Starting phenix.real_space_refine (version: dev)
on Sat Feb 18 17:05:44 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2023/7ljd_23391_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2023/7ljd_23391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2023/7ljd_23391.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2023/7ljd_23391.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2023/7ljd_23391_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2023/7ljd_23391_updated.pdb"
  }
  resolution = 3.2
  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=  -0.000 sd=   0.013
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
Process input model

  Symmetric amino acids flipped
    Residue "R ARG   52": "NH1" <-> "NH2"
    Residue "R ARG   55": "NH1" <-> "NH2"
    Residue "R ARG  130": "NH1" <-> "NH2"
    Residue "R ARG  216": "NH1" <-> "NH2"
    Residue "R ARG  219": "NH1" <-> "NH2"
    Residue "R ARG  226": "NH1" <-> "NH2"
    Residue "R ARG  233": "NH1" <-> "NH2"
    Residue "R ARG  266": "NH1" <-> "NH2"
    Residue "R ARG  338": "NH1" <-> "NH2"
    Residue "A ARG   38": "NH1" <-> "NH2"
    Residue "A ARG   90": "NH1" <-> "NH2"
    Residue "A ARG  169": "NH1" <-> "NH2"
    Residue "B ARG   42": "NH1" <-> "NH2"
    Residue "B ARG   96": "NH1" <-> "NH2"
    Residue "B ARG  256": "NH1" <-> "NH2"
    Residue "N ARG   19": "NH1" <-> "NH2"
    Residue "N ARG   72": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 8518
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2269
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 10, 'TRANS': 274}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1987
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 253
          Unusual residues: {'CLR': 5, 'G4C': 1, 'LDP': 1, 'PLM': 4}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1  LDP R 501 " occ=0.50
      ... (9 atoms not shown)
      pdb=" O2  LDP R 501 " occ=0.50
  Time building chain proxies: 5.50, per 1000 atoms: 0.65
  Number of scatterers: 8518
  At special positions: 0
  Unit cell: (95.316, 99.372, 121.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      56     16.00
     O    1545      8.00
     N    1447      7.00
     C    5468      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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: 3.24
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1984

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      39.5% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'R' and resid 22 through 49
    Processing helix  chain 'R' and resid 53 through 56
      No H-bonds generated for 'chain 'R' and resid 53 through 56'
    Processing helix  chain 'R' and resid 59 through 76
      removed outlier: 3.596A  pdb=" N   VAL R  68 " --> pdb=" O   SER R  65 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER R  69 " --> pdb=" O   LEU R  66 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP R  70 " --> pdb=" O   ALA R  67 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL R  73 " --> pdb=" O   ASP R  70 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL R  75 " --> pdb=" O   LEU R  72 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU R  76 " --> pdb=" O   VAL R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 87
    Processing helix  chain 'R' and resid 93 through 126
      removed outlier: 3.753A  pdb=" N   VAL R 100 " --> pdb=" O   ASN R  97 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE R 104 " --> pdb=" O   ALA R 101 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   MET R 105 " --> pdb=" O   PHE R 102 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   CYS R 106 " --> pdb=" O   ASP R 103 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER R 107 " --> pdb=" O   ILE R 104 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR R 108 " --> pdb=" O   MET R 105 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA R 109 " --> pdb=" O   CYS R 106 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU R 112 " --> pdb=" O   ALA R 109 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN R 113 " --> pdb=" O   SER R 110 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ILE R 117 " --> pdb=" O   LEU R 114 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA R 124 " --> pdb=" O   ARG R 121 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE R 125 " --> pdb=" O   TYR R 122 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   SER R 126 " --> pdb=" O   TRP R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 128 through 134
      removed outlier: 3.676A  pdb=" N   GLU R 132 " --> pdb=" O   PRO R 128 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG R 133 " --> pdb=" O   PHE R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 161
      removed outlier: 4.784A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 192 through 202
      removed outlier: 3.599A  pdb=" N   ILE R 196 " --> pdb=" O   ARG R 192 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 204 through 241
    Processing helix  chain 'R' and resid 265 through 297
      removed outlier: 3.576A  pdb=" N   LEU R 274 " --> pdb=" O   VAL R 270 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
      removed outlier: 4.145A  pdb=" N   LEU R 291 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   CYS R 293 " --> pdb=" O   PHE R 289 " (cutoff:3.500A)
      Proline residue:  R 296  - end of helix
    Processing helix  chain 'R' and resid 310 through 331
      removed outlier: 3.648A  pdb=" N   TRP R 318 " --> pdb=" O   ASP R 314 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE R 319 " --> pdb=" O   VAL R 315 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASN R 323 " --> pdb=" O   PHE R 319 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   SER R 325 " --> pdb=" O   TRP R 321 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 335 through 345
    Processing helix  chain 'A' and resid 10 through 39
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 3.666A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ASP A 102 " --> pdb=" O   CYS A  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 98 through 102'
    Processing helix  chain 'A' and resid 118 through 130
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.706A  pdb=" N   LEU A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA A 155 " --> pdb=" O   GLU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 184 through 204
      removed outlier: 3.559A  pdb=" N   PHE A 197 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 242
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 35
      removed outlier: 3.662A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 23
      removed outlier: 3.919A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'N' and resid 29 through 31
      No H-bonds generated for 'chain 'N' and resid 29 through 31'
    Processing helix  chain 'N' and resid 62 through 64
      No H-bonds generated for 'chain 'N' and resid 62 through 64'
    Processing sheet with id=  A, first strand: chain 'A' and resid 211 through 214
      removed outlier: 7.260A  pdb=" N   VAL A 139 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 8.251A  pdb=" N   HIS A 214 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU A 141 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A  80 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 62
      removed outlier: 7.211A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.600A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.680A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.006A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.778A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.602A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.779A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.576A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.698A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU N  45 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1014 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: 2.27

  Time building geometry restraints manager: 3.53 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2114
        1.33 -     1.45: 1750
        1.45 -     1.58: 4760
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8702
  Sorted by residual:
  bond pdb=" C05 G4C R 502 "
       pdb=" N04 G4C R 502 "
    ideal  model  delta    sigma   weight residual
    1.355  1.497 -0.142 2.00e-02 2.50e+03 5.03e+01
  bond pdb=" C03 G4C R 502 "
       pdb=" N04 G4C R 502 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 2.00e-02 2.50e+03 3.36e+00
  bond pdb=" C   ILE R 205 "
       pdb=" N   PRO R 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.28e-02 6.10e+03 3.31e+00
  bond pdb=" C   MET R  78 "
       pdb=" N   PRO R  79 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.30e-02 5.92e+03 3.19e+00
  bond pdb=" C5  CLR R 505 "
       pdb=" C6  CLR R 505 "
    ideal  model  delta    sigma   weight residual
    1.332  1.300  0.032 2.00e-02 2.50e+03 2.53e+00
  ... (remaining 8697 not shown)

  Histogram of bond angle deviations from ideal:
      100.03 -   107.05: 225
      107.05 -   114.07: 5030
      114.07 -   121.08: 3977
      121.08 -   128.10: 2488
      128.10 -   135.12: 75
  Bond angle restraints: 11795
  Sorted by residual:
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  130.97   -9.43 1.91e+00 2.74e-01 2.44e+01
  angle pdb=" C   ILE R 294 "
        pdb=" N   LEU R 295 "
        pdb=" CA  LEU R 295 "
      ideal   model   delta    sigma   weight residual
     121.62  127.01   -5.39 1.57e+00 4.06e-01 1.18e+01
  angle pdb=" CA  ASN B 119 "
        pdb=" CB  ASN B 119 "
        pdb=" CG  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     112.60  115.60   -3.00 1.00e+00 1.00e+00 8.97e+00
  angle pdb=" C   ASP B 163 "
        pdb=" N   THR B 164 "
        pdb=" CA  THR B 164 "
      ideal   model   delta    sigma   weight residual
     122.40  126.70   -4.30 1.45e+00 4.76e-01 8.78e+00
  angle pdb=" N   MET R  78 "
        pdb=" CA  MET R  78 "
        pdb=" C   MET R  78 "
      ideal   model   delta    sigma   weight residual
     112.75  116.65   -3.90 1.36e+00 5.41e-01 8.23e+00
  ... (remaining 11790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 5033
       17.89 -    35.77: 90
       35.77 -    53.65: 23
       53.65 -    71.54: 1
       71.54 -    89.42: 5
  Dihedral angle restraints: 5152
    sinusoidal: 2097
      harmonic: 3055
  Sorted by residual:
  dihedral pdb=" CB  CYS R 298 "
           pdb=" SG  CYS R 298 "
           pdb=" SG  CYS R 307 "
           pdb=" CB  CYS R 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.67  -87.33     1      1.00e+01 1.00e-02 9.15e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.82  -73.82     1      1.00e+01 1.00e-02 6.93e+01
  dihedral pdb=" CA  LEU B 198 "
           pdb=" C   LEU B 198 "
           pdb=" N   PHE B 199 "
           pdb=" CA  PHE B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.61   20.39     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 5149 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1173
       0.082 -    0.163: 126
       0.163 -    0.245: 19
       0.245 -    0.327: 6
       0.327 -    0.408: 5
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" C14 CLR R 507 "
            pdb=" C13 CLR R 507 "
            pdb=" C15 CLR R 507 "
            pdb=" C8  CLR R 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.73    0.41 2.00e-01 2.50e+01 4.17e+00
  chirality pdb=" C14 CLR R 504 "
            pdb=" C13 CLR R 504 "
            pdb=" C15 CLR R 504 "
            pdb=" C8  CLR R 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" C14 CLR R 503 "
            pdb=" C13 CLR R 503 "
            pdb=" C15 CLR R 503 "
            pdb=" C8  CLR R 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.39 2.00e-01 2.50e+01 3.73e+00
  ... (remaining 1326 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C03 G4C R 502 "   -0.215 2.00e-02 2.50e+03   1.50e-01 3.37e+02
        pdb=" C05 G4C R 502 "    0.047 2.00e-02 2.50e+03
        pdb=" C06 G4C R 502 "   -0.169 2.00e-02 2.50e+03
        pdb=" C16 G4C R 502 "    0.029 2.00e-02 2.50e+03
        pdb=" N04 G4C R 502 "    0.222 2.00e-02 2.50e+03
        pdb=" O15 G4C R 502 "    0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 207 "    0.014 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   VAL R 207 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   VAL R 207 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA R 208 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  93 "   -0.035 5.00e-02 4.00e+02   5.38e-02 4.64e+00
        pdb=" N   PRO B  94 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B  94 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  94 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 2240
        2.82 -     3.34: 7350
        3.34 -     3.86: 13173
        3.86 -     4.38: 15319
        4.38 -     4.90: 27065
  Nonbonded interactions: 65147
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.294 2.440
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.309 2.440
  nonbonded pdb=" OH  TYR A 170 "
            pdb=" OD2 ASP A 195 "
     model   vdw
     2.322 2.440
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.337 2.440
  nonbonded pdb=" OG  SER R 198 "
            pdb=" O2  LDP R 501 "
     model   vdw
     2.349 2.440
  ... (remaining 65142 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
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     Cl      2      4.86       5
     C    5468      2.51       5
     N    1447      2.21       5
     O    1545      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.530
  Check model and map are aligned:         0.130
  Process input model:                     24.640
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.090
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
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      :  0.004   0.142   8702  Z= 0.267
  Angle     :  0.853  10.120  11795  Z= 0.463
  Chirality :  0.062   0.408   1329
  Planarity :  0.007   0.150   1463
  Dihedral  :  8.494  89.425   3156
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  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: -2.10 (0.23), residues: 1030
  helix: -1.11 (0.24), residues: 402
  sheet: -0.32 (0.34), residues: 218
  loop : -2.18 (0.25), residues: 410

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.834 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2774
  time to fit residues: 74.2479
Evaluate side-chains
  133 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.902 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2887
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
R  41 ASN
R  60 ASN
R 113 ASN
R 242 GLN
A  14 ASN
A  82 HIS
A 242 GLN
B  91 HIS
B 239 ASN
B 268 ASN
N  82 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8702  Z= 0.334
  Angle     :  0.643   7.122  11795  Z= 0.342
  Chirality :  0.044   0.164   1329
  Planarity :  0.005   0.046   1463
  Dihedral  :  6.600  85.896   1249
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer Outliers :  1.55 %
  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: -0.54 (0.25), residues: 1030
  helix:  0.72 (0.25), residues: 397
  sheet: -0.22 (0.34), residues: 225
  loop : -1.47 (0.28), residues: 408

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.950 
Fit side-chains
  outliers start: 14
  outliers final: 7
  residues processed: 151
  average time/residue: 0.2319
  time to fit residues: 47.0902
Evaluate side-chains
  124 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.086 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1239
  time to fit residues: 2.7768
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 76 optimal weight:    0.3980
   chunk 62 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 81 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 73 optimal weight:    0.3980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A  66 ASN
A 239 HIS
G  44 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8702  Z= 0.148
  Angle     :  0.495   7.281  11795  Z= 0.263
  Chirality :  0.040   0.159   1329
  Planarity :  0.004   0.046   1463
  Dihedral  :  6.074  82.059   1249
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer Outliers :  1.66 %
  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:  0.11 (0.26), residues: 1030
  helix:  1.43 (0.26), residues: 397
  sheet:  0.11 (0.34), residues: 227
  loop : -1.32 (0.28), residues: 406

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 7
  residues processed: 140
  average time/residue: 0.2322
  time to fit residues: 44.9110
Evaluate side-chains
  122 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.919 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0867
  time to fit residues: 2.5661
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 43 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 97 optimal weight:    0.4980
   chunk 48 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
B  62 HIS
B 259 GLN
G  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8702  Z= 0.290
  Angle     :  0.587  10.286  11795  Z= 0.307
  Chirality :  0.042   0.156   1329
  Planarity :  0.004   0.052   1463
  Dihedral  :  6.344  77.190   1249
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer Outliers :  2.00 %
  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:  0.11 (0.26), residues: 1030
  helix:  1.41 (0.26), residues: 398
  sheet:  0.01 (0.34), residues: 219
  loop : -1.20 (0.29), residues: 413

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.087 
Fit side-chains
  outliers start: 18
  outliers final: 10
  residues processed: 125
  average time/residue: 0.2264
  time to fit residues: 38.7500
Evaluate side-chains
  117 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 1.026 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1185
  time to fit residues: 3.3292
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 67 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0570
   overall best weight:    1.0702

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8702  Z= 0.183
  Angle     :  0.515   7.500  11795  Z= 0.269
  Chirality :  0.040   0.139   1329
  Planarity :  0.004   0.053   1463
  Dihedral  :  6.126  73.948   1249
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer Outliers :  0.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1030
  helix:  1.61 (0.26), residues: 400
  sheet:  0.08 (0.34), residues: 220
  loop : -1.15 (0.29), residues: 410

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 6
  residues processed: 115
  average time/residue: 0.2212
  time to fit residues: 35.0456
Evaluate side-chains
  115 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.939 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0928
  time to fit residues: 2.2570
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.1980
   chunk 19 optimal weight:    0.7980
   chunk 57 optimal weight:    0.4980
   chunk 24 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
G  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8702  Z= 0.229
  Angle     :  0.541   9.790  11795  Z= 0.281
  Chirality :  0.041   0.145   1329
  Planarity :  0.004   0.054   1463
  Dihedral  :  6.112  70.741   1249
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer Outliers :  1.66 %
  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 (0.26), residues: 1030
  helix:  1.61 (0.26), residues: 400
  sheet:  0.14 (0.34), residues: 220
  loop : -1.11 (0.29), residues: 410

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.985 
Fit side-chains
  outliers start: 15
  outliers final: 12
  residues processed: 118
  average time/residue: 0.2222
  time to fit residues: 36.2638
Evaluate side-chains
  116 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.987 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0863
  time to fit residues: 3.2864
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0270
   chunk 59 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.3844

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
B 295 ASN
G  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8702  Z= 0.342
  Angle     :  0.609   7.237  11795  Z= 0.318
  Chirality :  0.043   0.195   1329
  Planarity :  0.004   0.053   1463
  Dihedral  :  6.145  65.397   1249
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer Outliers :  0.89 %
  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:  0.09 (0.26), residues: 1030
  helix:  1.40 (0.26), residues: 399
  sheet: -0.05 (0.34), residues: 216
  loop : -1.19 (0.29), residues: 415

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 118
  average time/residue: 0.2452
  time to fit residues: 39.2499
Evaluate side-chains
  112 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.948 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1132
  time to fit residues: 2.1783
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
G  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8702  Z= 0.172
  Angle     :  0.527   9.000  11795  Z= 0.275
  Chirality :  0.041   0.157   1329
  Planarity :  0.004   0.052   1463
  Dihedral  :  5.780  62.900   1249
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer Outliers :  0.33 %
  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:  0.28 (0.26), residues: 1030
  helix:  1.64 (0.26), residues: 400
  sheet: -0.10 (0.34), residues: 213
  loop : -1.08 (0.30), residues: 417

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 116
  average time/residue: 0.2449
  time to fit residues: 38.6712
Evaluate side-chains
  107 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 1.030 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0860
  time to fit residues: 1.9371
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0570
   chunk 81 optimal weight:    1.9990
   chunk 85 optimal weight:    7.9990
   chunk 59 optimal weight:    0.3980
   chunk 95 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.0904

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

Flipped N/Q/H residues before XYZ refinement:
** R  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.5008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8702  Z= 0.314
  Angle     :  0.597   7.192  11795  Z= 0.314
  Chirality :  0.043   0.175   1329
  Planarity :  0.004   0.054   1463
  Dihedral  :  5.955  58.066   1249
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer Outliers :  1.00 %
  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:  0.07 (0.26), residues: 1030
  helix:  1.32 (0.26), residues: 406
  sheet: -0.07 (0.35), residues: 209
  loop : -1.16 (0.30), residues: 415

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 8
  residues processed: 112
  average time/residue: 0.2423
  time to fit residues: 36.7648
Evaluate side-chains
  110 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.959 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0890
  time to fit residues: 2.5512
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 100 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R  41 ASN
A  75 GLN
G  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8702  Z= 0.170
  Angle     :  0.530   7.873  11795  Z= 0.277
  Chirality :  0.040   0.153   1329
  Planarity :  0.004   0.052   1463
  Dihedral  :  5.670  56.661   1249
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer Outliers :  0.33 %
  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:  0.26 (0.26), residues: 1030
  helix:  1.54 (0.26), residues: 406
  sheet:  0.04 (0.35), residues: 209
  loop : -1.12 (0.30), residues: 415

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 111
  average time/residue: 0.2857
  time to fit residues: 43.3351
Evaluate side-chains
  104 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 1.011 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0801
  time to fit residues: 1.5978
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0060
   chunk 4 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0050
   overall best weight:    0.4410

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.177588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.132759 restraints weight = 8931.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.99
r_work: 0.3302 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3952 r_free = 0.3952    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3949 r_free = 0.3949    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8702  Z= 0.137
  Angle     :  0.500   7.373  11795  Z= 0.264
  Chirality :  0.040   0.145   1329
  Planarity :  0.004   0.051   1463
  Dihedral  :  5.371  57.417   1249
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer Outliers :  0.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1030
  helix:  1.72 (0.26), residues: 407
  sheet:  0.13 (0.35), residues: 207
  loop : -1.05 (0.29), residues: 416

===============================================================================
Job complete
usr+sys time: 2068.61 seconds
wall clock time: 38 minutes 32.52 seconds (2312.52 seconds total)