Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Aug 10 09:20:00 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/08_2023/8jlz_36409_updated.pdb"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.050
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: 5
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     Cl      1      4.86       5
     C    4917      2.51       5
     N    1336      2.21       5
     O    1420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  344": "OE1" <-> "OE2"
    Residue "B TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  303": "OD1" <-> "OD2"
    Residue "N ASP   90": "OD1" <-> "OD2"
    Residue "R PHE  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib"
  Total number of atoms: 7730
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1831
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 46
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "B"
      Number of atoms: 2533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2533
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 54
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "G"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 420
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 953
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 1993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 1993
          Unusual residues: {'UQL': 1}
          Classifications: {'peptide': 268, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 15, 'TRANS': 252, None: 1}
            Not linked:
              pdbres="GLY R 332 "
              pdbres="UQL R 501 "
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 60
  Time building chain proxies: 4.37, per 1000 atoms: 0.57
  Number of scatterers: 7730
  At special positions: 0
  Unit cell: (96.05, 107.1, 116.45, 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      1     17.00
     S      56     16.00
     O    1420      8.00
     N    1336      7.00
     C    4917      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  99 " - pdb=" SG  CYS R 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 294 " - pdb=" SG  CYS R 296 " 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: 3.38
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1904

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      21 helices and 10 sheets defined
      36.7% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 38
      removed outlier: 3.974A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 58
    Processing helix  chain 'A' and resid 236 through 238
      No H-bonds generated for 'chain 'A' and resid 236 through 238'
    Processing helix  chain 'A' and resid 265 through 277
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 4.322A  pdb=" N   VAL A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 4.105A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 307 through 311'
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 332 through 352
      removed outlier: 4.495A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 390
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'G' and resid 10 through 23
    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 'R' and resid 28 through 53
      removed outlier: 3.848A  pdb=" N   VAL R  36 " --> pdb=" O   ALA R  32 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU R  39 " --> pdb=" O   VAL R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 88
      removed outlier: 4.640A  pdb=" N   PHE R  64 " --> pdb=" O   SER R  61 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU R  65 " --> pdb=" O   ASN R  62 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL R  66 " --> pdb=" O   PHE R  63 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LEU R  77 " --> pdb=" O   MET R  74 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   VAL R  78 " --> pdb=" O   VAL R  75 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   VAL R  79 " --> pdb=" O   GLY R  76 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   MET R  80 " --> pdb=" O   LEU R  77 " (cutoff:3.500A)
      Proline residue:  R  81  - end of helix
    Processing helix  chain 'R' and resid 96 through 128
      removed outlier: 4.002A  pdb=" N   LEU R 100 " --> pdb=" O   GLY R  97 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS R 110 " --> pdb=" O   VAL R 107 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE R 114 " --> pdb=" O   SER R 111 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ASN R 116 " --> pdb=" O   SER R 113 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   CYS R 118 " --> pdb=" O   LEU R 115 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ILE R 120 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ARG R 124 " --> pdb=" O   SER R 121 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   TYR R 125 " --> pdb=" O   LEU R 122 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU R 126 " --> pdb=" O   ASP R 123 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU R 127 " --> pdb=" O   ARG R 124 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE R 128 " --> pdb=" O   TYR R 125 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 164
      Proline residue:  R 161  - end of helix
    Processing helix  chain 'R' and resid 186 through 223
      removed outlier: 4.133A  pdb=" N   SER R 193 " --> pdb=" O   VAL R 189 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLY R 194 " --> pdb=" O   LEU R 190 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
    Processing helix  chain 'R' and resid 265 through 293
      removed outlier: 3.788A  pdb=" N   PHE R 277 " --> pdb=" O   LEU R 273 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
      removed outlier: 4.233A  pdb=" N   ILE R 289 " --> pdb=" O   PHE R 285 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL R 290 " --> pdb=" O   VAL R 286 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 301 through 323
      removed outlier: 3.807A  pdb=" N   LEU R 308 " --> pdb=" O   VAL R 304 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   SER R 313 " --> pdb=" O   GLY R 309 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR R 314 " --> pdb=" O   TYR R 310 " (cutoff:3.500A)
      Proline residue:  R 317  - end of helix
      Proline residue:  R 321  - end of helix
    Processing helix  chain 'R' and resid 325 through 331
    Processing sheet with id=  A, first strand: chain 'A' and resid 359 through 363
      removed outlier: 7.010A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASN A 218 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   HIS A 220 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   LEU A  45 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.604A  pdb=" N   TYR B  59 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.397A  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: 7.236A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 178 through 180
      removed outlier: 3.632A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.104A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.422A  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: 7.076A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.145A  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: 6.536A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 336 through 339
      removed outlier: 3.595A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.522A  pdb=" N   VAL N 124 " --> pdb=" O   ALA N  92 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA N  92 " --> pdb=" O   VAL N 124 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    336 hydrogen bonds defined for protein.
    870 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: 2.08

  Time building geometry restraints manager: 3.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2524
        1.34 -     1.46: 1884
        1.46 -     1.59: 3398
        1.59 -     1.71: 0
        1.71 -     1.83: 78
  Bond restraints: 7884
  Sorted by residual:
  bond pdb=" C7  UQL R 501 "
       pdb=" C8  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.377  1.272  0.105 2.00e-02 2.50e+03 2.75e+01
  bond pdb=" C7  UQL R 501 "
       pdb=" N1  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.357  1.258  0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" C3  UQL R 501 "
       pdb=" C4  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.368  1.462 -0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" C2  UQL R 501 "
       pdb=" C3  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.360  0.046 2.00e-02 2.50e+03 5.39e+00
  bond pdb=" C4  UQL R 501 "
       pdb=" C5  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.373  0.033 2.00e-02 2.50e+03 2.72e+00
  ... (remaining 7879 not shown)

  Histogram of bond angle deviations from ideal:
       99.02 -   107.74: 266
      107.74 -   116.47: 5084
      116.47 -   125.19: 5240
      125.19 -   133.92: 116
      133.92 -   142.64: 11
  Bond angle restraints: 10717
  Sorted by residual:
  angle pdb=" C9  UQL R 501 "
        pdb=" C7  UQL R 501 "
        pdb=" N1  UQL R 501 "
      ideal   model   delta    sigma   weight residual
     100.49  128.88  -28.39 3.00e+00 1.11e-01 8.96e+01
  angle pdb=" C8  UQL R 501 "
        pdb=" C7  UQL R 501 "
        pdb=" C9  UQL R 501 "
      ideal   model   delta    sigma   weight residual
     151.42  129.77   21.65 3.00e+00 1.11e-01 5.21e+01
  angle pdb=" C   ILE R 319 "
        pdb=" N   TYR R 320 "
        pdb=" CA  TYR R 320 "
      ideal   model   delta    sigma   weight residual
     120.09  114.63    5.46 1.25e+00 6.40e-01 1.91e+01
  angle pdb=" C10 UQL R 501 "
        pdb=" C8  UQL R 501 "
        pdb=" C4  UQL R 501 "
      ideal   model   delta    sigma   weight residual
     132.69  120.69   12.00 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" C4  UQL R 501 "
        pdb=" C8  UQL R 501 "
        pdb=" C7  UQL R 501 "
      ideal   model   delta    sigma   weight residual
     107.95  119.43  -11.48 3.00e+00 1.11e-01 1.46e+01
  ... (remaining 10712 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 4221
       16.36 -    32.72: 345
       32.72 -    49.08: 93
       49.08 -    65.44: 12
       65.44 -    81.80: 11
  Dihedral angle restraints: 4682
    sinusoidal: 1744
      harmonic: 2938
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -19.05  -66.95     1      1.00e+01 1.00e-02 5.84e+01
  dihedral pdb=" CB  CYS R 294 "
           pdb=" SG  CYS R 294 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.57   54.57     1      1.00e+01 1.00e-02 4.04e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4679 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 868
       0.042 -    0.084: 292
       0.084 -    0.126: 76
       0.126 -    0.167: 8
       0.167 -    0.209: 1
  Chirality restraints: 1245
  Sorted by residual:
  chirality pdb=" CA  TYR R 320 "
            pdb=" N   TYR R 320 "
            pdb=" C   TYR R 320 "
            pdb=" CB  TYR R 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ILE B 229 "
            pdb=" N   ILE B 229 "
            pdb=" C   ILE B 229 "
            pdb=" CB  ILE B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CA  ARG A 317 "
            pdb=" N   ARG A 317 "
            pdb=" C   ARG A 317 "
            pdb=" CB  ARG A 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 1242 not shown)

  Planarity restraints: 1363
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 316 "    0.065 5.00e-02 4.00e+02   9.80e-02 1.54e+01
        pdb=" N   PRO R 317 "   -0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO R 317 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO R 317 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  81 "   -0.047 5.00e-02 4.00e+02   7.06e-02 7.98e+00
        pdb=" N   PRO R  82 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO R  82 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO R  82 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.041 5.00e-02 4.00e+02   6.21e-02 6.16e+00
        pdb=" N   PRO G  49 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1360 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 252
        2.72 -     3.26: 7489
        3.26 -     3.81: 11654
        3.81 -     4.35: 14086
        4.35 -     4.90: 24786
  Nonbonded interactions: 58267
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.170 2.440
  nonbonded pdb=" O   PRO A 361 "
            pdb=" ND1 HIS A 362 "
     model   vdw
     2.201 2.520
  nonbonded pdb=" O   TYR A 318 "
            pdb=" NH1 ARG A 336 "
     model   vdw
     2.283 2.520
  nonbonded pdb=" O   MET R 276 "
            pdb=" OG1 THR R 280 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" NH1 ARG N  67 "
            pdb=" O   SER N  85 "
     model   vdw
     2.300 2.520
  ... (remaining 58262 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:             0.400
  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:          2.410
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     23.110
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:2.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
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   0.105   7884  Z= 0.304
  Angle     :  0.786  28.393  10717  Z= 0.407
  Chirality :  0.044   0.209   1245
  Planarity :  0.006   0.098   1363
  Dihedral  : 13.378  81.800   2766
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer Outliers :  0.12 %
  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: -0.56 (0.27), residues: 997
  helix:  0.64 (0.28), residues: 370
  sheet: -0.20 (0.35), residues: 219
  loop : -1.36 (0.29), residues: 408

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.938 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2531
  time to fit residues: 52.1511
Evaluate side-chains
  152 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.866 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2238
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0060
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0670
   chunk 46 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.7538

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 218 ASN
N  31 ASN
** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.0824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7884  Z= 0.174
  Angle     :  0.527   7.413  10717  Z= 0.278
  Chirality :  0.040   0.172   1245
  Planarity :  0.005   0.063   1363
  Dihedral  :  4.617  36.316   1090
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer Outliers :  0.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.27), residues: 997
  helix:  0.96 (0.28), residues: 365
  sheet: -0.15 (0.34), residues: 233
  loop : -1.22 (0.30), residues: 399

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 163
  time to evaluate  : 0.847 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 164
  average time/residue: 0.2796
  time to fit residues: 59.3499
Evaluate side-chains
  162 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 157
  time to evaluate  : 0.899 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1723
  time to fit residues: 2.4350
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 89 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 279 ASN
N  31 ASN
** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7884  Z= 0.156
  Angle     :  0.491   7.315  10717  Z= 0.257
  Chirality :  0.040   0.155   1245
  Planarity :  0.004   0.055   1363
  Dihedral  :  4.329  34.636   1090
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer Outliers :  1.48 %
  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: -0.12 (0.27), residues: 997
  helix:  1.15 (0.29), residues: 364
  sheet: -0.05 (0.35), residues: 228
  loop : -1.20 (0.30), residues: 405

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.878 
Fit side-chains
  outliers start: 12
  outliers final: 10
  residues processed: 155
  average time/residue: 0.2489
  time to fit residues: 49.3596
Evaluate side-chains
  158 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.839 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0772
  time to fit residues: 2.5836
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0770
   chunk 89 optimal weight:    0.3980
   chunk 94 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 25 optimal weight:    0.4980
   chunk 78 optimal weight:   10.0000
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
N  31 ASN
R 291 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7884  Z= 0.146
  Angle     :  0.476   7.387  10717  Z= 0.248
  Chirality :  0.039   0.145   1245
  Planarity :  0.004   0.055   1363
  Dihedral  :  4.209  34.598   1090
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer Outliers :  1.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.27), residues: 997
  helix:  1.30 (0.29), residues: 363
  sheet:  0.04 (0.35), residues: 228
  loop : -1.16 (0.30), residues: 406

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.823 
Fit side-chains
  outliers start: 16
  outliers final: 9
  residues processed: 155
  average time/residue: 0.2505
  time to fit residues: 49.6663
Evaluate side-chains
  152 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.839 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1282
  time to fit residues: 2.8083
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    0.4980
   chunk 1 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0970
   chunk 39 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.0780

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

Flipped N/Q/H residues before XYZ refinement:
N  31 ASN
** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7884  Z= 0.205
  Angle     :  0.507   7.775  10717  Z= 0.266
  Chirality :  0.041   0.143   1245
  Planarity :  0.004   0.055   1363
  Dihedral  :  4.377  37.134   1090
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer Outliers :  0.86 %
  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 (0.27), residues: 997
  helix:  1.28 (0.29), residues: 364
  sheet: -0.04 (0.34), residues: 237
  loop : -1.02 (0.31), residues: 396

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 149
  time to evaluate  : 0.826 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 154
  average time/residue: 0.2522
  time to fit residues: 49.5770
Evaluate side-chains
  153 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 149
  time to evaluate  : 0.765 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0785
  time to fit residues: 1.6436
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 94 optimal weight:    0.8980
   chunk 78 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0770
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.5742

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
N  31 ASN
N  74 ASN
** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 316 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7884  Z= 0.274
  Angle     :  0.556   7.876  10717  Z= 0.292
  Chirality :  0.042   0.152   1245
  Planarity :  0.004   0.055   1363
  Dihedral  :  4.580  38.710   1090
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer Outliers :  1.11 %
  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:  0.01 (0.27), residues: 997
  helix:  1.23 (0.29), residues: 363
  sheet: -0.04 (0.35), residues: 229
  loop : -1.05 (0.30), residues: 405

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 0.900 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 148
  average time/residue: 0.2607
  time to fit residues: 49.0841
Evaluate side-chains
  150 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 144
  time to evaluate  : 0.773 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1591
  time to fit residues: 2.5613
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 54 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0870
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
N  31 ASN
N  74 ASN
R 291 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7884  Z= 0.144
  Angle     :  0.488   8.585  10717  Z= 0.252
  Chirality :  0.039   0.142   1245
  Planarity :  0.004   0.057   1363
  Dihedral  :  4.170  33.721   1090
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer Outliers :  0.37 %
  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:  0.13 (0.27), residues: 997
  helix:  1.38 (0.29), residues: 364
  sheet:  0.04 (0.34), residues: 229
  loop : -1.05 (0.30), residues: 404

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 146
  time to evaluate  : 0.835 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 149
  average time/residue: 0.2620
  time to fit residues: 49.4475
Evaluate side-chains
  145 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.838 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1174
  time to fit residues: 1.3771
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   chunk 85 optimal weight:    0.3980
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
N  31 ASN
N  74 ASN
** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7884  Z= 0.225
  Angle     :  0.536   8.683  10717  Z= 0.278
  Chirality :  0.041   0.157   1245
  Planarity :  0.004   0.056   1363
  Dihedral  :  4.369  36.866   1090
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer Outliers :  0.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.27), residues: 997
  helix:  1.39 (0.29), residues: 362
  sheet:  0.01 (0.34), residues: 229
  loop : -1.05 (0.30), residues: 406

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 0.771 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 152
  average time/residue: 0.2526
  time to fit residues: 48.6479
Evaluate side-chains
  155 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.765 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1800
  time to fit residues: 2.0478
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.0370
   chunk 88 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 38 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.8260

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

Flipped N/Q/H residues before XYZ refinement:
N  31 ASN
N  74 ASN
** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7884  Z= 0.176
  Angle     :  0.521   9.109  10717  Z= 0.269
  Chirality :  0.040   0.144   1245
  Planarity :  0.004   0.058   1363
  Dihedral  :  4.279  36.157   1090
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer Outliers :  0.37 %
  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:  0.16 (0.27), residues: 997
  helix:  1.42 (0.29), residues: 363
  sheet:  0.03 (0.34), residues: 229
  loop : -1.03 (0.31), residues: 405

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 150
  time to evaluate  : 0.870 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 152
  average time/residue: 0.2641
  time to fit residues: 51.0704
Evaluate side-chains
  148 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 0.884 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0908
  time to fit residues: 1.4988
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.2980
   chunk 56 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 64 optimal weight:    0.4980
   chunk 97 optimal weight:    0.0040
   chunk 89 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
N  31 ASN
** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7884  Z= 0.139
  Angle     :  0.502   9.445  10717  Z= 0.258
  Chirality :  0.039   0.191   1245
  Planarity :  0.004   0.059   1363
  Dihedral  :  4.058  34.298   1090
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer Outliers :  0.25 %
  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 (0.27), residues: 997
  helix:  1.52 (0.29), residues: 363
  sheet:  0.10 (0.34), residues: 234
  loop : -0.98 (0.31), residues: 400

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.880 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 150
  average time/residue: 0.2628
  time to fit residues: 49.9820
Evaluate side-chains
  149 residues out of total 856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.732 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0640
  time to fit residues: 1.1692
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 71 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
N  31 ASN
** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.141217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.120593 restraints weight = 11243.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.11
r_work: 0.3432 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7884  Z= 0.173
  Angle     :  0.520   9.787  10717  Z= 0.267
  Chirality :  0.040   0.171   1245
  Planarity :  0.004   0.058   1363
  Dihedral  :  4.138  35.607   1090
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer Outliers :  0.25 %
  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:  0.27 (0.27), residues: 997
  helix:  1.53 (0.29), residues: 363
  sheet:  0.09 (0.34), residues: 230
  loop : -0.99 (0.31), residues: 404
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2099.92 seconds
wall clock time: 38 minutes 30.22 seconds (2310.22 seconds total)