Starting phenix.real_space_refine
on Fri Nov 15 11:07:57 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/11_2024/8fu6_29453_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/11_2024/8fu6_29453.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/8fu6_29453/11_2024/8fu6_29453.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/11_2024/8fu6_29453.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/11_2024/8fu6_29453_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/11_2024/8fu6_29453_neut.cif"
  }
  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=  -0.001 sd=   0.038
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      53      5.16       5
     C    5608      2.51       5
     N    1552      2.21       5
     O    1621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8834
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1773
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 205}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2597
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "P"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 240
          Classifications: {'peptide': 29}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 28}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "R"
      Number of atoms: 2809
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2800
          Classifications: {'peptide': 346}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 337}
          Chain breaks: 3
          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
      Conformer: "B"
        Number of residues, atoms: 346, 2800
          Classifications: {'peptide': 346}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 337}
          Chain breaks: 3
          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
          bond proxies already assigned to first conformer: 2870
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLN R  42 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN R  42 " occ=0.50
  Time building chain proxies: 6.88, per 1000 atoms: 0.78
  Number of scatterers: 8834
  At special positions: 0
  Unit cell: (84.348, 166.992, 101.388, 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      53     16.00
     O    1621      8.00
     N    1552      7.00
     C    5608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, 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  81 " - pdb=" SG  CYS R 121 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      41.4% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 4.178A  pdb=" N   ARG A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.752A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 233 through 239'
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.744A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.763A  pdb=" N   ASP A 343 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.573A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.582A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.780A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.710A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.536A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   MET G  38 " --> pdb=" O   ALA G  34 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.575A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 29
      removed outlier: 3.516A  pdb=" N   SER P  16 " --> pdb=" O   LYS P  12 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 27 through 43
      removed outlier: 3.571A  pdb=" N   PHE R  31 " --> pdb=" O   GLN R  27 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   CYS R  43 " --> pdb=" O   TYR R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 124 through 166
      removed outlier: 3.539A  pdb=" N   GLU R 133 " --> pdb=" O   GLU R 129 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL R 134 " --> pdb=" O   VAL R 130 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA R 135 " --> pdb=" O   GLN R 131 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   LYS R 136 " --> pdb=" O   LYS R 132 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   MET R 137 " --> pdb=" O   GLU R 133 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR R 138 " --> pdb=" O   VAL R 134 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU R 151 " --> pdb=" O   VAL R 147 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER R 152 " --> pdb=" O   GLY R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 197
    Processing helix  chain 'R' and resid 208 through 212
      removed outlier: 3.667A  pdb=" N   VAL R 212 " --> pdb=" O   ASP R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 221 through 255
      removed outlier: 3.687A  pdb=" N   ARG R 225 " --> pdb=" O   VAL R 221 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   VAL R 226 " --> pdb=" O   ALA R 222 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA R 227 " --> pdb=" O   GLY R 223 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL R 236 " --> pdb=" O   GLN R 232 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR R 239 " --> pdb=" O   ILE R 235 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   CYS R 240 " --> pdb=" O   VAL R 236 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   TRP R 241 " --> pdb=" O   ALA R 237 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU R 242 " --> pdb=" O   ASN R 238 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU R 243 " --> pdb=" O   TYR R 239 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LEU R 253 " --> pdb=" O   LEU R 249 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLY R 254 " --> pdb=" O   HIS R 250 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LEU R 255 " --> pdb=" O   ASN R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 274
      removed outlier: 3.781A  pdb=" N   ALA R 274 " --> pdb=" O   ILE R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 275 through 289
      removed outlier: 3.789A  pdb=" N   VAL R 280 " --> pdb=" O   MET R 276 " (cutoff:3.500A)
      Proline residue:  R 281  - end of helix
    Processing helix  chain 'R' and resid 292 through 296
      removed outlier: 4.225A  pdb=" N   THR R 296 " --> pdb=" O   GLN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 305
    Processing helix  chain 'R' and resid 308 through 335
      removed outlier: 3.588A  pdb=" N   ILE R 315 " --> pdb=" O   VAL R 311 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   PHE R 320 " --> pdb=" O   LEU R 316 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE R 321 " --> pdb=" O   ILE R 317 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 344 through 359
      removed outlier: 4.149A  pdb=" N   THR R 351 " --> pdb=" O   LEU R 347 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU R 352 " --> pdb=" O   ALA R 348 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR R 353 " --> pdb=" O   LYS R 349 " (cutoff:3.500A)
      Proline residue:  R 356  - end of helix
    Processing helix  chain 'R' and resid 360 through 365
      removed outlier: 4.097A  pdb=" N   PHE R 365 " --> pdb=" O   HIS R 361 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 375 through 389
      removed outlier: 3.705A  pdb=" N   SER R 379 " --> pdb=" O   GLY R 375 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS R 381 " --> pdb=" O   LEU R 377 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LEU R 386 " --> pdb=" O   LEU R 382 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 391 through 401
    Processing helix  chain 'R' and resid 404 through 421
      removed outlier: 3.564A  pdb=" N   GLU R 410 " --> pdb=" O   GLU R 406 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG R 412 " --> pdb=" O   GLN R 408 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ARG R 413 " --> pdb=" O   SER R 409 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG R 414 " --> pdb=" O   GLU R 410 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TRP R 415 " --> pdb=" O   LEU R 411 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 3.611A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 9.136A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.854A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.806A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.945A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.684A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.776A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.915A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.738A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.001A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.558A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.584A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA N  97 " --> pdb=" O   ASN N  35 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 122 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1095 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: 2.44

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2902
        1.35 -     1.47: 2266
        1.47 -     1.59: 3787
        1.59 -     1.71: 0
        1.71 -     1.83: 73
  Bond restraints: 9028
  Sorted by residual:
  bond pdb=" C   ALA R 274 "
       pdb=" N   PRO R 275 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.021 1.28e-02 6.10e+03 2.57e+00
  bond pdb=" CA  VAL A 224 "
       pdb=" CB  VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.528  1.543 -0.015 1.34e-02 5.57e+03 1.30e+00
  bond pdb=" CA  VAL R 280 "
       pdb=" C   VAL R 280 "
    ideal  model  delta    sigma   weight residual
    1.520  1.529 -0.009 8.80e-03 1.29e+04 1.13e+00
  bond pdb=" C   GLY N   9 "
       pdb=" O   GLY N   9 "
    ideal  model  delta    sigma   weight residual
    1.232  1.243 -0.011 1.03e-02 9.43e+03 1.11e+00
  bond pdb=" C   PHE B 235 "
       pdb=" N   PRO B 236 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.013 1.36e-02 5.41e+03 9.18e-01
  ... (remaining 9023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 11557
        1.20 -     2.40: 553
        2.40 -     3.60: 87
        3.60 -     4.80: 20
        4.80 -     6.00: 6
  Bond angle restraints: 12223
  Sorted by residual:
  angle pdb=" N   VAL N 110 "
        pdb=" CA  VAL N 110 "
        pdb=" C   VAL N 110 "
      ideal   model   delta    sigma   weight residual
     111.91  106.81    5.10 8.90e-01 1.26e+00 3.28e+01
  angle pdb=" N   VAL R 360 "
        pdb=" CA  VAL R 360 "
        pdb=" C   VAL R 360 "
      ideal   model   delta    sigma   weight residual
     113.39  108.93    4.46 1.47e+00 4.63e-01 9.20e+00
  angle pdb=" N   PHE A 315 "
        pdb=" CA  PHE A 315 "
        pdb=" C   PHE A 315 "
      ideal   model   delta    sigma   weight residual
     112.57  109.27    3.30 1.13e+00 7.83e-01 8.53e+00
  angle pdb=" N   TYR A  37 "
        pdb=" CA  TYR A  37 "
        pdb=" C   TYR A  37 "
      ideal   model   delta    sigma   weight residual
     111.28  114.37   -3.09 1.09e+00 8.42e-01 8.02e+00
  angle pdb=" CA  VAL R 360 "
        pdb=" C   VAL R 360 "
        pdb=" N   HIS R 361 "
      ideal   model   delta    sigma   weight residual
     118.55  116.14    2.41 8.60e-01 1.35e+00 7.87e+00
  ... (remaining 12218 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 4899
       17.67 -    35.34: 368
       35.34 -    53.02: 47
       53.02 -    70.69: 7
       70.69 -    88.36: 6
  Dihedral angle restraints: 5327
    sinusoidal: 2102
      harmonic: 3225
  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    1.91  -87.91     1      1.00e+01 1.00e-02 9.25e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.80  -38.80     1      1.00e+01 1.00e-02 2.12e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.07  -19.93     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 5324 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 755
       0.025 -    0.050: 346
       0.050 -    0.076: 142
       0.076 -    0.101: 61
       0.101 -    0.126: 44
  Chirality restraints: 1348
  Sorted by residual:
  chirality pdb=" CA  VAL N 110 "
            pdb=" N   VAL N 110 "
            pdb=" C   VAL N 110 "
            pdb=" CB  VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  TYR R 145 "
            pdb=" N   TYR R 145 "
            pdb=" C   TYR R 145 "
            pdb=" CB  TYR R 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 1345 not shown)

  Planarity restraints: 1562
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS R  81 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.87e+00
        pdb=" N   PRO R  82 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO R  82 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R  82 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 274 "   -0.039 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO R 275 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO R 275 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 275 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 327 "    0.038 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO A 328 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 328 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 328 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1559 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 553
        2.74 -     3.28: 8226
        3.28 -     3.82: 13185
        3.82 -     4.36: 15566
        4.36 -     4.90: 28274
  Nonbonded interactions: 65804
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" NH1 ARG A  38 "
            pdb=" O   GLU R 260 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   ARG B  22 "
            pdb=" NE2 GLN B 259 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OG1 THR B 221 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" NH2 ARG R 201 "
            pdb=" OE1 GLN R 293 "
     model   vdw
     2.298 3.120
  ... (remaining 65799 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.320
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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   0.037   9028  Z= 0.162
  Angle     :  0.598   6.000  12223  Z= 0.367
  Chirality :  0.040   0.126   1348
  Planarity :  0.004   0.061   1562
  Dihedral  : 12.459  88.360   3232
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1091
  helix:  1.36 (0.26), residues: 425
  sheet:  0.43 (0.35), residues: 218
  loop : -1.48 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.014   0.001   PHE N 108 
 TYR   0.014   0.001   TYR R 145 
 ARG   0.006   0.000   ARG R 201 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.949 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 1.2976
  time to fit residues: 159.2593
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0050
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.5332

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B 237 ASN
R 131 GLN
R 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9028  Z= 0.149
  Angle     :  0.524   7.011  12223  Z= 0.283
  Chirality :  0.041   0.136   1348
  Planarity :  0.005   0.055   1562
  Dihedral  :  4.007  17.954   1213
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.09 %
    Favored  : 91.75 %
  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:  0.34 (0.25), residues: 1091
  helix:  1.70 (0.26), residues: 429
  sheet:  0.51 (0.34), residues: 219
  loop : -1.46 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.028   0.001   TYR R 145 
 ARG   0.006   0.000   ARG R 201 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.936 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.6653 (ttp-170) cc_final: 0.6060 (ttp80)
REVERT: B  152 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8086 (tt)
REVERT: N    3 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7149 (tt0)
REVERT: P   17 ARG cc_start: 0.6745 (mmp-170) cc_final: 0.6014 (ttp-170)
REVERT: R  419 ARG cc_start: 0.6549 (ttp-170) cc_final: 0.6192 (tpp-160)
  outliers start: 11
  outliers final: 4
  residues processed: 109
  average time/residue: 1.2465
  time to fit residues: 145.2976
Evaluate side-chains
  90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0670
   chunk 97 optimal weight:    0.6980
   chunk 105 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9028  Z= 0.156
  Angle     :  0.513   8.941  12223  Z= 0.275
  Chirality :  0.040   0.134   1348
  Planarity :  0.004   0.053   1562
  Dihedral  :  4.013  18.592   1213
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  9.10 %
    Favored  : 88.99 %
  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:  0.52 (0.25), residues: 1091
  helix:  1.90 (0.26), residues: 425
  sheet:  0.59 (0.34), residues: 222
  loop : -1.38 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.015   0.001   PHE N 108 
 TYR   0.027   0.001   TYR R 145 
 ARG   0.005   0.000   ARG R 201 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A  317 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6990 (mtm-85)
REVERT: B   19 ARG cc_start: 0.6652 (ttp-170) cc_final: 0.6202 (ttp80)
REVERT: B  152 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8048 (tt)
REVERT: R  334 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5195 (ttm170)
REVERT: R  419 ARG cc_start: 0.6497 (ttp-170) cc_final: 0.6123 (tpp-160)
  outliers start: 18
  outliers final: 6
  residues processed: 102
  average time/residue: 1.3248
  time to fit residues: 144.3355
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  334 ARG
Chi-restraints excluded: chain R residue  403 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 46 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0370
   chunk 97 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
R 300 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9028  Z= 0.150
  Angle     :  0.498   7.875  12223  Z= 0.268
  Chirality :  0.040   0.133   1348
  Planarity :  0.004   0.051   1562
  Dihedral  :  3.985  19.689   1213
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.58 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.25), residues: 1091
  helix:  2.03 (0.26), residues: 424
  sheet:  0.70 (0.34), residues: 222
  loop : -1.38 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.014   0.001   PHE N 108 
 TYR   0.026   0.001   TYR R 145 
 ARG   0.003   0.000   ARG R 201 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A  317 ARG cc_start: 0.7272 (mtm-85) cc_final: 0.6994 (mtm-85)
REVERT: B   19 ARG cc_start: 0.6681 (ttp-170) cc_final: 0.6220 (ttp80)
REVERT: B  152 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8052 (tt)
REVERT: B  234 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7971 (t80)
REVERT: R  419 ARG cc_start: 0.6479 (ttp-170) cc_final: 0.6071 (tpp-160)
  outliers start: 15
  outliers final: 6
  residues processed: 97
  average time/residue: 1.1853
  time to fit residues: 123.4670
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 77 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
R 120 GLN
R 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9028  Z= 0.168
  Angle     :  0.519   7.746  12223  Z= 0.278
  Chirality :  0.040   0.134   1348
  Planarity :  0.004   0.050   1562
  Dihedral  :  4.071  20.800   1213
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 11.85 %
    Favored  : 86.56 %
  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:  0.69 (0.25), residues: 1091
  helix:  2.10 (0.26), residues: 424
  sheet:  0.73 (0.34), residues: 222
  loop : -1.39 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.018   0.001   PHE N 108 
 TYR   0.026   0.001   TYR R 145 
 ARG   0.005   0.000   ARG B 197 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A  279 ASN cc_start: 0.8591 (t0) cc_final: 0.8369 (t0)
REVERT: A  317 ARG cc_start: 0.7328 (mtm-85) cc_final: 0.7056 (mtm-85)
REVERT: B   19 ARG cc_start: 0.6711 (ttp-170) cc_final: 0.6250 (ttp80)
REVERT: B   38 ASP cc_start: 0.7678 (p0) cc_final: 0.7316 (p0)
REVERT: B  152 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8014 (tt)
REVERT: B  234 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8052 (t80)
REVERT: P   17 ARG cc_start: 0.6682 (mmp-170) cc_final: 0.5783 (ttp-170)
REVERT: R  334 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5170 (ttm170)
REVERT: R  419 ARG cc_start: 0.6584 (ttp-170) cc_final: 0.6126 (tpp-160)
  outliers start: 15
  outliers final: 9
  residues processed: 100
  average time/residue: 1.3428
  time to fit residues: 143.0366
Evaluate side-chains
  101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  296 THR
Chi-restraints excluded: chain R residue  334 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0980
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9028  Z= 0.158
  Angle     :  0.505   7.700  12223  Z= 0.270
  Chirality :  0.040   0.133   1348
  Planarity :  0.004   0.049   1562
  Dihedral  :  4.043  20.499   1213
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.02 %
    Favored  : 85.50 %
  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:  0.76 (0.25), residues: 1091
  helix:  2.18 (0.26), residues: 425
  sheet:  0.77 (0.34), residues: 222
  loop : -1.38 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.016   0.001   PHE N 108 
 TYR   0.025   0.001   TYR R 145 
 ARG   0.009   0.000   ARG B 197 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A  279 ASN cc_start: 0.8587 (t0) cc_final: 0.8341 (t0)
REVERT: A  317 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.7072 (mtm-85)
REVERT: B   19 ARG cc_start: 0.6703 (ttp-170) cc_final: 0.6245 (ttp80)
REVERT: B   38 ASP cc_start: 0.7699 (p0) cc_final: 0.7269 (p0)
REVERT: B  152 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8015 (tt)
REVERT: B  234 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8038 (t80)
REVERT: P   17 ARG cc_start: 0.6693 (mmp-170) cc_final: 0.5761 (ttp-170)
REVERT: R  296 THR cc_start: 0.7881 (m) cc_final: 0.7510 (m)
REVERT: R  334 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5149 (ttm170)
REVERT: R  419 ARG cc_start: 0.6630 (ttp-170) cc_final: 0.6083 (tpp-160)
  outliers start: 14
  outliers final: 8
  residues processed: 103
  average time/residue: 1.4615
  time to fit residues: 159.8163
Evaluate side-chains
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  334 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0570
   chunk 57 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.7304

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9028  Z= 0.287
  Angle     :  0.624   8.683  12223  Z= 0.332
  Chirality :  0.044   0.172   1348
  Planarity :  0.005   0.048   1562
  Dihedral  :  4.529  24.255   1213
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.12 %
    Favored  : 85.08 %
  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:  0.49 (0.25), residues: 1091
  helix:  1.90 (0.25), residues: 424
  sheet:  0.57 (0.34), residues: 222
  loop : -1.41 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.005   0.001   HIS A 362 
 PHE   0.027   0.002   PHE N 108 
 TYR   0.030   0.002   TYR R 145 
 ARG   0.008   0.001   ARG B 197 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.7036 (mtm-85)
REVERT: B   19 ARG cc_start: 0.6681 (ttp-170) cc_final: 0.6226 (ttp80)
REVERT: B  152 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7994 (tt)
REVERT: B  234 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8119 (t80)
REVERT: R  296 THR cc_start: 0.7958 (m) cc_final: 0.7596 (m)
REVERT: R  334 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.5455 (ttm170)
REVERT: R  419 ARG cc_start: 0.6679 (ttp-170) cc_final: 0.6187 (tpp-160)
  outliers start: 17
  outliers final: 10
  residues processed: 114
  average time/residue: 1.4564
  time to fit residues: 176.0663
Evaluate side-chains
  104 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  334 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9028  Z= 0.205
  Angle     :  0.559   7.822  12223  Z= 0.299
  Chirality :  0.042   0.139   1348
  Planarity :  0.004   0.048   1562
  Dihedral  :  4.413  23.418   1213
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.76 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1091
  helix:  1.97 (0.26), residues: 425
  sheet:  0.61 (0.34), residues: 220
  loop : -1.41 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.021   0.002   PHE N 108 
 TYR   0.026   0.001   TYR R 145 
 ARG   0.007   0.000   ARG B 197 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.6653 (ttp-170) cc_final: 0.6200 (ttp80)
REVERT: B   38 ASP cc_start: 0.7745 (p0) cc_final: 0.7140 (p0)
REVERT: B  152 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7999 (tt)
REVERT: B  234 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8066 (t80)
REVERT: P   17 ARG cc_start: 0.6712 (mmp-170) cc_final: 0.5890 (ttp-170)
REVERT: R  296 THR cc_start: 0.7951 (m) cc_final: 0.7597 (m)
REVERT: R  334 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5336 (ttm170)
REVERT: R  419 ARG cc_start: 0.6672 (ttp-170) cc_final: 0.6120 (tpp-160)
  outliers start: 16
  outliers final: 11
  residues processed: 105
  average time/residue: 1.3975
  time to fit residues: 156.0617
Evaluate side-chains
  105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  334 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0670
   chunk 86 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 101 optimal weight:    0.0970
   overall best weight:    0.5516

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 357 HIS
B 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9028  Z= 0.143
  Angle     :  0.496   6.459  12223  Z= 0.268
  Chirality :  0.040   0.130   1348
  Planarity :  0.004   0.049   1562
  Dihedral  :  4.144  20.853   1213
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.18 %
    Favored  : 84.44 %
  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:  0.75 (0.25), residues: 1091
  helix:  2.23 (0.26), residues: 425
  sheet:  0.69 (0.34), residues: 220
  loop : -1.39 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.009   0.001   HIS B 225 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.023   0.001   TYR R 145 
 ARG   0.007   0.000   ARG B 197 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.220 
Fit side-chains
REVERT: A  279 ASN cc_start: 0.8668 (t0) cc_final: 0.8417 (t0)
REVERT: B   19 ARG cc_start: 0.6649 (ttp-170) cc_final: 0.6200 (ttp80)
REVERT: B   38 ASP cc_start: 0.7677 (p0) cc_final: 0.7196 (p0)
REVERT: B  152 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8006 (tt)
REVERT: B  234 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8010 (t80)
REVERT: P   17 ARG cc_start: 0.6593 (mmp-170) cc_final: 0.5714 (ttp-170)
REVERT: R  296 THR cc_start: 0.7903 (m) cc_final: 0.7601 (m)
REVERT: R  334 ARG cc_start: 0.6240 (OUTLIER) cc_final: 0.5204 (ttm170)
REVERT: R  419 ARG cc_start: 0.6699 (ttp-170) cc_final: 0.6091 (tpp-160)
  outliers start: 13
  outliers final: 9
  residues processed: 98
  average time/residue: 1.3316
  time to fit residues: 139.3185
Evaluate side-chains
  97 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  334 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0020
   chunk 106 optimal weight:    0.6980
   chunk 98 optimal weight:    0.2980
   chunk 84 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9028  Z= 0.143
  Angle     :  0.489   5.890  12223  Z= 0.264
  Chirality :  0.040   0.130   1348
  Planarity :  0.004   0.049   1562
  Dihedral  :  4.040  19.531   1213
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.60 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.25), residues: 1091
  helix:  2.26 (0.26), residues: 428
  sheet:  0.76 (0.34), residues: 219
  loop : -1.40 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.013   0.001   PHE R 289 
 TYR   0.024   0.001   TYR R 145 
 ARG   0.007   0.000   ARG B 197 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A  279 ASN cc_start: 0.8612 (t0) cc_final: 0.8397 (t0)
REVERT: B   19 ARG cc_start: 0.6648 (ttp-170) cc_final: 0.6201 (ttp80)
REVERT: B   38 ASP cc_start: 0.7685 (p0) cc_final: 0.7256 (p0)
REVERT: B  152 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7993 (tt)
REVERT: B  234 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8059 (t80)
REVERT: P   17 ARG cc_start: 0.6591 (mmp-170) cc_final: 0.5707 (ttp-170)
REVERT: R  296 THR cc_start: 0.7843 (m) cc_final: 0.7553 (m)
REVERT: R  334 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5186 (ttm170)
REVERT: R  419 ARG cc_start: 0.6740 (ttp-170) cc_final: 0.6123 (tpp-160)
  outliers start: 13
  outliers final: 8
  residues processed: 94
  average time/residue: 1.3942
  time to fit residues: 139.9383
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  334 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    9.9990
   chunk 85 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.167543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.125329 restraints weight = 21274.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 4.21
r_work: 0.3134 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9028  Z= 0.198
  Angle     :  0.537   6.428  12223  Z= 0.288
  Chirality :  0.041   0.138   1348
  Planarity :  0.004   0.049   1562
  Dihedral  :  4.210  20.865   1213
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.60 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.25), residues: 1091
  helix:  2.14 (0.25), residues: 428
  sheet:  0.66 (0.34), residues: 220
  loop : -1.36 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.011   0.001   HIS A 357 
 PHE   0.020   0.002   PHE N 108 
 TYR   0.027   0.001   TYR R 145 
 ARG   0.007   0.000   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3272.48 seconds
wall clock time: 59 minutes 23.40 seconds (3563.40 seconds total)