Starting phenix.real_space_refine (version: dev)
on Fri Feb 17 19:49:49 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/02_2023/6z3z_11067.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/02_2023/6z3z_11067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/02_2023/6z3z_11067.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/02_2023/6z3z_11067.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/02_2023/6z3z_11067.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/02_2023/6z3z_11067.pdb"
  }
  resolution = 3.19
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Process input model

  Symmetric amino acids flipped
    Residue "B ARG   45": "NH1" <-> "NH2"
    Residue "B TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  129": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  207": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  282": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  286": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  292": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  307": "OE1" <-> "OE2"
    Residue "B PHE  324": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  328": "OE1" <-> "OE2"
    Residue "B PHE  340": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  350": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  367": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  446": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  451": "NH1" <-> "NH2"
    Residue "B GLU  454": "OE1" <-> "OE2"
    Residue "B PHE  476": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  486": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  487": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   41": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   45": "NH1" <-> "NH2"
    Residue "A TYR   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  134": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  203": "OD1" <-> "OD2"
    Residue "A PHE  207": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  225": "OE1" <-> "OE2"
    Residue "A GLU  239": "OE1" <-> "OE2"
    Residue "A TYR  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  282": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  286": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  292": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  328": "OE1" <-> "OE2"
    Residue "A PHE  365": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  367": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  373": "OE1" <-> "OE2"
    Residue "A PHE  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  405": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  451": "NH1" <-> "NH2"
    Residue "A TYR  486": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 6115
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3061
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3061
          Classifications: {'peptide': 385}
          Link IDs: {'PTRANS': 10, 'TRANS': 374}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 3054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3054
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 9, 'TRANS': 374}
          Chain breaks: 5
  Time building chain proxies: 3.86, per 1000 atoms: 0.63
  Number of scatterers: 6115
  At special positions: 0
  Unit cell: (77.8125, 87.15, 102.713, 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      44     16.00
     O    1019      8.00
     N     931      7.00
     C    4121      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 994.7 milliseconds
  

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      82.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 25 through 44
      removed outlier: 3.629A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LEU B  36 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 59
      removed outlier: 3.596A  pdb=" N   VAL B  57 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 66
      removed outlier: 3.862A  pdb=" N   LEU B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE B  65 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 60 through 66'
    Processing helix  chain 'B' and resid 125 through 129
    Processing helix  chain 'B' and resid 131 through 136
    Processing helix  chain 'B' and resid 139 through 149
      removed outlier: 3.674A  pdb=" N   HIS B 145 " --> pdb=" O   PRO B 141 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA B 146 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 165
    Processing helix  chain 'B' and resid 165 through 188
      removed outlier: 4.086A  pdb=" N   GLY B 169 " --> pdb=" O   TYR B 165 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   THR B 170 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLY B 178 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B 179 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   TYR B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   PHE B 184 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL B 185 " --> pdb=" O   MET B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 211
    Processing helix  chain 'B' and resid 216 through 227
    Processing helix  chain 'B' and resid 229 through 256
      removed outlier: 4.317A  pdb=" N   ASP B 244 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ALA B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL B 249 " --> pdb=" O   ALA B 245 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR B 252 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER B 253 " --> pdb=" O   VAL B 249 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B 254 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 303
      removed outlier: 3.622A  pdb=" N   ALA B 293 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 331
      removed outlier: 3.760A  pdb=" N   PHE B 324 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA B 327 " --> pdb=" O   ALA B 323 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLU B 328 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 341
      removed outlier: 3.571A  pdb=" N   LEU B 339 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 353
      removed outlier: 3.589A  pdb=" N   ALA B 346 " --> pdb=" O   GLY B 342 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   TYR B 350 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   ASN B 351 " --> pdb=" O   HIS B 347 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   LEU B 353 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 371
      removed outlier: 4.270A  pdb=" N   ARG B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS B 362 " --> pdb=" O   LYS B 358 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   MET B 368 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 385
      removed outlier: 4.085A  pdb=" N   VAL B 375 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   MET B 380 " --> pdb=" O   ILE B 376 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA B 383 " --> pdb=" O   TYR B 379 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B 384 " --> pdb=" O   MET B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 410
      removed outlier: 3.992A  pdb=" N   PHE B 405 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG B 408 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 422
      removed outlier: 3.827A  pdb=" N   GLY B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 431
      removed outlier: 3.843A  pdb=" N   PHE B 431 " --> pdb=" O   PRO B 428 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 428 through 431'
    Processing helix  chain 'B' and resid 432 through 438
      removed outlier: 4.246A  pdb=" N   MET B 436 " --> pdb=" O   GLN B 432 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   SER B 438 " --> pdb=" O   MET B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 450
      removed outlier: 3.837A  pdb=" N   LEU B 448 " --> pdb=" O   ILE B 444 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B 449 " --> pdb=" O   ALA B 445 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE B 450 " --> pdb=" O   PHE B 446 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 444 through 450'
    Processing helix  chain 'B' and resid 458 through 474
      removed outlier: 3.965A  pdb=" N   SER B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   TRP B 474 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 479
      removed outlier: 3.567A  pdb=" N   GLY B 478 " --> pdb=" O   TRP B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 488
    Processing helix  chain 'A' and resid 25 through 44
      removed outlier: 3.504A  pdb=" N   PHE A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU A  33 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 68
      removed outlier: 4.449A  pdb=" N   GLY A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LEU A  60 " --> pdb=" O   MET A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 128
      removed outlier: 3.555A  pdb=" N   THR A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 124 through 128'
    Processing helix  chain 'A' and resid 131 through 139
      removed outlier: 3.792A  pdb=" N   ASN A 136 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
      removed outlier: 3.537A  pdb=" N   ILE A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   HIS A 145 " --> pdb=" O   PRO A 141 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A 146 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 165
      removed outlier: 3.611A  pdb=" N   TYR A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 188
      removed outlier: 3.515A  pdb=" N   ILE A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   GLY A 178 " --> pdb=" O   CYS A 174 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A 185 " --> pdb=" O   MET A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 212
      removed outlier: 3.693A  pdb=" N   PHE A 206 " --> pdb=" O   THR A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 229 through 257
      removed outlier: 3.806A  pdb=" N   GLU A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL A 241 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASP A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 245 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TYR A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER A 253 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 303
      removed outlier: 3.930A  pdb=" N   SER A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 330
      removed outlier: 3.891A  pdb=" N   THR A 313 " --> pdb=" O   PRO A 309 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   GLY A 314 " --> pdb=" O   MET A 310 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   PHE A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 341
    Processing helix  chain 'A' and resid 343 through 348
      removed outlier: 3.764A  pdb=" N   HIS A 347 " --> pdb=" O   VAL A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 4.543A  pdb=" N   ARG A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 385
      removed outlier: 4.137A  pdb=" N   TYR A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   MET A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE A 385 " --> pdb=" O   GLY A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 391
      removed outlier: 3.766A  pdb=" N   ILE A 391 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 408
      removed outlier: 3.629A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   PHE A 405 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 406 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG A 408 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 420
    Processing helix  chain 'A' and resid 432 through 437
      removed outlier: 3.830A  pdb=" N   MET A 436 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE A 437 " --> pdb=" O   HIS A 433 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 432 through 437'
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 4.193A  pdb=" N   LEU A 448 " --> pdb=" O   ILE A 444 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA A 449 " --> pdb=" O   ALA A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 479
      removed outlier: 3.593A  pdb=" N   LEU A 468 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 475 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   PHE A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 488
      removed outlier: 4.182A  pdb=" N   GLU A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)

    346 hydrogen bonds defined for protein.
    1026 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: 1.59

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1758
        1.34 -     1.46: 1130
        1.46 -     1.57: 3318
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 6282
  Sorted by residual:
  bond pdb=" N   ARG A 408 "
       pdb=" CA  ARG A 408 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.32e-02 5.74e+03 7.60e+00
  bond pdb=" N   ARG B 441 "
       pdb=" CA  ARG B 441 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.19e-02 7.06e+03 7.32e+00
  bond pdb=" N   PHE B 129 "
       pdb=" CA  PHE B 129 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.92e+00
  bond pdb=" N   THR B 128 "
       pdb=" CA  THR B 128 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.030 1.32e-02 5.74e+03 5.13e+00
  bond pdb=" N   ASP B 130 "
       pdb=" CA  ASP B 130 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.41e-02 5.03e+03 5.09e+00
  ... (remaining 6277 not shown)

  Histogram of bond angle deviations from ideal:
       99.47 -   106.37: 127
      106.37 -   113.28: 3266
      113.28 -   120.18: 2424
      120.18 -   127.09: 2639
      127.09 -   133.99: 50
  Bond angle restraints: 8506
  Sorted by residual:
  angle pdb=" N   MET B 127 "
        pdb=" CA  MET B 127 "
        pdb=" C   MET B 127 "
      ideal   model   delta    sigma   weight residual
     112.87  108.14    4.73 1.20e+00 6.94e-01 1.56e+01
  angle pdb=" C   VAL B 228 "
        pdb=" N   ASP B 229 "
        pdb=" CA  ASP B 229 "
      ideal   model   delta    sigma   weight residual
     121.80  129.62   -7.82 2.44e+00 1.68e-01 1.03e+01
  angle pdb=" CA  GLU B 132 "
        pdb=" C   GLU B 132 "
        pdb=" O   GLU B 132 "
      ideal   model   delta    sigma   weight residual
     120.90  117.52    3.38 1.07e+00 8.73e-01 9.97e+00
  angle pdb=" CA  ARG B 441 "
        pdb=" C   ARG B 441 "
        pdb=" O   ARG B 441 "
      ideal   model   delta    sigma   weight residual
     120.65  116.93    3.72 1.23e+00 6.61e-01 9.17e+00
  angle pdb=" CB  ARG B 441 "
        pdb=" CG  ARG B 441 "
        pdb=" CD  ARG B 441 "
      ideal   model   delta    sigma   weight residual
     111.30  117.76   -6.46 2.30e+00 1.89e-01 7.88e+00
  ... (remaining 8501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3206
       17.91 -    35.81: 285
       35.81 -    53.72: 43
       53.72 -    71.63: 4
       71.63 -    89.53: 6
  Dihedral angle restraints: 3544
    sinusoidal: 1329
      harmonic: 2215
  Sorted by residual:
  dihedral pdb=" CA  ASP B 452 "
           pdb=" C   ASP B 452 "
           pdb=" N   THR B 453 "
           pdb=" CA  THR B 453 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.61   22.39     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CB  GLU B 483 "
           pdb=" CG  GLU B 483 "
           pdb=" CD  GLU B 483 "
           pdb=" OE1 GLU B 483 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.53   89.53     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU B 239 "
           pdb=" CG  GLU B 239 "
           pdb=" CD  GLU B 239 "
           pdb=" OE1 GLU B 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.34   87.34     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 3541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 597
       0.030 -    0.059: 292
       0.059 -    0.089: 63
       0.089 -    0.119: 23
       0.119 -    0.148: 6
  Chirality restraints: 981
  Sorted by residual:
  chirality pdb=" CA  MET B 127 "
            pdb=" N   MET B 127 "
            pdb=" C   MET B 127 "
            pdb=" CB  MET B 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  PRO B 131 "
            pdb=" N   PRO B 131 "
            pdb=" C   PRO B 131 "
            pdb=" CB  PRO B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.87   -0.15 2.00e-01 2.50e+01 5.39e-01
  chirality pdb=" CB  ILE A 450 "
            pdb=" CA  ILE A 450 "
            pdb=" CG1 ILE A 450 "
            pdb=" CG2 ILE A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 978 not shown)

  Planarity restraints: 1032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 308 "    0.039 5.00e-02 4.00e+02   5.94e-02 5.64e+00
        pdb=" N   PRO A 309 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 309 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 309 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 139 "    0.036 5.00e-02 4.00e+02   5.45e-02 4.76e+00
        pdb=" N   PRO B 140 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 140 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 140 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 413 "   -0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO A 414 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 414 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 414 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1029 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 356
        2.74 -     3.28: 6872
        3.28 -     3.82: 9676
        3.82 -     4.36: 11671
        4.36 -     4.90: 18847
  Nonbonded interactions: 47422
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 382 "
            pdb=" OG1 THR A 386 "
     model   vdw
     2.198 2.440
  nonbonded pdb=" N   GLU B 132 "
            pdb=" OE1 GLU B 132 "
     model   vdw
     2.202 2.520
  nonbonded pdb=" O   LYS A  42 "
            pdb=" NH1 ARG A  45 "
     model   vdw
     2.257 2.520
  nonbonded pdb=" O   LEU A 299 "
            pdb=" OG1 THR A 303 "
     model   vdw
     2.274 2.440
  nonbonded pdb=" OG  SER A 455 "
            pdb=" OE1 GLN A 459 "
     model   vdw
     2.283 2.440
  ... (remaining 47417 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 23 through 258 or resid 269 through 488))
}

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      44      5.16       5
     C    4121      2.51       5
     N     931      2.21       5
     O    1019      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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          3.610
  Check model and map are aligned:         0.100
  Process input model:                     19.730
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.070
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
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      :  0.003   0.051   6282  Z= 0.162
  Angle     :  0.621   8.408   8506  Z= 0.326
  Chirality :  0.037   0.148    981
  Planarity :  0.004   0.059   1032
  Dihedral  : 13.781  89.534   2114
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer Outliers :  0.31 %
  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 (0.32), residues: 745
  helix:  0.30 (0.23), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.12 (0.45), residues: 216

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 179
  time to evaluate  : 0.703 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1499
  time to fit residues: 36.7529
Evaluate side-chains
  135 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.675 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8707
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    0.4980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6282  Z= 0.247
  Angle     :  0.706   9.995   8506  Z= 0.362
  Chirality :  0.041   0.153    981
  Planarity :  0.004   0.053   1032
  Dihedral  :  4.416  21.249    801
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer Outliers :  1.69 %
  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: -0.17 (0.32), residues: 745
  helix:  0.49 (0.22), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.90 (0.49), residues: 179

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.740 
Fit side-chains
  outliers start: 11
  outliers final: 8
  residues processed: 153
  average time/residue: 0.1432
  time to fit residues: 30.7354
Evaluate side-chains
  142 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.796 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0721
  time to fit residues: 2.0439
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 411 ASN
A 433 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6282  Z= 0.250
  Angle     :  0.692   9.304   8506  Z= 0.350
  Chirality :  0.042   0.222    981
  Planarity :  0.004   0.055   1032
  Dihedral  :  4.639  18.648    801
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer Outliers :  1.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.32), residues: 745
  helix:  0.46 (0.22), residues: 573
  sheet:  None (None), residues: 0
  loop : -1.68 (0.53), residues: 172

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 0.725 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 164
  average time/residue: 0.1361
  time to fit residues: 31.5614
Evaluate side-chains
  142 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 138
  time to evaluate  : 0.895 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0682
  time to fit residues: 1.3960
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0010
   chunk 36 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.0388

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

Flipped N/Q/H residues before XYZ refinement:
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.4041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6282  Z= 0.212
  Angle     :  0.681   9.152   8506  Z= 0.340
  Chirality :  0.041   0.148    981
  Planarity :  0.004   0.057   1032
  Dihedral  :  4.579  18.035    801
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer Outliers :  2.47 %
  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: -0.03 (0.32), residues: 745
  helix:  0.53 (0.22), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.59 (0.52), residues: 179

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 9
  residues processed: 157
  average time/residue: 0.1366
  time to fit residues: 30.2781
Evaluate side-chains
  152 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.677 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0643
  time to fit residues: 1.9877
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 0 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6282  Z= 0.195
  Angle     :  0.701  10.661   8506  Z= 0.343
  Chirality :  0.041   0.169    981
  Planarity :  0.004   0.057   1032
  Dihedral  :  4.536  18.265    801
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer Outliers :  2.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.32), residues: 745
  helix:  0.56 (0.22), residues: 565
  sheet:  None (None), residues: 0
  loop : -1.60 (0.51), residues: 180

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 4
  residues processed: 160
  average time/residue: 0.1398
  time to fit residues: 31.3576
Evaluate side-chains
  153 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 149
  time to evaluate  : 0.738 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0609
  time to fit residues: 1.3971
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0970
   chunk 61 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6282  Z= 0.195
  Angle     :  0.687   8.620   8506  Z= 0.341
  Chirality :  0.041   0.147    981
  Planarity :  0.004   0.058   1032
  Dihedral  :  4.501  18.433    801
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 15.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer Outliers :  2.16 %
  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:  0.05 (0.32), residues: 745
  helix:  0.56 (0.22), residues: 571
  sheet:  None (None), residues: 0
  loop : -1.50 (0.53), residues: 174

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 0.949 
Fit side-chains
  outliers start: 14
  outliers final: 8
  residues processed: 170
  average time/residue: 0.1563
  time to fit residues: 37.6434
Evaluate side-chains
  151 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 0.772 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0591
  time to fit residues: 1.8086
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.4980
   chunk 43 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6282  Z= 0.202
  Angle     :  0.738  11.392   8506  Z= 0.360
  Chirality :  0.041   0.177    981
  Planarity :  0.004   0.057   1032
  Dihedral  :  4.488  18.243    801
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer Outliers :  2.16 %
  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:  0.08 (0.32), residues: 745
  helix:  0.53 (0.22), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.30 (0.54), residues: 173

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 0.761 
Fit side-chains
  outliers start: 14
  outliers final: 8
  residues processed: 161
  average time/residue: 0.1374
  time to fit residues: 31.1941
Evaluate side-chains
  151 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 0.773 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0752
  time to fit residues: 2.0554
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0370
   chunk 64 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6282  Z= 0.196
  Angle     :  0.724  10.780   8506  Z= 0.356
  Chirality :  0.041   0.153    981
  Planarity :  0.004   0.058   1032
  Dihedral  :  4.561  17.977    801
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer Outliers :  1.85 %
  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: -0.00 (0.32), residues: 745
  helix:  0.52 (0.22), residues: 574
  sheet:  None (None), residues: 0
  loop : -1.53 (0.52), residues: 171

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 4
  residues processed: 160
  average time/residue: 0.1434
  time to fit residues: 32.1932
Evaluate side-chains
  148 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.716 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0573
  time to fit residues: 1.4143
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.0770
   chunk 53 optimal weight:    0.5980
   chunk 20 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6282  Z= 0.205
  Angle     :  0.779  12.008   8506  Z= 0.374
  Chirality :  0.041   0.141    981
  Planarity :  0.004   0.058   1032
  Dihedral  :  4.486  17.646    801
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 17.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer Outliers :  1.08 %
  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: -0.03 (0.32), residues: 745
  helix:  0.53 (0.22), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.65 (0.52), residues: 173

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 145
  time to evaluate  : 0.761 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 147
  average time/residue: 0.1401
  time to fit residues: 29.0929
Evaluate side-chains
  145 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 141
  time to evaluate  : 0.683 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0692
  time to fit residues: 1.5455
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 388 GLN
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.4758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6282  Z= 0.221
  Angle     :  0.792  10.463   8506  Z= 0.384
  Chirality :  0.042   0.150    981
  Planarity :  0.005   0.057   1032
  Dihedral  :  4.555  18.715    801
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer Outliers :  0.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.32), residues: 745
  helix:  0.47 (0.22), residues: 573
  sheet:  None (None), residues: 0
  loop : -1.75 (0.51), residues: 172

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.791 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1375
  time to fit residues: 30.1915
Evaluate side-chains
  142 residues out of total 649 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.715 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9635
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.115313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.105108 restraints weight = 18528.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 3.95
r_work: 0.3686 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.5013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6282  Z= 0.281
  Angle     :  0.836  11.835   8506  Z= 0.410
  Chirality :  0.046   0.207    981
  Planarity :  0.005   0.055   1032
  Dihedral  :  4.864  21.021    801
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 21.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer Outliers :  0.31 %
  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: -0.20 (0.32), residues: 745
  helix:  0.45 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.86 (0.50), residues: 177

===============================================================================
Job complete
usr+sys time: 1583.43 seconds
wall clock time: 29 minutes 45.43 seconds (1785.43 seconds total)