Starting phenix.real_space_refine (version: dev)
on Mon Dec 12 05:07:20 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/12_2022/7tyo_26190_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/12_2022/7tyo_26190.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/12_2022/7tyo_26190.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/12_2022/7tyo_26190.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/12_2022/7tyo_26190_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/12_2022/7tyo_26190_updated.pdb"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   15": "OE1" <-> "OE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   20": "NH1" <-> "NH2"
    Residue "A GLU   27": "OE1" <-> "OE2"
    Residue "A ARG   42": "NH1" <-> "NH2"
    Residue "A ARG  228": "NH1" <-> "NH2"
    Residue "A ARG  231": "NH1" <-> "NH2"
    Residue "A ARG  265": "NH1" <-> "NH2"
    Residue "A ASP  274": "OD1" <-> "OD2"
    Residue "A ARG  385": "NH1" <-> "NH2"
    Residue "A GLU  392": "OE1" <-> "OE2"
    Residue "B GLU    3": "OE1" <-> "OE2"
    Residue "B GLU   10": "OE1" <-> "OE2"
    Residue "B ARG   46": "NH1" <-> "NH2"
    Residue "B ARG   96": "NH1" <-> "NH2"
    Residue "B GLU  172": "OE1" <-> "OE2"
    Residue "B ARG  214": "NH1" <-> "NH2"
    Residue "B GLU  226": "OE1" <-> "OE2"
    Residue "B ARG  304": "NH1" <-> "NH2"
    Residue "G GLU   42": "OE1" <-> "OE2"
    Residue "G GLU   58": "OE1" <-> "OE2"
    Residue "G ARG   62": "NH1" <-> "NH2"
    Residue "N GLU    6": "OE1" <-> "OE2"
    Residue "N GLU   46": "OE1" <-> "OE2"
    Residue "N TYR   60": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ARG   98": "NH1" <-> "NH2"
    Residue "R GLU  204": "OE1" <-> "OE2"
    Residue "R ARG  258": "NH1" <-> "NH2"
    Residue "R ARG  321": "NH1" <-> "NH2"
    Residue "R ARG  362": "NH1" <-> "NH2"
    Residue "R GLU  397": "OE1" <-> "OE2"
    Residue "R ARG  404": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib"
  Total number of atoms: 9052
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1889
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 2606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2606
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "P"
      Number of atoms: 239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 239
          Unusual residues: {'NH2': 1}
          Classifications: {'peptide': 32, 'undetermined': 1}
          Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 29}
    Chain: "R"
      Number of atoms: 2921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2921
          Unusual residues: {'NAG': 1, 'Y01': 2}
          Classifications: {'peptide': 359, 'undetermined': 3}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 14, 'TRANS': 344, None: 3}
            Not linked:
              pdbres="PHE R 409 "
              pdbres="NAG R 501 "
            Not linked:
              pdbres="NAG R 501 "
              pdbres="Y01 R 502 "
            Not linked:
              pdbres="Y01 R 502 "
              pdbres="Y01 R 503 "
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 208
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 97
  Time building chain proxies: 5.70, per 1000 atoms: 0.63
  Number of scatterers: 9052
  At special positions: 0
  Unit cell: (116.086, 100.547, 140.766, 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      64     16.00
     O    1646      8.00
     N    1561      7.00
     C    5781      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P   1 " - pdb=" SG  CYS P   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  55 " - pdb=" SG  CYS R  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  72 " - pdb=" SG  CYS R 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 219 " - pdb=" SG  CYS R 289 " 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
  Links applied
    NAG-ASN
      " NAG R 501 " - " ASN R 130 "
  Time building additional restraints: 3.42
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      36.7% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
    Processing helix  chain 'A' and resid 53 through 59
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.526A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 277
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 3.710A  pdb=" N   VAL A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 315
      No H-bonds generated for 'chain 'A' and resid 313 through 315'
    Processing helix  chain 'A' and resid 332 through 352
      removed outlier: 3.507A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 390
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 4.068A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 10 through 23
    Processing helix  chain 'G' and resid 30 through 43
      removed outlier: 3.516A  pdb=" N   TYR G  40 " --> pdb=" O   ASP G  36 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 29 through 31
      No H-bonds generated for 'chain 'N' and resid 29 through 31'
    Processing helix  chain 'N' and resid 62 through 64
      No H-bonds generated for 'chain 'N' and resid 62 through 64'
    Processing helix  chain 'N' and resid 88 through 90
      No H-bonds generated for 'chain 'N' and resid 88 through 90'
    Processing helix  chain 'P' and resid 8 through 19
      removed outlier: 3.556A  pdb=" N   LYS P  18 " --> pdb=" O   GLN P  14 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   PHE P  19 " --> pdb=" O   ASP P  15 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 59
    Processing helix  chain 'R' and resid 141 through 172
    Processing helix  chain 'R' and resid 174 through 176
      No H-bonds generated for 'chain 'R' and resid 174 through 176'
    Processing helix  chain 'R' and resid 179 through 204
      removed outlier: 3.671A  pdb=" N   LEU R 183 " --> pdb=" O   GLN R 179 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE R 199 " --> pdb=" O   SER R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 214
    Processing helix  chain 'R' and resid 217 through 248
      removed outlier: 3.666A  pdb=" N   MET R 237 " --> pdb=" O   ASN R 233 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 266
    Processing helix  chain 'R' and resid 269 through 283
      Proline residue:  R 273  - end of helix
      removed outlier: 3.773A  pdb=" N   ILE R 276 " --> pdb=" O   PRO R 273 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA R 278 " --> pdb=" O   THR R 275 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE R 279 " --> pdb=" O   ILE R 276 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG R 281 " --> pdb=" O   ALA R 278 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL R 283 " --> pdb=" O   THR R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 290
      No H-bonds generated for 'chain 'R' and resid 288 through 290'
    Processing helix  chain 'R' and resid 297 through 328
      removed outlier: 3.922A  pdb=" N   HIS R 302 " --> pdb=" O   TYR R 299 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   GLY R 303 " --> pdb=" O   ILE R 300 " (cutoff:3.500A)
      Proline residue:  R 304  - end of helix
      removed outlier: 3.710A  pdb=" N   LEU R 317 " --> pdb=" O   PHE R 314 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE R 319 " --> pdb=" O   LEU R 316 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL R 320 " --> pdb=" O   LEU R 317 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU R 323 " --> pdb=" O   VAL R 320 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL R 324 " --> pdb=" O   ARG R 321 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS R 326 " --> pdb=" O   LEU R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 334 through 352
      removed outlier: 4.353A  pdb=" N   LEU R 339 " --> pdb=" O   SER R 335 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL R 342 " --> pdb=" O   TYR R 338 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS R 343 " --> pdb=" O   LEU R 339 " (cutoff:3.500A)
      Proline residue:  R 350  - end of helix
    Processing helix  chain 'R' and resid 354 through 358
      removed outlier: 3.993A  pdb=" N   VAL R 358 " --> pdb=" O   GLN R 355 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 381
    Processing helix  chain 'R' and resid 383 through 391
    Processing helix  chain 'R' and resid 396 through 408
      removed outlier: 3.526A  pdb=" N   THR R 401 " --> pdb=" O   GLU R 397 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG R 404 " --> pdb=" O   THR R 400 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA R 407 " --> pdb=" O   LYS R 403 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 359 through 363
      removed outlier: 7.245A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   ASN A 218 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   HIS A 220 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   LEU A  45 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.993A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.699A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.642A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.826A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.503A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.578A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.551A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.061A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU N  45 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'R' and resid 75 through 77
      removed outlier: 3.651A  pdb=" N   THR R  75 " --> pdb=" O   TRP R  82 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TRP R  82 " --> pdb=" O   THR R  75 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU R  80 " --> pdb=" O   ASP R  77 " (cutoff:3.500A)

    377 hydrogen bonds defined for protein.
    1014 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.86

  Time building geometry restraints manager: 3.73 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1454
        1.32 -     1.44: 2621
        1.44 -     1.57: 5100
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 9265
  Sorted by residual:
  bond pdb=" N   LYS A 280 "
       pdb=" CA  LYS A 280 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.27e-02 6.20e+03 6.96e+00
  bond pdb=" N   THR A 285 "
       pdb=" CA  THR A 285 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.22e-02 6.72e+03 5.00e+00
  bond pdb=" N   ASP A 284 "
       pdb=" CA  ASP A 284 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.16e-02 7.43e+03 4.80e+00
  bond pdb=" N   LYS A 271 "
       pdb=" CA  LYS A 271 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.23e-02 6.61e+03 4.23e+00
  bond pdb=" C   VAL R 206 "
       pdb=" N   PRO R 207 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 9.40e-03 1.13e+04 3.79e+00
  ... (remaining 9260 not shown)

  Histogram of bond angle deviations from ideal:
       99.62 -   106.50: 232
      106.50 -   113.38: 4992
      113.38 -   120.26: 3361
      120.26 -   127.14: 3884
      127.14 -   134.02: 108
  Bond angle restraints: 12577
  Sorted by residual:
  angle pdb=" CA  PRO P  32 "
        pdb=" N   PRO P  32 "
        pdb=" CD  PRO P  32 "
      ideal   model   delta    sigma   weight residual
     112.00  105.03    6.97 1.40e+00 5.10e-01 2.48e+01
  angle pdb=" CA  ASP A 274 "
        pdb=" C   ASP A 274 "
        pdb=" O   ASP A 274 "
      ideal   model   delta    sigma   weight residual
     120.82  117.05    3.77 1.05e+00 9.07e-01 1.29e+01
  angle pdb=" N   VAL R 357 "
        pdb=" CA  VAL R 357 "
        pdb=" C   VAL R 357 "
      ideal   model   delta    sigma   weight residual
     112.96  109.57    3.39 1.00e+00 1.00e+00 1.15e+01
  angle pdb=" C   ILE R 248 "
        pdb=" N   VAL R 249 "
        pdb=" CA  VAL R 249 "
      ideal   model   delta    sigma   weight residual
     122.97  120.20    2.77 9.80e-01 1.04e+00 7.99e+00
  angle pdb=" N   ALA A 226 "
        pdb=" CA  ALA A 226 "
        pdb=" C   ALA A 226 "
      ideal   model   delta    sigma   weight residual
     109.39  113.75   -4.36 1.59e+00 3.96e-01 7.53e+00
  ... (remaining 12572 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5049
       17.91 -    35.81: 316
       35.81 -    53.72: 73
       53.72 -    71.63: 14
       71.63 -    89.53: 7
  Dihedral angle restraints: 5459
    sinusoidal: 2135
      harmonic: 3324
  Sorted by residual:
  dihedral pdb=" CB  CYS P   1 "
           pdb=" SG  CYS P   1 "
           pdb=" SG  CYS P   7 "
           pdb=" CB  CYS P   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.74   42.26     1      1.00e+01 1.00e-02 2.49e+01
  dihedral pdb=" CB  CYS R 219 "
           pdb=" SG  CYS R 219 "
           pdb=" SG  CYS R 289 "
           pdb=" CB  CYS R 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.76   39.24     1      1.00e+01 1.00e-02 2.16e+01
  dihedral pdb=" CB  CYS R  55 "
           pdb=" SG  CYS R  55 "
           pdb=" SG  CYS R  81 "
           pdb=" CB  CYS R  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.65   35.65     1      1.00e+01 1.00e-02 1.80e+01
  ... (remaining 5456 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1101
       0.044 -    0.089: 232
       0.089 -    0.133: 63
       0.133 -    0.177: 4
       0.177 -    0.222: 1
  Chirality restraints: 1401
  Sorted by residual:
  chirality pdb=" CBE Y01 R 503 "
            pdb=" CAP Y01 R 503 "
            pdb=" CBB Y01 R 503 "
            pdb=" CBI Y01 R 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.35    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  LYS A 280 "
            pdb=" N   LYS A 280 "
            pdb=" C   LYS A 280 "
            pdb=" CB  LYS A 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.65e-01
  chirality pdb=" CA  PRO P  32 "
            pdb=" N   PRO P  32 "
            pdb=" C   PRO P  32 "
            pdb=" CB  PRO P  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.07e-01
  ... (remaining 1398 not shown)

  Planarity restraints: 1595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA P  31 "   -0.082 5.00e-02 4.00e+02   1.20e-01 2.32e+01
        pdb=" N   PRO P  32 "    0.208 5.00e-02 4.00e+02
        pdb=" CA  PRO P  32 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO P  32 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 138 "   -0.026 5.00e-02 4.00e+02   3.86e-02 2.38e+00
        pdb=" N   PRO R 139 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO R 139 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 139 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.023 5.00e-02 4.00e+02   3.55e-02 2.01e+00
        pdb=" N   PRO B 236 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1592 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 289
        2.72 -     3.27: 9140
        3.27 -     3.81: 14641
        3.81 -     4.36: 19346
        4.36 -     4.90: 31762
  Nonbonded interactions: 75178
  Sorted by model distance:
  nonbonded pdb=" OH  TYR P  12 "
            pdb=" O   ALA R 145 "
     model   vdw
     2.176 2.440
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.236 2.440
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.294 2.440
  nonbonded pdb=" OH  TYR R 149 "
            pdb=" O   LEU R 202 "
     model   vdw
     2.294 2.440
  nonbonded pdb=" O   PRO R 270 "
            pdb=" OG1 THR R 274 "
     model   vdw
     2.306 2.440
  ... (remaining 75173 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    5781      2.51       5
     N    1561      2.21       5
     O    1646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  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:          4.490
  Check model and map are aligned:         0.140
  Convert atoms to be neutral:             0.070
  Process input model:                     27.490
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:13.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
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   0.034   9265  Z= 0.129
  Angle     :  0.463   6.965  12577  Z= 0.287
  Chirality :  0.039   0.222   1401
  Planarity :  0.004   0.120   1594
  Dihedral  : 12.827  89.532   3290
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer Outliers :  1.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.21), residues: 1121
  helix: -2.90 (0.16), residues: 427
  sheet: -0.61 (0.31), residues: 239
  loop : -1.84 (0.27), residues: 455

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 160
  time to evaluate  : 1.134 
Fit side-chains
  outliers start: 13
  outliers final: 7
  residues processed: 169
  average time/residue: 1.3205
  time to fit residues: 237.0750
Evaluate side-chains
  119 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 1.163 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 6
  residues processed: 1
  average time/residue: 1.5273
  time to fit residues: 3.3051
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 64 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  31 GLN
A 294 GLN
B  17 GLN
B  36 ASN
B  75 GLN
G  24 ASN
N   5 GLN
N  13 GLN
P  14 GLN
R 135 ASN
R 144 ASN
R 179 GLN
R 201 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9265  Z= 0.204
  Angle     :  0.538   7.161  12577  Z= 0.290
  Chirality :  0.042   0.192   1401
  Planarity :  0.005   0.059   1594
  Dihedral  :  4.708  52.416   1271
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer Outliers :  4.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.24), residues: 1121
  helix: -0.31 (0.23), residues: 432
  sheet: -0.38 (0.31), residues: 237
  loop : -1.35 (0.28), residues: 452

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 1.155 
Fit side-chains
  outliers start: 39
  outliers final: 17
  residues processed: 146
  average time/residue: 1.2161
  time to fit residues: 189.5392
Evaluate side-chains
  126 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.981 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 13
  residues processed: 4
  average time/residue: 0.6181
  time to fit residues: 4.1557
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 100 optimal weight:    0.6980
   chunk 109 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
P  24 GLN
R 179 GLN
R 405 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9265  Z= 0.134
  Angle     :  0.460   5.571  12577  Z= 0.247
  Chirality :  0.040   0.183   1401
  Planarity :  0.003   0.048   1594
  Dihedral  :  4.458  48.079   1271
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer Outliers :  3.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.25), residues: 1121
  helix:  0.78 (0.25), residues: 432
  sheet:  0.12 (0.33), residues: 211
  loop : -1.16 (0.27), residues: 478

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 116
  time to evaluate  : 1.057 
Fit side-chains
  outliers start: 34
  outliers final: 18
  residues processed: 140
  average time/residue: 1.1028
  time to fit residues: 165.9729
Evaluate side-chains
  129 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.096 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 16
  residues processed: 2
  average time/residue: 0.6157
  time to fit residues: 2.8005
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0870
   chunk 48 optimal weight:    0.0370
   chunk 67 optimal weight:    9.9990
   chunk 101 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 89 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    0.9240

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9265  Z= 0.138
  Angle     :  0.470   6.433  12577  Z= 0.250
  Chirality :  0.041   0.183   1401
  Planarity :  0.003   0.042   1594
  Dihedral  :  4.423  44.187   1271
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer Outliers :  3.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.25), residues: 1121
  helix:  1.16 (0.26), residues: 433
  sheet:  0.24 (0.33), residues: 211
  loop : -0.98 (0.28), residues: 477

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 109
  time to evaluate  : 1.089 
Fit side-chains
  outliers start: 37
  outliers final: 22
  residues processed: 134
  average time/residue: 1.1775
  time to fit residues: 169.0828
Evaluate side-chains
  118 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 1.051 
Switching outliers to nearest non-outliers
  outliers start: 22
  outliers final: 17
  residues processed: 5
  average time/residue: 0.8959
  time to fit residues: 6.3276
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 79 optimal weight:   30.0000
   chunk 44 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.9988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9265  Z= 0.208
  Angle     :  0.526   6.599  12577  Z= 0.280
  Chirality :  0.043   0.200   1401
  Planarity :  0.004   0.064   1594
  Dihedral  :  4.815  49.107   1271
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer Outliers :  3.38 %
  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: 1121
  helix:  1.16 (0.26), residues: 434
  sheet:  0.17 (0.34), residues: 210
  loop : -1.03 (0.27), residues: 477

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 1.018 
Fit side-chains
  outliers start: 32
  outliers final: 22
  residues processed: 131
  average time/residue: 1.2361
  time to fit residues: 173.1698
Evaluate side-chains
  123 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 1.109 
Switching outliers to nearest non-outliers
  outliers start: 22
  outliers final: 20
  residues processed: 2
  average time/residue: 0.6103
  time to fit residues: 2.7283
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 35 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.2186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9265  Z= 0.152
  Angle     :  0.478   6.847  12577  Z= 0.254
  Chirality :  0.041   0.185   1401
  Planarity :  0.003   0.050   1594
  Dihedral  :  4.625  45.058   1271
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer Outliers :  3.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.25), residues: 1121
  helix:  1.33 (0.26), residues: 434
  sheet:  0.23 (0.34), residues: 210
  loop : -0.91 (0.28), residues: 477

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 1.037 
Fit side-chains
  outliers start: 32
  outliers final: 21
  residues processed: 133
  average time/residue: 1.2278
  time to fit residues: 174.6152
Evaluate side-chains
  121 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 1.053 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 20
  residues processed: 1
  average time/residue: 0.1325
  time to fit residues: 1.6505
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 90 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 106 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0570
   chunk 42 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    1.6106

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9265  Z= 0.182
  Angle     :  0.508   8.019  12577  Z= 0.270
  Chirality :  0.042   0.188   1401
  Planarity :  0.004   0.044   1594
  Dihedral  :  4.733  45.038   1271
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer Outliers :  4.02 %
  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:  0.26 (0.25), residues: 1121
  helix:  1.32 (0.26), residues: 434
  sheet:  0.25 (0.34), residues: 210
  loop : -0.91 (0.28), residues: 477

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 105
  time to evaluate  : 1.073 
Fit side-chains
  outliers start: 38
  outliers final: 24
  residues processed: 135
  average time/residue: 1.2069
  time to fit residues: 174.4768
Evaluate side-chains
  127 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 1.082 
Switching outliers to nearest non-outliers
  outliers start: 24
  outliers final: 21
  residues processed: 3
  average time/residue: 0.7401
  time to fit residues: 3.9134
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0870
   chunk 102 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.9964

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9265  Z= 0.141
  Angle     :  0.475   7.174  12577  Z= 0.252
  Chirality :  0.041   0.185   1401
  Planarity :  0.003   0.043   1594
  Dihedral  :  4.575  41.644   1271
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer Outliers :  3.28 %
  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:  0.48 (0.25), residues: 1121
  helix:  1.48 (0.26), residues: 434
  sheet:  0.39 (0.34), residues: 212
  loop : -0.77 (0.28), residues: 475

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 1.069 
Fit side-chains
  outliers start: 31
  outliers final: 21
  residues processed: 128
  average time/residue: 1.1955
  time to fit residues: 163.8055
Evaluate side-chains
  121 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.971 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 19
  residues processed: 2
  average time/residue: 0.0765
  time to fit residues: 1.6477
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 65 optimal weight:    0.3980
   chunk 105 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0040
   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 405 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9265  Z= 0.134
  Angle     :  0.479   9.256  12577  Z= 0.251
  Chirality :  0.040   0.184   1401
  Planarity :  0.003   0.042   1594
  Dihedral  :  4.481  38.915   1271
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer Outliers :  2.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1121
  helix:  1.56 (0.26), residues: 433
  sheet:  0.44 (0.34), residues: 211
  loop : -0.69 (0.28), residues: 477

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 1.056 
Fit side-chains
  outliers start: 20
  outliers final: 19
  residues processed: 122
  average time/residue: 1.2006
  time to fit residues: 157.3693
Evaluate side-chains
  116 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 1.087 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 19
  residues processed: 0
  time to fit residues: 1.4077
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 73 optimal weight:    8.9990
   chunk 110 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 68 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9265  Z= 0.176
  Angle     :  0.512   8.799  12577  Z= 0.269
  Chirality :  0.042   0.189   1401
  Planarity :  0.004   0.043   1594
  Dihedral  :  4.684  40.215   1271
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer Outliers :  2.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1121
  helix:  1.45 (0.26), residues: 434
  sheet:  0.28 (0.34), residues: 212
  loop : -0.82 (0.28), residues: 475

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 1.042 
Fit side-chains
  outliers start: 22
  outliers final: 20
  residues processed: 122
  average time/residue: 1.2524
  time to fit residues: 163.4128
Evaluate side-chains
  119 residues out of total 992 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.070 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 19
  residues processed: 1
  average time/residue: 1.6353
  time to fit residues: 3.2188
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0010
   chunk 24 optimal weight:    0.3980
   chunk 88 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 11 optimal weight:    0.4980
   chunk 16 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
R 179 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.165735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.128668 restraints weight = 10823.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.90
r_work: 0.3405 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9265  Z= 0.121
  Angle     :  0.459   7.989  12577  Z= 0.243
  Chirality :  0.040   0.184   1401
  Planarity :  0.003   0.041   1594
  Dihedral  :  4.391  37.716   1271
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer Outliers :  2.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1121
  helix:  1.71 (0.26), residues: 433
  sheet:  0.53 (0.34), residues: 211
  loop : -0.64 (0.28), residues: 477

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Job complete
usr+sys time: 3451.67 seconds
wall clock time: 62 minutes 1.06 seconds (3721.06 seconds total)