  Dihedral  :  6.056  22.751    780
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 18.66 %
    Favored  : 77.14 %
  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: -3.91 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.006   0.001   HIS 1 110 
 PHE   0.023   0.003   PHE C 197 
 TYR   0.032   0.003   TYR C 217 
 ARG   0.005   0.000   ARG B 135 

*********************** 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
  157 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.659 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8275 (ttm) cc_final: 0.7808 (ttm)
REVERT: 1  206 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7409 (tm-30)
REVERT: A  145 GLU cc_start: 0.8364 (mp0) cc_final: 0.7993 (mp0)
REVERT: A  155 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7152 (mpp80)
REVERT: A  197 PHE cc_start: 0.6728 (m-10) cc_final: 0.6524 (m-10)
REVERT: A  211 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8115 (mt0)
REVERT: A  226 ASP cc_start: 0.7816 (p0) cc_final: 0.7542 (p0)
REVERT: A  229 ARG cc_start: 0.8089 (mmt-90) cc_final: 0.7768 (mmt-90)
REVERT: B  135 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5171 (pmt170)
REVERT: B  137 MET cc_start: 0.8685 (ttp) cc_final: 0.8417 (ttt)
REVERT: B  140 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6884 (m-10)
REVERT: B  145 GLU cc_start: 0.8351 (mp0) cc_final: 0.8083 (mp0)
REVERT: B  155 ARG cc_start: 0.8091 (mtt180) cc_final: 0.6600 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7599 (tm-30)
REVERT: B  207 ARG cc_start: 0.7931 (mtt180) cc_final: 0.6301 (ttp80)
REVERT: B  210 GLU cc_start: 0.4455 (OUTLIER) cc_final: 0.4117 (pm20)
REVERT: B  212 MET cc_start: 0.8026 (tpp) cc_final: 0.7730 (ttm)
REVERT: B  219 LYS cc_start: 0.8230 (mttt) cc_final: 0.6636 (pmtt)
REVERT: B  220 GLU cc_start: 0.8220 (mp0) cc_final: 0.7495 (pp20)
REVERT: B  228 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.6289 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8365 (m-40)
REVERT: C  128 MET cc_start: 0.8972 (mtp) cc_final: 0.8678 (mtp)
REVERT: C  137 MET cc_start: 0.8211 (ttm) cc_final: 0.7830 (ttm)
REVERT: C  220 GLU cc_start: 0.8886 (mp0) cc_final: 0.8378 (mp0)
REVERT: C  229 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7025 (mtp85)
REVERT: D  100 LYS cc_start: 0.7811 (mtmt) cc_final: 0.6914 (mmtt)
REVERT: D  133 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6763 (mpt)
REVERT: D  135 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7421 (tpm170)
REVERT: D  140 PHE cc_start: 0.8221 (m-80) cc_final: 0.6097 (p90)
REVERT: D  145 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8060 (mt-10)
REVERT: D  153 MET cc_start: 0.8285 (mmm) cc_final: 0.6736 (ptt)
REVERT: D  155 ARG cc_start: 0.7954 (mtt180) cc_final: 0.6899 (ptt90)
REVERT: D  158 ASN cc_start: 0.8787 (m110) cc_final: 0.8537 (m-40)
REVERT: D  163 ARG cc_start: 0.8755 (mtt180) cc_final: 0.7018 (pmt170)
REVERT: D  207 ARG cc_start: 0.8308 (mtt180) cc_final: 0.6267 (mmp-170)
REVERT: D  212 MET cc_start: 0.8350 (tpp) cc_final: 0.7000 (pmt)
REVERT: D  229 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7246 (pmt170)
  outliers start: 25
  outliers final: 7
  residues processed: 144
  average time/residue: 1.6384
  time to fit residues: 243.2578
Evaluate side-chains
  147 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain B residue  210 GLU
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
B 142 ASN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5710  Z= 0.299
  Angle     :  0.712   7.349   7720  Z= 0.380
  Chirality :  0.050   0.147    780
  Planarity :  0.003   0.019   1020
  Dihedral  :  5.882  21.942    780
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.33 %
    Favored  : 76.97 %
  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: -3.93 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.018   0.003   PHE 1 197 
 TYR   0.030   0.002   TYR C 217 
 ARG   0.003   0.000   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
  162 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.673 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8273 (ttm) cc_final: 0.7879 (ttm)
REVERT: 1  205 MET cc_start: 0.8585 (mtm) cc_final: 0.8102 (mtt)
REVERT: 1  206 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6948 (tm-30)
REVERT: A  145 GLU cc_start: 0.8421 (mp0) cc_final: 0.8032 (mp0)
REVERT: A  155 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7064 (mpp80)
REVERT: A  226 ASP cc_start: 0.7788 (p0) cc_final: 0.7509 (p0)
REVERT: A  229 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7754 (mmt-90)
REVERT: B  137 MET cc_start: 0.8663 (ttp) cc_final: 0.8394 (ttt)
REVERT: B  140 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6847 (m-10)
REVERT: B  145 GLU cc_start: 0.8354 (mp0) cc_final: 0.8072 (mp0)
REVERT: B  155 ARG cc_start: 0.8048 (mtt180) cc_final: 0.6594 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7463 (tm-30)
REVERT: B  207 ARG cc_start: 0.7869 (mtt180) cc_final: 0.6309 (ttp80)
REVERT: B  210 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.4214 (pm20)
REVERT: B  212 MET cc_start: 0.8020 (tpp) cc_final: 0.7655 (ttt)
REVERT: B  219 LYS cc_start: 0.8206 (mttt) cc_final: 0.6723 (pmtt)
REVERT: B  220 GLU cc_start: 0.8208 (mp0) cc_final: 0.7562 (pp20)
REVERT: B  228 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.6367 (pmt170)
REVERT: C  107 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8359 (m-40)
REVERT: C  128 MET cc_start: 0.8950 (mtp) cc_final: 0.8651 (mtp)
REVERT: C  137 MET cc_start: 0.8157 (ttm) cc_final: 0.7801 (ttm)
REVERT: C  195 GLU cc_start: 0.6029 (tm-30) cc_final: 0.4927 (tt0)
REVERT: C  211 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7972 (mt0)
REVERT: C  220 GLU cc_start: 0.8891 (mp0) cc_final: 0.8338 (mp0)
REVERT: C  229 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.6962 (mtp85)
REVERT: D  100 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7073 (mmtt)
REVERT: D  133 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6720 (mpt)
REVERT: D  135 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7362 (tpm170)
REVERT: D  140 PHE cc_start: 0.8191 (m-80) cc_final: 0.6112 (p90)
REVERT: D  145 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7952 (mt-10)
REVERT: D  153 MET cc_start: 0.8265 (mmm) cc_final: 0.6744 (ptt)
REVERT: D  155 ARG cc_start: 0.7937 (mtt180) cc_final: 0.6854 (ptt90)
REVERT: D  158 ASN cc_start: 0.8737 (m110) cc_final: 0.8456 (m-40)
REVERT: D  163 ARG cc_start: 0.8737 (mtt180) cc_final: 0.6994 (pmt170)
REVERT: D  207 ARG cc_start: 0.8331 (mtt180) cc_final: 0.6245 (mmp-170)
REVERT: D  212 MET cc_start: 0.8342 (tpp) cc_final: 0.7026 (pmt)
REVERT: D  229 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7228 (pmt170)
  outliers start: 22
  outliers final: 7
  residues processed: 149
  average time/residue: 1.6084
  time to fit residues: 247.1962
Evaluate side-chains
  145 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain B residue  210 GLU
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  211 GLN
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   overall best weight:    2.6388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5710  Z= 0.295
  Angle     :  0.713   7.883   7720  Z= 0.382
  Chirality :  0.050   0.145    780
  Planarity :  0.003   0.019   1020
  Dihedral  :  5.834  22.744    780
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.83 %
    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: -3.95 (0.24), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.021   0.003   PHE 1 197 
 TYR   0.032   0.002   TYR C 217 
 ARG   0.003   0.000   ARG B 135 

*********************** 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
  160 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.674 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8258 (ttm) cc_final: 0.7884 (ttm)
REVERT: 1  204 MET cc_start: 0.7332 (mtp) cc_final: 0.6877 (tmt)
REVERT: 1  229 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7785 (mtm-85)
REVERT: A  145 GLU cc_start: 0.8432 (mp0) cc_final: 0.8026 (mp0)
REVERT: A  155 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7056 (mpp80)
REVERT: A  226 ASP cc_start: 0.7846 (p0) cc_final: 0.7479 (p0)
REVERT: A  229 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7778 (mmt-90)
REVERT: B  135 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5431 (pmt170)
REVERT: B  137 MET cc_start: 0.8646 (ttp) cc_final: 0.8371 (ttt)
REVERT: B  140 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6872 (m-10)
REVERT: B  145 GLU cc_start: 0.8317 (mp0) cc_final: 0.8042 (mp0)
REVERT: B  155 ARG cc_start: 0.8005 (mtt180) cc_final: 0.6569 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: B  207 ARG cc_start: 0.7854 (mtt180) cc_final: 0.6187 (tmm160)
REVERT: B  210 GLU cc_start: 0.4606 (OUTLIER) cc_final: 0.4219 (pm20)
REVERT: B  212 MET cc_start: 0.7993 (tpp) cc_final: 0.7695 (ttm)
REVERT: B  219 LYS cc_start: 0.8155 (mttt) cc_final: 0.6674 (pmtt)
REVERT: B  220 GLU cc_start: 0.8200 (mp0) cc_final: 0.7557 (pp20)
REVERT: B  228 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.6302 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8368 (m-40)
REVERT: C  128 MET cc_start: 0.8953 (mtp) cc_final: 0.8676 (mtp)
REVERT: C  137 MET cc_start: 0.8162 (ttm) cc_final: 0.7797 (ttm)
REVERT: C  195 GLU cc_start: 0.5844 (tm-30) cc_final: 0.4857 (tt0)
REVERT: C  220 GLU cc_start: 0.8873 (mp0) cc_final: 0.8374 (mp0)
REVERT: C  229 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.6980 (mtp85)
REVERT: D  100 LYS cc_start: 0.7914 (mtmt) cc_final: 0.6991 (mmtt)
REVERT: D  133 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6707 (mpt)
REVERT: D  135 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7374 (tpm170)
REVERT: D  140 PHE cc_start: 0.8174 (m-80) cc_final: 0.6072 (p90)
REVERT: D  145 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7913 (mt-10)
REVERT: D  153 MET cc_start: 0.8230 (mmm) cc_final: 0.6728 (ptt)
REVERT: D  155 ARG cc_start: 0.7966 (mtt180) cc_final: 0.6860 (ptt90)
REVERT: D  158 ASN cc_start: 0.8735 (m110) cc_final: 0.8472 (m-40)
REVERT: D  163 ARG cc_start: 0.8750 (mtt180) cc_final: 0.6998 (pmt170)
REVERT: D  207 ARG cc_start: 0.8308 (mtt180) cc_final: 0.6238 (mmp-170)
REVERT: D  212 MET cc_start: 0.8285 (tpp) cc_final: 0.6946 (pmt)
REVERT: D  229 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7209 (pmt170)
  outliers start: 21
  outliers final: 7
  residues processed: 149
  average time/residue: 1.6163
  time to fit residues: 248.4405
Evaluate side-chains
  146 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  128 MET
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain 1 residue  229 ARG
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain B residue  210 GLU
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 39 optimal weight:    9.9990
   chunk 42 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 54 optimal weight:    0.4980
   chunk 58 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5710  Z= 0.353
  Angle     :  0.764   8.059   7720  Z= 0.409
  Chirality :  0.051   0.148    780
  Planarity :  0.003   0.028   1020
  Dihedral  :  5.967  22.961    780
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.17 %
    Favored  : 76.13 %
  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: -4.00 (0.24), 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   0.007   0.001   TRP A  98 
 HIS   0.005   0.001   HIS 1 110 
 PHE   0.016   0.003   PHE A 197 
 TYR   0.034   0.002   TYR C 217 
 ARG   0.004   0.000   ARG B 135 

*********************** 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
  155 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.667 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8259 (ttm) cc_final: 0.7805 (ttm)
REVERT: 1  229 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7784 (mtm-85)
REVERT: A  145 GLU cc_start: 0.8488 (mp0) cc_final: 0.8054 (mp0)
REVERT: A  155 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7074 (mpp80)
REVERT: A  211 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.7805 (mt0)
REVERT: A  226 ASP cc_start: 0.7837 (p0) cc_final: 0.7484 (p0)
REVERT: A  229 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7755 (mmt-90)
REVERT: B  137 MET cc_start: 0.8618 (ttp) cc_final: 0.8332 (ttt)
REVERT: B  140 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6858 (m-10)
REVERT: B  145 GLU cc_start: 0.8338 (mp0) cc_final: 0.8057 (mp0)
REVERT: B  155 ARG cc_start: 0.8035 (mtt180) cc_final: 0.6567 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7456 (tm-30)
REVERT: B  207 ARG cc_start: 0.7861 (mtt180) cc_final: 0.6338 (ttp80)
REVERT: B  210 GLU cc_start: 0.4532 (OUTLIER) cc_final: 0.4212 (pm20)
REVERT: B  212 MET cc_start: 0.7999 (tpp) cc_final: 0.7699 (ttm)
REVERT: B  219 LYS cc_start: 0.8174 (mttt) cc_final: 0.6690 (pmtt)
REVERT: B  220 GLU cc_start: 0.8182 (mp0) cc_final: 0.7469 (pp20)
REVERT: B  228 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.6326 (pmt-80)
REVERT: C  128 MET cc_start: 0.8969 (mtp) cc_final: 0.8685 (mtp)
REVERT: C  137 MET cc_start: 0.8178 (ttm) cc_final: 0.7813 (ttm)
REVERT: C  147 ARG cc_start: 0.8333 (ptp-170) cc_final: 0.8109 (ptp-110)
REVERT: C  195 GLU cc_start: 0.6082 (tm-30) cc_final: 0.4902 (tt0)
REVERT: C  210 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7581 (tm-30)
REVERT: C  220 GLU cc_start: 0.8892 (mp0) cc_final: 0.8375 (mp0)
REVERT: C  229 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7003 (mtp85)
REVERT: D  100 LYS cc_start: 0.7893 (mtmt) cc_final: 0.6959 (mmtt)
REVERT: D  133 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6712 (mpt)
REVERT: D  135 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7383 (tpm170)
REVERT: D  140 PHE cc_start: 0.8217 (m-80) cc_final: 0.6017 (p90)
REVERT: D  145 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7921 (mt-10)
REVERT: D  153 MET cc_start: 0.8219 (mmm) cc_final: 0.6691 (ptt)
REVERT: D  155 ARG cc_start: 0.7991 (mtt180) cc_final: 0.6852 (ptt90)
REVERT: D  158 ASN cc_start: 0.8747 (m110) cc_final: 0.8477 (m-40)
REVERT: D  163 ARG cc_start: 0.8803 (mtt180) cc_final: 0.7089 (pmt170)
REVERT: D  207 ARG cc_start: 0.8300 (mtt180) cc_final: 0.6180 (mmp-170)
REVERT: D  212 MET cc_start: 0.8312 (tpp) cc_final: 0.6937 (pmt)
REVERT: D  229 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7226 (pmt170)
  outliers start: 22
  outliers final: 9
  residues processed: 144
  average time/residue: 1.6462
  time to fit residues: 244.4335
Evaluate side-chains
  147 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  190 THR
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain 1 residue  229 ARG
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain B residue  210 GLU
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    2.9990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5710  Z= 0.329
  Angle     :  0.780   7.860   7720  Z= 0.418
  Chirality :  0.051   0.148    780
  Planarity :  0.003   0.026   1020
  Dihedral  :  5.971  23.144    780
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.84 %
    Favored  : 75.97 %
  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 (0.24), 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   0.007   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.026   0.003   PHE 1 197 
 TYR   0.032   0.002   TYR C 217 
 ARG   0.004   0.000   ARG B 135 

*********************** 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
  152 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.643 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8253 (ttm) cc_final: 0.7880 (ttm)
REVERT: 1  229 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7779 (mtm-85)
REVERT: A  145 GLU cc_start: 0.8493 (mp0) cc_final: 0.8057 (mp0)
REVERT: A  155 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7071 (mpp80)
REVERT: A  195 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6393 (tm-30)
REVERT: A  226 ASP cc_start: 0.7864 (p0) cc_final: 0.7474 (p0)
REVERT: A  229 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7768 (mmt-90)
REVERT: B  137 MET cc_start: 0.8608 (ttp) cc_final: 0.8323 (ttt)
REVERT: B  140 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6885 (m-10)
REVERT: B  145 GLU cc_start: 0.8338 (mp0) cc_final: 0.8055 (mp0)
REVERT: B  155 ARG cc_start: 0.8026 (mtt180) cc_final: 0.6580 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7574 (tm-30)
REVERT: B  207 ARG cc_start: 0.7875 (mtt180) cc_final: 0.6263 (tmm160)
REVERT: B  210 GLU cc_start: 0.4543 (OUTLIER) cc_final: 0.4232 (pm20)
REVERT: B  212 MET cc_start: 0.7984 (tpp) cc_final: 0.7533 (ttp)
REVERT: B  219 LYS cc_start: 0.8162 (mttt) cc_final: 0.6691 (pmtt)
REVERT: B  220 GLU cc_start: 0.8175 (mp0) cc_final: 0.7469 (pp20)
REVERT: B  228 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.6301 (pmt-80)
REVERT: C  128 MET cc_start: 0.8961 (mtp) cc_final: 0.8676 (mtp)
REVERT: C  137 MET cc_start: 0.8177 (ttm) cc_final: 0.7811 (ttm)
REVERT: C  146 ASP cc_start: 0.8292 (t0) cc_final: 0.8054 (t0)
REVERT: C  147 ARG cc_start: 0.8340 (ptp-170) cc_final: 0.8083 (ptp-110)
REVERT: C  195 GLU cc_start: 0.6048 (tm-30) cc_final: 0.5071 (tt0)
REVERT: C  220 GLU cc_start: 0.8882 (mp0) cc_final: 0.8370 (mp0)
REVERT: C  229 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7007 (mtp85)
REVERT: D  100 LYS cc_start: 0.7902 (mtmt) cc_final: 0.6982 (mmtt)
REVERT: D  133 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6707 (mpt)
REVERT: D  135 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7390 (tpm170)
REVERT: D  140 PHE cc_start: 0.8223 (m-80) cc_final: 0.6020 (p90)
REVERT: D  145 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7881 (mt-10)
REVERT: D  153 MET cc_start: 0.8212 (mmm) cc_final: 0.6683 (ptt)
REVERT: D  155 ARG cc_start: 0.7998 (mtt180) cc_final: 0.6857 (ptt90)
REVERT: D  158 ASN cc_start: 0.8747 (m110) cc_final: 0.8463 (m-40)
REVERT: D  163 ARG cc_start: 0.8757 (mtt180) cc_final: 0.7065 (pmt170)
REVERT: D  207 ARG cc_start: 0.8336 (mtt180) cc_final: 0.6192 (mmp-170)
REVERT: D  212 MET cc_start: 0.8296 (tpp) cc_final: 0.6948 (pmt)
REVERT: D  219 LYS cc_start: 0.8758 (ttmm) cc_final: 0.7753 (tptt)
REVERT: D  229 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7252 (pmt170)
  outliers start: 19
  outliers final: 11
  residues processed: 144
  average time/residue: 1.6829
  time to fit residues: 249.5211
Evaluate side-chains
  149 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  128 MET
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  190 THR
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain 1 residue  229 ARG
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain B residue  210 GLU
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 64 optimal weight:    0.0370
   chunk 59 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0010
   chunk 15 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.9468

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5710  Z= 0.265
  Angle     :  0.785   8.710   7720  Z= 0.420
  Chirality :  0.051   0.165    780
  Planarity :  0.003   0.022   1020
  Dihedral  :  5.887  22.975    780
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.85 %
    Favored  : 75.29 %
  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: -3.98 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 144 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.014   0.002   PHE B 174 
 TYR   0.032   0.002   TYR C 217 
 ARG   0.003   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: 17
    poor density    : 137
  time to evaluate  : 0.671 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8251 (ttm) cc_final: 0.7928 (ttm)
REVERT: A  145 GLU cc_start: 0.8395 (mp0) cc_final: 0.7990 (mp0)
REVERT: A  155 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7050 (mpp80)
REVERT: A  195 GLU cc_start: 0.6550 (tm-30) cc_final: 0.6334 (tm-30)
REVERT: A  211 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7654 (mt0)
REVERT: A  226 ASP cc_start: 0.7769 (p0) cc_final: 0.7358 (p0)
REVERT: A  229 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7717 (mmt-90)
REVERT: B  137 MET cc_start: 0.8586 (ttp) cc_final: 0.8296 (ttt)
REVERT: B  140 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6751 (m-10)
REVERT: B  145 GLU cc_start: 0.8334 (mp0) cc_final: 0.8044 (mp0)
REVERT: B  155 ARG cc_start: 0.7998 (mtt180) cc_final: 0.6569 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: B  207 ARG cc_start: 0.7817 (mtt180) cc_final: 0.6202 (tmm160)
REVERT: B  210 GLU cc_start: 0.4485 (OUTLIER) cc_final: 0.4135 (pm20)
REVERT: B  212 MET cc_start: 0.7984 (tpp) cc_final: 0.7679 (ttt)
REVERT: B  219 LYS cc_start: 0.8141 (mttt) cc_final: 0.6679 (pmtt)
REVERT: B  220 GLU cc_start: 0.8212 (mp0) cc_final: 0.7594 (pp20)
REVERT: B  228 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.6247 (pmt-80)
REVERT: C  128 MET cc_start: 0.8953 (mtp) cc_final: 0.8639 (mtp)
REVERT: C  137 MET cc_start: 0.8155 (ttm) cc_final: 0.7777 (ttm)
REVERT: C  147 ARG cc_start: 0.8291 (ptp-170) cc_final: 0.8075 (ptp-170)
REVERT: C  195 GLU cc_start: 0.5988 (tm-30) cc_final: 0.4861 (tt0)
REVERT: C  220 GLU cc_start: 0.8868 (mp0) cc_final: 0.8326 (mp0)
REVERT: C  229 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.6978 (mtp85)
REVERT: D  100 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7004 (mmtt)
REVERT: D  133 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6711 (mpt)
REVERT: D  135 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7408 (tpm170)
REVERT: D  140 PHE cc_start: 0.8155 (m-80) cc_final: 0.6048 (p90)
REVERT: D  145 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7847 (mt-10)
REVERT: D  153 MET cc_start: 0.8197 (mmm) cc_final: 0.6757 (ptt)
REVERT: D  155 ARG cc_start: 0.7987 (mtt180) cc_final: 0.6880 (ptt90)
REVERT: D  158 ASN cc_start: 0.8726 (m110) cc_final: 0.8452 (m-40)
REVERT: D  163 ARG cc_start: 0.8752 (mtt180) cc_final: 0.7114 (pmt170)
REVERT: D  207 ARG cc_start: 0.8302 (mtt180) cc_final: 0.6211 (mmp-170)
REVERT: D  212 MET cc_start: 0.8275 (tpp) cc_final: 0.6931 (pmt)
REVERT: D  219 LYS cc_start: 0.8797 (ttmm) cc_final: 0.7767 (tptt)
REVERT: D  229 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7197 (pmt170)
  outliers start: 17
  outliers final: 9
  residues processed: 147
  average time/residue: 1.5800
  time to fit residues: 239.7802
Evaluate side-chains
  150 residues out of total 595 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  128 MET
Chi-restraints excluded: chain 1 residue  190 THR
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain B residue  210 GLU
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 21 optimal weight:    0.4980
   chunk 53 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    2.2186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.112973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.096713 restraints weight = 10011.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 2.94
r_work: 0.3880 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5710  Z= 0.281
  Angle     :  0.802   9.251   7720  Z= 0.428
  Chirality :  0.051   0.156    780
  Planarity :  0.003   0.027   1020
  Dihedral  :  5.909  23.045    780
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 22.18 %
    Favored  : 74.62 %
  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 A 144 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.028   0.003   PHE B 197 
 TYR   0.032   0.002   TYR C 217 
 ARG   0.005   0.000   ARG 1 135 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3889.42 seconds
wall clock time: 67 minutes 51.11 seconds (4071.11 seconds total)