Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 08:11:51 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwh_27754/04_2023/8dwh_27754_updated.pdb"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    4136      2.51       5
     N    1103      2.21       5
     O    1161      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B ARG   15": "NH1" <-> "NH2"
    Residue "B ARG   24": "NH1" <-> "NH2"
    Residue "B ARG   32": "NH1" <-> "NH2"
    Residue "B PHE  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  111": "OD1" <-> "OD2"
    Residue "B ARG  117": "NH1" <-> "NH2"
    Residue "B PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  167": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  243": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   68": "NH1" <-> "NH2"
    Residue "C TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  134": "NH1" <-> "NH2"
    Residue "C ARG  137": "NH1" <-> "NH2"
    Residue "C PHE  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  154": "OD1" <-> "OD2"
    Residue "C PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  212": "OD1" <-> "OD2"
    Residue "C PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  256": "NH1" <-> "NH2"
    Residue "C TYR  264": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  298": "OD1" <-> "OD2"
    Residue "C ASP  323": "OD1" <-> "OD2"
    Residue "D TYR   40": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   61": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ARG   55": "NH1" <-> "NH2"
    Residue "R PHE   73": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR   99": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  107": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  178": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  225": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  239": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  272": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  274": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 6444
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1704
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 6, 'TRANS': 214}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 67
    Chain: "C"
      Number of atoms: 2480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2480
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 92
    Chain: "D"
      Number of atoms: 350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 350
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 1910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1910
          Unusual residues: {'U2U': 1}
          Classifications: {'peptide': 248, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 241, None: 1}
            Not linked:
              pdbres="PHE R 278 "
              pdbres="U2U R 401 "
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 46
  Time building chain proxies: 3.92, per 1000 atoms: 0.61
  Number of scatterers: 6444
  At special positions: 0
  Unit cell: (90.64, 101.2, 121.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1161      8.00
     N    1103      7.00
     C    4136      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 161 " - pdb=" SG  CYS R 173 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1622

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      41.4% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 31
      removed outlier: 3.603A  pdb=" N   GLU B  28 " --> pdb=" O   ARG B  24 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LYS B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 101
    Processing helix  chain 'B' and resid 118 through 130
    Processing helix  chain 'B' and resid 132 through 134
      No H-bonds generated for 'chain 'B' and resid 132 through 134'
    Processing helix  chain 'B' and resid 146 through 155
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 165 through 169
      removed outlier: 3.756A  pdb=" N   ALA B 168 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 203
      removed outlier: 3.710A  pdb=" N   ALA B 189 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE B 197 " --> pdb=" O   ILE B 193 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER B 201 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 242
    Processing helix  chain 'C' and resid 4 through 24
    Processing helix  chain 'C' and resid 30 through 33
      No H-bonds generated for 'chain 'C' and resid 30 through 33'
    Processing helix  chain 'D' and resid 12 through 23
    Processing helix  chain 'D' and resid 30 through 43
    Processing helix  chain 'R' and resid 26 through 54
      removed outlier: 4.027A  pdb=" N   GLY R  53 " --> pdb=" O   LEU R  49 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   CYS R  54 " --> pdb=" O   TRP R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 87
      removed outlier: 3.829A  pdb=" N   TYR R  64 " --> pdb=" O   ALA R  60 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE R  87 " --> pdb=" O   SER R  83 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 125
      removed outlier: 4.397A  pdb=" N   LEU R  98 " --> pdb=" O   SER R  95 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   TYR R  99 " --> pdb=" O   LYS R  96 " (cutoff:3.500A)
      Proline residue:  R 100  - end of helix
      removed outlier: 5.558A  pdb=" N   MET R 103 " --> pdb=" O   PRO R 100 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE R 107 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA R 108 " --> pdb=" O   SER R 105 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU R 110 " --> pdb=" O   PHE R 107 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   SER R 114 " --> pdb=" O   SER R 111 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL R 116 " --> pdb=" O   LEU R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 131
    Processing helix  chain 'R' and resid 136 through 160
      removed outlier: 4.446A  pdb=" N   SER R 139 " --> pdb=" O   THR R 136 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA R 140 " --> pdb=" O   HIS R 137 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL R 142 " --> pdb=" O   SER R 139 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   CYS R 143 " --> pdb=" O   ALA R 140 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU R 146 " --> pdb=" O   CYS R 143 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG R 153 " --> pdb=" O   SER R 150 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE R 155 " --> pdb=" O   LEU R 152 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   MET R 159 " --> pdb=" O   LEU R 156 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU R 160 " --> pdb=" O   GLU R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 203
    Processing helix  chain 'R' and resid 212 through 228
      removed outlier: 3.873A  pdb=" N   PHE R 225 " --> pdb=" O   THR R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 231 through 234
      No H-bonds generated for 'chain 'R' and resid 231 through 234'
    Processing helix  chain 'R' and resid 238 through 241
      No H-bonds generated for 'chain 'R' and resid 238 through 241'
    Processing helix  chain 'R' and resid 246 through 251
      removed outlier: 4.125A  pdb=" N   PHE R 250 " --> pdb=" O   ARG R 246 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   CYS R 251 " --> pdb=" O   GLU R 247 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 246 through 251'
    Processing helix  chain 'R' and resid 255 through 272
      removed outlier: 3.524A  pdb=" N   SER R 265 " --> pdb=" O   SER R 261 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   SER R 266 " --> pdb=" O   ALA R 262 " (cutoff:3.500A)
      Proline residue:  R 269  - end of helix
    Processing sheet with id=  A, first strand: chain 'B' and resid 33 through 35
      removed outlier: 6.829A  pdb=" N   ASN B  80 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 38 through 40
      removed outlier: 8.178A  pdb=" N   LEU B  39 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ILE B 107 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   SER B 138 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   PHE B 108 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   ILE B 140 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   VAL B 110 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE B 142 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.861A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.965A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.675A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.662A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.718A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE C 241 " --> pdb=" O   PHE C 253 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'C' and resid 276 through 278
      removed outlier: 3.525A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'C' and resid 46 through 51
      removed outlier: 6.628A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE C 335 " --> pdb=" O   SER C 331 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    759 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: 1.88

  Time building geometry restraints manager: 2.58 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: 2079
        1.34 -     1.46: 1452
        1.46 -     1.58: 2990
        1.58 -     1.69: 1
        1.69 -     1.81: 56
  Bond restraints: 6578
  Sorted by residual:
  bond pdb=" C22 U2U R 401 "
       pdb=" N3  U2U R 401 "
    ideal  model  delta    sigma   weight residual
    1.453  1.341  0.112 2.00e-02 2.50e+03 3.15e+01
  bond pdb=" N1  U2U R 401 "
       pdb=" S1  U2U R 401 "
    ideal  model  delta    sigma   weight residual
    1.713  1.628  0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C17 U2U R 401 "
       pdb=" C18 U2U R 401 "
    ideal  model  delta    sigma   weight residual
    1.351  1.414 -0.063 2.00e-02 2.50e+03 9.81e+00
  bond pdb=" C7  U2U R 401 "
       pdb=" S1  U2U R 401 "
    ideal  model  delta    sigma   weight residual
    1.817  1.760  0.057 2.00e-02 2.50e+03 8.06e+00
  bond pdb=" C2  U2U R 401 "
       pdb=" O1  U2U R 401 "
    ideal  model  delta    sigma   weight residual
    1.403  1.358  0.045 2.00e-02 2.50e+03 5.15e+00
  ... (remaining 6573 not shown)

  Histogram of bond angle deviations from ideal:
      100.61 -   107.30: 169
      107.30 -   114.00: 3760
      114.00 -   120.69: 2781
      120.69 -   127.38: 2186
      127.38 -   134.08: 68
  Bond angle restraints: 8964
  Sorted by residual:
  angle pdb=" C17 U2U R 401 "
        pdb=" C22 U2U R 401 "
        pdb=" N3  U2U R 401 "
      ideal   model   delta    sigma   weight residual
     147.58  121.24   26.34 3.00e+00 1.11e-01 7.71e+01
  angle pdb=" N2  U2U R 401 "
        pdb=" C22 U2U R 401 "
        pdb=" N3  U2U R 401 "
      ideal   model   delta    sigma   weight residual
      92.15  117.90  -25.75 3.00e+00 1.11e-01 7.37e+01
  angle pdb=" C19 U2U R 401 "
        pdb=" C14 U2U R 401 "
        pdb=" O4  U2U R 401 "
      ideal   model   delta    sigma   weight residual
     140.79  120.36   20.43 3.00e+00 1.11e-01 4.64e+01
  angle pdb=" C12 U2U R 401 "
        pdb=" C13 U2U R 401 "
        pdb=" O4  U2U R 401 "
      ideal   model   delta    sigma   weight residual
     101.58  120.28  -18.70 3.00e+00 1.11e-01 3.88e+01
  angle pdb=" C15 U2U R 401 "
        pdb=" C14 U2U R 401 "
        pdb=" O4  U2U R 401 "
      ideal   model   delta    sigma   weight residual
      99.20  117.63  -18.43 3.00e+00 1.11e-01 3.78e+01
  ... (remaining 8959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 3493
       17.84 -    35.68: 278
       35.68 -    53.52: 49
       53.52 -    71.36: 4
       71.36 -    89.19: 1
  Dihedral angle restraints: 3825
    sinusoidal: 1330
      harmonic: 2495
  Sorted by residual:
  dihedral pdb=" C7  U2U R 401 "
           pdb=" N1  U2U R 401 "
           pdb=" S1  U2U R 401 "
           pdb=" C8  U2U R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.27  111.08   89.19     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CA  PRO R 100 "
           pdb=" C   PRO R 100 "
           pdb=" N   VAL R 101 "
           pdb=" CA  VAL R 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.80   16.20     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  ASN B 223 "
           pdb=" CB  ASN B 223 "
           pdb=" CG  ASN B 223 "
           pdb=" OD1 ASN B 223 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -175.31  -64.69     2      2.00e+01 2.50e-03 9.81e+00
  ... (remaining 3822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 619
       0.030 -    0.060: 296
       0.060 -    0.090: 90
       0.090 -    0.120: 46
       0.120 -    0.150: 10
  Chirality restraints: 1061
  Sorted by residual:
  chirality pdb=" CA  PRO R 231 "
            pdb=" N   PRO R 231 "
            pdb=" C   PRO R 231 "
            pdb=" CB  PRO R 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.63e-01
  chirality pdb=" CG  LEU R 191 "
            pdb=" CB  LEU R 191 "
            pdb=" CD1 LEU R 191 "
            pdb=" CD2 LEU R 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  ASN B  43 "
            pdb=" N   ASN B  43 "
            pdb=" C   ASN B  43 "
            pdb=" CB  ASN B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1058 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 230 "    0.035 5.00e-02 4.00e+02   5.22e-02 4.36e+00
        pdb=" N   PRO R 231 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO R 231 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 231 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 235 "    0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO C 236 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO C 236 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 236 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  48 "    0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO D  49 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO D  49 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D  49 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 117
        2.68 -     3.24: 6341
        3.24 -     3.79: 9809
        3.79 -     4.35: 13375
        4.35 -     4.90: 22176
  Nonbonded interactions: 51818
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R  64 "
            pdb=" OE2 GLU R 119 "
     model   vdw
     2.129 2.440
  nonbonded pdb=" OD1 ASP C 153 "
            pdb=" N   ASP C 154 "
     model   vdw
     2.133 2.520
  nonbonded pdb=" OH  TYR B 243 "
            pdb=" OH  TYR R 130 "
     model   vdw
     2.159 2.440
  nonbonded pdb=" OE1 GLU B 182 "
            pdb=" OG1 THR B 187 "
     model   vdw
     2.214 2.440
  nonbonded pdb=" OH  TYR R 106 "
            pdb=" O   PHE R 232 "
     model   vdw
     2.216 2.440
  ... (remaining 51813 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  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:             0.000
  Extract box with map and model:          5.300
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     20.360
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
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      :  0.005   0.112   6578  Z= 0.304
  Angle     :  0.848  26.345   8964  Z= 0.374
  Chirality :  0.042   0.150   1061
  Planarity :  0.003   0.052   1122
  Dihedral  : 13.054  89.195   2200
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer Outliers :  0.00 %
  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: -0.94 (0.29), residues: 844
  helix:  0.07 (0.28), residues: 356
  sheet: -0.32 (0.45), residues: 145
  loop : -1.41 (0.32), residues: 343

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.722 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2386
  time to fit residues: 48.4864
Evaluate side-chains
  145 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.737 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0832
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0670
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6122

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6578  Z= 0.248
  Angle     :  0.571   8.751   8964  Z= 0.293
  Chirality :  0.042   0.142   1061
  Planarity :  0.004   0.035   1122
  Dihedral  :  5.277  97.245    917
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer Outliers :  1.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.29), residues: 844
  helix:  0.78 (0.28), residues: 359
  sheet: -0.23 (0.40), residues: 164
  loop : -1.38 (0.33), residues: 321

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 172
  time to evaluate  : 0.789 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 174
  average time/residue: 0.2383
  time to fit residues: 51.8694
Evaluate side-chains
  157 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 151
  time to evaluate  : 0.749 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1126
  time to fit residues: 2.0216
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0040
   chunk 51 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6578  Z= 0.221
  Angle     :  0.552   8.717   8964  Z= 0.279
  Chirality :  0.041   0.130   1061
  Planarity :  0.004   0.039   1122
  Dihedral  :  5.174  98.523    917
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer Outliers :  2.02 %
  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: -0.08 (0.29), residues: 844
  helix:  1.18 (0.29), residues: 360
  sheet: -0.18 (0.41), residues: 163
  loop : -1.39 (0.32), residues: 321

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.730 
Fit side-chains
  outliers start: 13
  outliers final: 5
  residues processed: 166
  average time/residue: 0.2430
  time to fit residues: 49.9042
Evaluate side-chains
  163 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 158
  time to evaluate  : 0.724 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0614
  time to fit residues: 1.5659
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 51 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6578  Z= 0.249
  Angle     :  0.545   8.131   8964  Z= 0.278
  Chirality :  0.042   0.134   1061
  Planarity :  0.004   0.032   1122
  Dihedral  :  5.186  99.404    917
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer Outliers :  2.64 %
  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:  0.06 (0.30), residues: 844
  helix:  1.37 (0.29), residues: 357
  sheet: -0.19 (0.40), residues: 169
  loop : -1.35 (0.33), residues: 318

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 12
  residues processed: 170
  average time/residue: 0.2620
  time to fit residues: 55.4690
Evaluate side-chains
  164 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.786 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0695
  time to fit residues: 2.5555
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0010
   chunk 0 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0970
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  82 HIS
C 119 ASN
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6578  Z= 0.208
  Angle     :  0.534   7.930   8964  Z= 0.272
  Chirality :  0.041   0.128   1061
  Planarity :  0.004   0.040   1122
  Dihedral  :  5.121  99.902    917
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer Outliers :  2.02 %
  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:  0.22 (0.30), residues: 844
  helix:  1.53 (0.29), residues: 358
  sheet: -0.17 (0.39), residues: 171
  loop : -1.28 (0.33), residues: 315

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 7
  residues processed: 161
  average time/residue: 0.2586
  time to fit residues: 51.0672
Evaluate side-chains
  160 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 153
  time to evaluate  : 0.722 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0624
  time to fit residues: 1.7984
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 67 optimal weight:    0.1980
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6578  Z= 0.228
  Angle     :  0.536   7.573   8964  Z= 0.272
  Chirality :  0.041   0.130   1061
  Planarity :  0.004   0.040   1122
  Dihedral  :  5.156 100.391    917
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer Outliers :  1.24 %
  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:  0.33 (0.30), residues: 844
  helix:  1.66 (0.30), residues: 358
  sheet: -0.12 (0.39), residues: 171
  loop : -1.26 (0.33), residues: 315

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 156
  average time/residue: 0.2665
  time to fit residues: 51.1995
Evaluate side-chains
  154 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 150
  time to evaluate  : 0.686 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0668
  time to fit residues: 1.5345
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 68 optimal weight:    0.2980
   chunk 80 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  98 GLN
C 119 ASN
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6578  Z= 0.211
  Angle     :  0.524   7.513   8964  Z= 0.267
  Chirality :  0.041   0.128   1061
  Planarity :  0.004   0.040   1122
  Dihedral  :  5.143 101.127    917
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer Outliers :  1.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.30), residues: 844
  helix:  1.73 (0.30), residues: 359
  sheet: -0.09 (0.40), residues: 171
  loop : -1.22 (0.34), residues: 314

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 0.751 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 160
  average time/residue: 0.2657
  time to fit residues: 52.6152
Evaluate side-chains
  157 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 151
  time to evaluate  : 0.733 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0643
  time to fit residues: 1.7521
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0570
   chunk 51 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0870
   overall best weight:    0.3474

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6578  Z= 0.173
  Angle     :  0.530   7.575   8964  Z= 0.267
  Chirality :  0.042   0.220   1061
  Planarity :  0.003   0.039   1122
  Dihedral  :  5.098 101.557    917
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer Outliers :  0.16 %
  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:  0.44 (0.30), residues: 844
  helix:  1.77 (0.30), residues: 358
  sheet: -0.12 (0.39), residues: 171
  loop : -1.19 (0.34), residues: 315

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.745 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 152
  average time/residue: 0.2513
  time to fit residues: 47.4353
Evaluate side-chains
  147 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.657 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0622
  time to fit residues: 1.1494
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0060
   chunk 59 optimal weight:    0.0970
   chunk 23 optimal weight:    2.9990
   chunk 68 optimal weight:    0.3980
   chunk 71 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6578  Z= 0.170
  Angle     :  0.529   6.812   8964  Z= 0.267
  Chirality :  0.042   0.271   1061
  Planarity :  0.003   0.041   1122
  Dihedral  :  5.074 101.784    917
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer Outliers :  0.47 %
  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:  0.60 (0.30), residues: 844
  helix:  1.91 (0.30), residues: 354
  sheet: -0.05 (0.39), residues: 171
  loop : -1.07 (0.34), residues: 319

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 0.852 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 157
  average time/residue: 0.2539
  time to fit residues: 49.2424
Evaluate side-chains
  158 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.727 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0702
  time to fit residues: 1.1293
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
C 239 ASN
** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6578  Z= 0.242
  Angle     :  0.554   7.401   8964  Z= 0.278
  Chirality :  0.043   0.335   1061
  Planarity :  0.004   0.047   1122
  Dihedral  :  5.216 102.084    917
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer Outliers :  0.47 %
  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:  0.51 (0.30), residues: 844
  helix:  1.79 (0.30), residues: 358
  sheet: -0.12 (0.39), residues: 171
  loop : -1.08 (0.34), residues: 315

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 146
  time to evaluate  : 0.790 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 147
  average time/residue: 0.2550
  time to fit residues: 46.4989
Evaluate side-chains
  147 residues out of total 742 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 145
  time to evaluate  : 0.726 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0635
  time to fit residues: 1.2839
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 239 ASN
** R 264 ASN ** 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 = 0.3467 r_free = 0.3467 target = 0.117122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.100364 restraints weight = 9295.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.29
r_work: 0.3101 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6578  Z= 0.260
  Angle     :  0.577   9.803   8964  Z= 0.291
  Chirality :  0.044   0.323   1061
  Planarity :  0.004   0.044   1122
  Dihedral  :  5.289 102.553    917
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer Outliers :  0.47 %
  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:  0.39 (0.30), residues: 844
  helix:  1.65 (0.30), residues: 366
  sheet: -0.15 (0.39), residues: 171
  loop : -1.20 (0.35), residues: 307

===============================================================================
Job complete
usr+sys time: 1940.58 seconds
wall clock time: 35 minutes 32.89 seconds (2132.89 seconds total)