Starting phenix.real_space_refine (version: 1.21rc1)
on Wed Oct  4 02:05:21 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/10_2023/7xms_33303.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/10_2023/7xms_33303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/10_2023/7xms_33303.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/10_2023/7xms_33303.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/10_2023/7xms_33303.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/10_2023/7xms_33303.pdb"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5336      2.51       5
     N    1413      2.21       5
     O    1564      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R GLU   94": "OE1" <-> "OE2"
    Residue "R ARG  110": "NH1" <-> "NH2"
    Residue "R ARG  120": "NH1" <-> "NH2"
    Residue "R ARG  153": "NH1" <-> "NH2"
    Residue "R ARG  159": "NH1" <-> "NH2"
    Residue "R ARG  252": "NH1" <-> "NH2"
    Residue "R TYR  276": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  216": "OE1" <-> "OE2"
    Residue "A ASP  261": "OD1" <-> "OD2"
    Residue "A ASP  315": "OD1" <-> "OD2"
    Residue "A ASP  341": "OD1" <-> "OD2"
    Residue "B ASP   27": "OD1" <-> "OD2"
    Residue "B ARG   46": "NH1" <-> "NH2"
    Residue "B ARG   52": "NH1" <-> "NH2"
    Residue "B TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  153": "OD1" <-> "OD2"
    Residue "B ASP  312": "OD1" <-> "OD2"
    Residue "S ARG   18": "NH1" <-> "NH2"
    Residue "S ASP   74": "OD1" <-> "OD2"
    Residue "S ARG   98": "NH1" <-> "NH2"
    Residue "S ARG  160": "NH1" <-> "NH2"
    Residue "S ASP  201": "OD1" <-> "OD2"
    Residue "S TYR  235": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib"
  Total number of atoms: 8370
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2021
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 11, 'TRANS': 264}
          Unresolved non-hydrogen bonds: 153
          Unresolved non-hydrogen angles: 191
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'PHE:plan': 6, 'GLN:plan1': 1, 'HIS:plan': 3, 'ARG:plan': 5, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 92
    Chain: "A"
      Number of atoms: 1721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1721
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 41
    Chain: "B"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2433
          Classifications: {'peptide': 325}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 5, 'TRANS': 319}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 331
          Classifications: {'peptide': 45}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 40}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "S"
      Number of atoms: 1764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1764
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "L"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 100
          Classifications: {'peptide': 12}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N   LEU A 234 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  LEU A 234 " occ=0.00
    residue:
      pdb=" N   ALA A 235 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 235 " occ=0.00
    residue:
      pdb=" N   GLU A 236 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 236 " occ=0.00
    residue:
      pdb=" N   ASP A 237 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ASP A 237 " occ=0.00
    residue:
      pdb=" N   GLU A 238 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 238 " occ=0.00
    residue:
      pdb=" N   GLU A 239 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 239 " occ=0.00
    residue:
      pdb=" N   MET A 240 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  MET A 240 " occ=0.00
  Time building chain proxies: 4.97, per 1000 atoms: 0.59
  Number of scatterers: 8370
  At special positions: 0
  Unit cell: (114.95, 112.86, 107.635, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1564      8.00
     N    1413      7.00
     C    5336      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 119 " - pdb=" SG  CYS R 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   3 " - pdb=" SG  CYS L  14 " distance=2.04

  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: 3.08
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2082

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 13 sheets defined
      32.5% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'R' and resid 47 through 76
      removed outlier: 3.671A  pdb=" N   ALA R  55 " --> pdb=" O   GLN R  51 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU R  56 " --> pdb=" O   CYS R  52 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   LEU R  67 " --> pdb=" O   VAL R  63 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE R  69 " --> pdb=" O   ASN R  65 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   PHE R  70 " --> pdb=" O   ALA R  66 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ARG R  74 " --> pdb=" O   PHE R  70 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR R  75 " --> pdb=" O   VAL R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 80 through 110
      removed outlier: 3.823A  pdb=" N   ILE R  84 " --> pdb=" O   THR R  80 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TYR R  85 " --> pdb=" O   ALA R  81 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU R  86 " --> pdb=" O   THR R  82 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER R  99 " --> pdb=" O   LEU R  95 " (cutoff:3.500A)
      Proline residue:  R 101  - end of helix
      removed outlier: 3.656A  pdb=" N   SER R 105 " --> pdb=" O   PRO R 101 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER R 106 " --> pdb=" O   PHE R 102 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA R 107 " --> pdb=" O   VAL R 103 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ALA R 108 " --> pdb=" O   ALA R 104 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 115 through 150
      removed outlier: 3.726A  pdb=" N   CYS R 119 " --> pdb=" O   GLY R 115 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ARG R 120 " --> pdb=" O   SER R 116 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY R 127 " --> pdb=" O   LEU R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 155
      removed outlier: 3.723A  pdb=" N   ALA R 155 " --> pdb=" O   PRO R 151 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 159 through 179
      removed outlier: 3.637A  pdb=" N   LEU R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU R 175 " --> pdb=" O   TRP R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 179 through 184
      removed outlier: 3.583A  pdb=" N   PHE R 184 " --> pdb=" O   PRO R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 204 through 218
      removed outlier: 3.777A  pdb=" N   SER R 208 " --> pdb=" O   HIS R 204 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA R 209 " --> pdb=" O   PRO R 205 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL R 210 " --> pdb=" O   ALA R 206 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE R 211 " --> pdb=" O   TRP R 207 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL R 213 " --> pdb=" O   ALA R 209 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   PHE R 216 " --> pdb=" O   VAL R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 220 through 245
    Processing helix  chain 'R' and resid 251 through 282
      removed outlier: 3.543A  pdb=" N   PHE R 264 " --> pdb=" O   LEU R 260 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL R 265 " --> pdb=" O   VAL R 261 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TRP R 272 " --> pdb=" O   PHE R 268 " (cutoff:3.500A)
      Proline residue:  R 274  - end of helix
      removed outlier: 3.650A  pdb=" N   VAL R 278 " --> pdb=" O   PRO R 274 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN R 279 " --> pdb=" O   PHE R 275 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU R 280 " --> pdb=" O   TYR R 276 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 292 through 313
      removed outlier: 3.610A  pdb=" N   ILE R 298 " --> pdb=" O   HIS R 294 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER R 300 " --> pdb=" O   SER R 296 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN R 303 " --> pdb=" O   LEU R 299 " (cutoff:3.500A)
      Proline residue:  R 308  - end of helix
    Processing helix  chain 'R' and resid 315 through 322
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.761A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 53
      removed outlier: 4.199A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 53'
    Processing helix  chain 'A' and resid 207 through 211
      removed outlier: 3.602A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.585A  pdb=" N   CYS A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.745A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.663A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 352
      removed outlier: 3.735A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 44
    Processing helix  chain 'S' and resid 74 through 76
      No H-bonds generated for 'chain 'S' and resid 74 through 76'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.573A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.868A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 185 through 187
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.624A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.206A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62
      removed outlier: 4.447A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.543A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.673A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192
      removed outlier: 4.146A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.873A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.923A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7
      removed outlier: 3.730A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.576A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147
      removed outlier: 3.536A  pdb=" N   TYR S 175 " --> pdb=" O   MET S 230 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 157

    333 hydrogen bonds defined for protein.
    939 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: 2.35

  Time building geometry restraints manager: 3.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2702
        1.34 -     1.46: 2050
        1.46 -     1.58: 3715
        1.58 -     1.69: 0
        1.69 -     1.81: 79
  Bond restraints: 8546
  Sorted by residual:
  bond pdb=" N   ASP B 258 "
       pdb=" CA  ASP B 258 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.45e+00
  bond pdb=" N   GLY S 209 "
       pdb=" CA  GLY S 209 "
    ideal  model  delta    sigma   weight residual
    1.449  1.463 -0.014 1.45e-02 4.76e+03 9.54e-01
  bond pdb=" C   VAL R 100 "
       pdb=" N   PRO R 101 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.19e-02 7.06e+03 7.77e-01
  bond pdb=" CA  ILE B  93 "
       pdb=" C   ILE B  93 "
    ideal  model  delta    sigma   weight residual
    1.528  1.533 -0.006 8.10e-03 1.52e+04 5.34e-01
  bond pdb=" CA  VAL R 100 "
       pdb=" C   VAL R 100 "
    ideal  model  delta    sigma   weight residual
    1.524  1.532 -0.008 1.05e-02 9.07e+03 5.30e-01
  ... (remaining 8541 not shown)

  Histogram of bond angle deviations from ideal:
      100.56 -   107.25: 226
      107.25 -   113.94: 4863
      113.94 -   120.62: 3341
      120.62 -   127.31: 3113
      127.31 -   134.00: 88
  Bond angle restraints: 11631
  Sorted by residual:
  angle pdb=" N   VAL C  30 "
        pdb=" CA  VAL C  30 "
        pdb=" C   VAL C  30 "
      ideal   model   delta    sigma   weight residual
     113.42  109.55    3.87 1.17e+00 7.31e-01 1.09e+01
  angle pdb=" CA  LEU R 179 "
        pdb=" CB  LEU R 179 "
        pdb=" CG  LEU R 179 "
      ideal   model   delta    sigma   weight residual
     116.30  126.52  -10.22 3.50e+00 8.16e-02 8.52e+00
  angle pdb=" C   ASP B 163 "
        pdb=" N   THR B 164 "
        pdb=" CA  THR B 164 "
      ideal   model   delta    sigma   weight residual
     121.54  126.21   -4.67 1.91e+00 2.74e-01 5.98e+00
  angle pdb=" CA  VAL C  30 "
        pdb=" C   VAL C  30 "
        pdb=" N   SER C  31 "
      ideal   model   delta    sigma   weight residual
     118.90  116.85    2.05 9.40e-01 1.13e+00 4.76e+00
  angle pdb=" C   ALA B 257 "
        pdb=" N   ASP B 258 "
        pdb=" CA  ASP B 258 "
      ideal   model   delta    sigma   weight residual
     121.54  125.65   -4.11 1.91e+00 2.74e-01 4.62e+00
  ... (remaining 11626 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.86: 4706
       15.86 -    31.72: 252
       31.72 -    47.58: 51
       47.58 -    63.43: 8
       63.43 -    79.29: 2
  Dihedral angle restraints: 5019
    sinusoidal: 1793
      harmonic: 3226
  Sorted by residual:
  dihedral pdb=" CB  CYS L   3 "
           pdb=" SG  CYS L   3 "
           pdb=" SG  CYS L  14 "
           pdb=" CB  CYS L  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.93   32.07     1      1.00e+01 1.00e-02 1.47e+01
  dihedral pdb=" CB  LYS A 330 "
           pdb=" CG  LYS A 330 "
           pdb=" CD  LYS A 330 "
           pdb=" CE  LYS A 330 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.21  -56.21     3      1.50e+01 4.44e-03 9.39e+00
  dihedral pdb=" CA  ASP B  27 "
           pdb=" CB  ASP B  27 "
           pdb=" CG  ASP B  27 "
           pdb=" OD1 ASP B  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.31   52.31     1      2.00e+01 2.50e-03 9.33e+00
  ... (remaining 5016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 840
       0.028 -    0.056: 353
       0.056 -    0.084: 86
       0.084 -    0.112: 64
       0.112 -    0.140: 13
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  ASP B 258 "
            pdb=" N   ASP B 258 "
            pdb=" C   ASP B 258 "
            pdb=" CB  ASP B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE S 157 "
            pdb=" N   ILE S 157 "
            pdb=" C   ILE S 157 "
            pdb=" CB  ILE S 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.68e-01
  ... (remaining 1353 not shown)

  Planarity restraints: 1472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.66e+00
        pdb=" N   PRO S  75 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR S 150 "    0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO S 151 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO S 151 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO S 151 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  59 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.46e+00
        pdb=" N   PRO C  60 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1469 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1872
        2.78 -     3.31: 7696
        3.31 -     3.84: 13897
        3.84 -     4.37: 16412
        4.37 -     4.90: 27954
  Nonbonded interactions: 67831
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.251 2.440
  nonbonded pdb=" O   PHE A 336 "
            pdb=" OG1 THR A 340 "
     model   vdw
     2.298 2.440
  nonbonded pdb=" OG  SER B 277 "
            pdb=" O   LEU B 318 "
     model   vdw
     2.300 2.440
  nonbonded pdb=" O   TYR R 311 "
            pdb=" OG  SER R 315 "
     model   vdw
     2.309 2.440
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.320 2.520
  ... (remaining 67826 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=0.00 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:             0.830
  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:          4.130
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     25.500
  Find NCS groups from input model:        0.230
  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:11.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6232
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8546  Z= 0.104
  Angle     :  0.455  10.217  11631  Z= 0.257
  Chirality :  0.038   0.140   1356
  Planarity :  0.003   0.032   1472
  Dihedral  : 10.087  79.292   2928
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.20), residues: 1097
  helix: -3.32 (0.18), residues: 313
  sheet: -2.11 (0.31), residues: 226
  loop : -2.52 (0.22), residues: 558

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 1.0426
  time to fit residues: 256.7480
Evaluate side-chains
  137 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.914 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2634
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    8.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
R  51 GLN
R 129 ASN
R 150 HIS
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 248 GLN
** R 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 307 ASN
A 188 HIS
A 306 GLN
A 333 GLN
B  36 ASN
B 125 ASN
B 295 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  13 GLN
S  39 GLN
S  77 ASN
S  82 GLN
S 113 GLN
S 142 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8546  Z= 0.248
  Angle     :  0.644   9.196  11631  Z= 0.324
  Chirality :  0.044   0.269   1356
  Planarity :  0.005   0.050   1472
  Dihedral  :  3.821  20.111   1189
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 15.88 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -2.46 (0.23), residues: 1097
  helix: -1.11 (0.25), residues: 340
  sheet: -1.81 (0.31), residues: 245
  loop : -1.79 (0.25), residues: 512

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 161
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
  outliers start: 34
  outliers final: 9
  residues processed: 177
  average time/residue: 1.0301
  time to fit residues: 195.8818
Evaluate side-chains
  130 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.978 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 6
  residues processed: 3
  average time/residue: 0.0795
  time to fit residues: 1.7957
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 82 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0070
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    9.9990
   chunk 107 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 79 optimal weight:    0.4980
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
R  83 ASN
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
A 333 GLN
B  75 GLN
B 125 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8546  Z= 0.188
  Angle     :  0.585   9.957  11631  Z= 0.287
  Chirality :  0.041   0.142   1356
  Planarity :  0.004   0.065   1472
  Dihedral  :  3.656  19.833   1189
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 18.30 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.66 (0.24), residues: 1097
  helix: -0.01 (0.28), residues: 339
  sheet: -1.40 (0.30), residues: 267
  loop : -1.63 (0.26), residues: 491

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 15
  residues processed: 149
  average time/residue: 1.0463
  time to fit residues: 167.9148
Evaluate side-chains
  131 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.939 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 11
  residues processed: 5
  average time/residue: 0.1705
  time to fit residues: 2.4588
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.0050
   chunk 74 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.8596

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

Flipped N/Q/H residues before XYZ refinement:
** R  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
A 333 GLN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.4677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8546  Z= 0.223
  Angle     :  0.607  11.408  11631  Z= 0.297
  Chirality :  0.042   0.141   1356
  Planarity :  0.004   0.050   1472
  Dihedral  :  3.879  20.849   1189
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.91 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.27 (0.25), residues: 1097
  helix:  0.44 (0.29), residues: 339
  sheet: -1.28 (0.30), residues: 266
  loop : -1.44 (0.26), residues: 492

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
  outliers start: 33
  outliers final: 13
  residues processed: 160
  average time/residue: 1.0879
  time to fit residues: 186.4928
Evaluate side-chains
  135 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.882 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 3
  average time/residue: 0.0961
  time to fit residues: 1.8099
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 1 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 89 optimal weight:    0.2980
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0870
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
** R  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
A 333 GLN
B  75 GLN
S 167 HIS
S 171 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.5029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8546  Z= 0.211
  Angle     :  0.617  12.127  11631  Z= 0.300
  Chirality :  0.041   0.138   1356
  Planarity :  0.004   0.045   1472
  Dihedral  :  3.898  22.148   1189
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.17 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.99 (0.25), residues: 1097
  helix:  0.71 (0.29), residues: 339
  sheet: -1.12 (0.31), residues: 254
  loop : -1.31 (0.27), residues: 504

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 125
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
  outliers start: 37
  outliers final: 15
  residues processed: 149
  average time/residue: 1.0231
  time to fit residues: 164.4188
Evaluate side-chains
  132 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.909 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 12
  residues processed: 3
  average time/residue: 0.0815
  time to fit residues: 1.6971
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0170
   chunk 105 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0870
   chunk 8 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0870
   overall best weight:    0.3574

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

Flipped N/Q/H residues before XYZ refinement:
** R  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
A 333 GLN
B  75 GLN
S  77 ASN
S 171 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8546  Z= 0.158
  Angle     :  0.587  10.867  11631  Z= 0.284
  Chirality :  0.041   0.137   1356
  Planarity :  0.004   0.047   1472
  Dihedral  :  3.781  20.910   1189
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.94 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.79 (0.25), residues: 1097
  helix:  0.91 (0.29), residues: 341
  sheet: -0.92 (0.32), residues: 257
  loop : -1.27 (0.27), residues: 499

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 15
  residues processed: 152
  average time/residue: 0.8971
  time to fit residues: 148.8842
Evaluate side-chains
  133 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.061 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 11
  residues processed: 4
  average time/residue: 0.2543
  time to fit residues: 2.9563
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0770
   chunk 59 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 105 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** R  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.5268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8546  Z= 0.172
  Angle     :  0.611  12.025  11631  Z= 0.293
  Chirality :  0.041   0.137   1356
  Planarity :  0.004   0.046   1472
  Dihedral  :  3.793  20.039   1189
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 24.40 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.67 (0.26), residues: 1097
  helix:  0.94 (0.29), residues: 343
  sheet: -0.83 (0.31), residues: 266
  loop : -1.16 (0.28), residues: 488

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
  outliers start: 31
  outliers final: 13
  residues processed: 145
  average time/residue: 0.9400
  time to fit residues: 147.7803
Evaluate side-chains
  126 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.863 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 3
  average time/residue: 0.1566
  time to fit residues: 1.8295
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0470
   chunk 20 optimal weight:    5.9990
   chunk 66 optimal weight:    0.2980
   chunk 71 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 95 optimal weight:    0.4980
   chunk 100 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
** R  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.5439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8546  Z= 0.180
  Angle     :  0.617  11.787  11631  Z= 0.294
  Chirality :  0.041   0.144   1356
  Planarity :  0.004   0.051   1472
  Dihedral  :  3.853  19.623   1189
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 26.01 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.58 (0.26), residues: 1097
  helix:  0.97 (0.29), residues: 344
  sheet: -0.75 (0.31), residues: 266
  loop : -1.10 (0.28), residues: 487

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 13
  residues processed: 142
  average time/residue: 0.8421
  time to fit residues: 130.6777
Evaluate side-chains
  128 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.838 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 12
  residues processed: 1
  average time/residue: 0.0785
  time to fit residues: 1.3217
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 100 optimal weight:    0.0000
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 92 optimal weight:    0.4980
   chunk 64 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
** R  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.5515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8546  Z= 0.176
  Angle     :  0.636  12.804  11631  Z= 0.298
  Chirality :  0.041   0.139   1356
  Planarity :  0.004   0.051   1472
  Dihedral  :  3.857  19.363   1189
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 26.81 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.48 (0.26), residues: 1097
  helix:  1.02 (0.29), residues: 343
  sheet: -0.54 (0.32), residues: 260
  loop : -1.11 (0.28), residues: 494

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 13
  residues processed: 131
  average time/residue: 0.8799
  time to fit residues: 126.2665
Evaluate side-chains
  128 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.916 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 12
  residues processed: 1
  average time/residue: 0.1356
  time to fit residues: 1.5135
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    0.0050
   chunk 71 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0070
   chunk 68 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0970
   chunk 26 optimal weight:    0.0010
   overall best weight:    0.1816

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

Flipped N/Q/H residues before XYZ refinement:
R  51 GLN
** R  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
S 171 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.5504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8546  Z= 0.147
  Angle     :  0.618  13.391  11631  Z= 0.290
  Chirality :  0.040   0.142   1356
  Planarity :  0.004   0.054   1472
  Dihedral  :  3.702  19.300   1189
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 26.81 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.35 (0.26), residues: 1097
  helix:  1.11 (0.29), residues: 342
  sheet: -0.44 (0.33), residues: 266
  loop : -1.03 (0.28), residues: 489

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 12
  residues processed: 146
  average time/residue: 0.7721
  time to fit residues: 124.4032
Evaluate side-chains
  132 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.945 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 12
  residues processed: 0
  time to fit residues: 1.3241
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** R  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.196407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.158141 restraints weight = 9203.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 1.82
r_work: 0.3884 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.5815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8546  Z= 0.251
  Angle     :  0.690  13.116  11631  Z= 0.329
  Chirality :  0.043   0.169   1356
  Planarity :  0.004   0.049   1472
  Dihedral  :  4.102  19.239   1189
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 28.19 %
    Favored  : 70.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.46 (0.26), residues: 1097
  helix:  1.00 (0.29), residues: 345
  sheet: -0.84 (0.31), residues: 276
  loop : -0.86 (0.29), residues: 476
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3689.66 seconds
wall clock time: 66 minutes 7.11 seconds (3967.11 seconds total)