Starting phenix.real_space_refine (version: dev)
on Fri Feb 17 19:49:30 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/02_2023/6z3y_11066.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/02_2023/6z3y_11066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/02_2023/6z3y_11066.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/02_2023/6z3y_11066.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/02_2023/6z3y_11066.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/02_2023/6z3y_11066.pdb"
  }
  resolution = 3.51
  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=   0.003
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   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  134": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  167": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  239": "OE1" <-> "OE2"
    Residue "B TYR  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  286": "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  367": "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 "A PHE   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   41": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   45": "NH1" <-> "NH2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  134": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  167": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  207": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  239": "OE1" <-> "OE2"
    Residue "A TYR  252": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  286": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  292": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  316": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  365": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  367": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  401": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  431": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  451": "NH1" <-> "NH2"
    Residue "A PHE  462": "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: 6131
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 3069
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 11, 'TRANS': 374}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 3062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3062
          Classifications: {'peptide': 385}
          Link IDs: {'PTRANS': 10, 'TRANS': 374}
          Chain breaks: 5
  Time building chain proxies: 4.05, per 1000 atoms: 0.66
  Number of scatterers: 6131
  At special positions: 0
  Unit cell: (76.775, 87.15, 106.862, 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      46     16.00
     O    1015      8.00
     N     933      7.00
     C    4137      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: 2.48
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1438

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 0 sheets defined
      83.8% 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: 4.148A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B  32 " --> pdb=" O   ASN B  28 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU B  33 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE B  41 " --> pdb=" O   THR B  37 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS B  42 " --> pdb=" O   ILE B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 56
      No H-bonds generated for 'chain 'B' and resid 54 through 56'
    Processing helix  chain 'B' and resid 57 through 66
      removed outlier: 4.473A  pdb=" N   ILE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE B  65 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 129
      removed outlier: 3.664A  pdb=" N   MET B 127 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE B 129 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 139
      removed outlier: 3.606A  pdb=" N   PHE B 135 " --> pdb=" O   PRO B 131 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASN B 136 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL B 137 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 148
      removed outlier: 3.593A  pdb=" N   ALA B 146 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 167
      removed outlier: 3.604A  pdb=" N   PHE B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 188
      removed outlier: 3.798A  pdb=" N   GLY B 178 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TYR B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL B 185 " --> pdb=" O   MET B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 212
    Processing helix  chain 'B' and resid 216 through 227
      removed outlier: 3.730A  pdb=" N   HIS B 227 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 256
      removed outlier: 4.125A  pdb=" N   ASP B 244 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   ALA B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL B 249 " --> pdb=" O   ALA B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 303
      removed outlier: 4.235A  pdb=" N   SER B 274 " --> pdb=" O   ALA B 270 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR B 292 " --> pdb=" O   MET B 288 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA B 293 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 307
      removed outlier: 3.882A  pdb=" N   GLU B 307 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 304 through 307'
    Processing helix  chain 'B' and resid 308 through 331
      removed outlier: 3.910A  pdb=" N   GLU B 328 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 341
    Processing helix  chain 'B' and resid 343 through 348
      removed outlier: 3.627A  pdb=" N   HIS B 347 " --> pdb=" O   VAL B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 370
      removed outlier: 4.041A  pdb=" N   ARG B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 386
      removed outlier: 4.162A  pdb=" N   VAL B 375 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TYR B 379 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   MET B 380 " --> pdb=" O   ILE B 376 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LEU B 384 " --> pdb=" O   MET B 380 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 410
      removed outlier: 3.508A  pdb=" N   ALA B 400 " --> pdb=" O   PHE B 396 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE B 405 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG B 408 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 409 " --> pdb=" O   PHE B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 422
      removed outlier: 4.156A  pdb=" N   GLY B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 4.236A  pdb=" N   ALA B 447 " --> pdb=" O   ALA B 443 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU B 448 " --> pdb=" O   ILE B 444 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE B 450 " --> pdb=" O   PHE B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 479
      removed outlier: 3.859A  pdb=" N   MET B 461 " --> pdb=" O   PRO B 457 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR B 464 " --> pdb=" O   MET B 460 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   VAL B 475 " --> pdb=" O   PHE B 471 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   PHE B 476 " --> pdb=" O   THR B 472 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLY B 477 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 487
      removed outlier: 4.410A  pdb=" N   LEU B 487 " --> pdb=" O   MET B 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 44
      removed outlier: 3.682A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU A  31 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ILE A  32 " --> pdb=" O   ASN A  28 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A  33 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   THR A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE A  41 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 56
      No H-bonds generated for 'chain 'A' and resid 54 through 56'
    Processing helix  chain 'A' and resid 57 through 68
      removed outlier: 3.616A  pdb=" N   TYR A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 129
      removed outlier: 3.664A  pdb=" N   MET A 127 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE A 129 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 139
      removed outlier: 3.805A  pdb=" N   ASN A 136 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 158 through 165
    Processing helix  chain 'A' and resid 165 through 189
      removed outlier: 3.923A  pdb=" N   GLY A 169 " --> pdb=" O   TYR A 165 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   THR A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLY A 178 " --> pdb=" O   CYS A 174 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 212
      removed outlier: 3.713A  pdb=" N   CYS A 204 " --> pdb=" O   HIS A 200 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   SER A 212 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 229 through 254
      removed outlier: 3.618A  pdb=" N   LEU A 235 " --> pdb=" O   ASP A 231 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   GLY A 238 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ASP A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 257
      No H-bonds generated for 'chain 'A' and resid 255 through 257'
    Processing helix  chain 'A' and resid 271 through 303
      removed outlier: 4.494A  pdb=" N   VAL A 275 " --> pdb=" O   PHE A 271 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   GLY A 276 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   PHE A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   THR A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 331
      removed outlier: 3.655A  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 342 through 348
      removed outlier: 3.971A  pdb=" N   ALA A 346 " --> pdb=" O   GLY A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 4.008A  pdb=" N   ARG A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 383
      removed outlier: 4.477A  pdb=" N   TYR A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   MET A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLY A 381 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A 382 " --> pdb=" O   CYS A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 391
      removed outlier: 3.532A  pdb=" N   ILE A 391 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 411
      removed outlier: 3.893A  pdb=" N   PHE A 405 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 406 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASN A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 422
      removed outlier: 3.509A  pdb=" N   LEU A 415 " --> pdb=" O   ASN A 411 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LEU A 418 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 437
      removed outlier: 3.815A  pdb=" N   MET A 436 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 450
      removed outlier: 3.854A  pdb=" N   ALA A 447 " --> pdb=" O   ALA A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 479
      removed outlier: 3.737A  pdb=" N   THR A 464 " --> pdb=" O   MET A 460 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 468 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A 475 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 488

    352 hydrogen bonds defined for protein.
    1050 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: 1.71

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1786
        1.34 -     1.46: 1696
        1.46 -     1.58: 2738
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 6300
  Sorted by residual:
  bond pdb=" N   ILE B 133 "
       pdb=" CA  ILE B 133 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.78e+00
  bond pdb=" N   VAL B 137 "
       pdb=" CA  VAL B 137 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.039 1.41e-02 5.03e+03 7.59e+00
  bond pdb=" N   ASN B 136 "
       pdb=" CA  ASN B 136 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.10e+00
  bond pdb=" N   GLU B 132 "
       pdb=" CA  GLU B 132 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.27e-02 6.20e+03 5.82e+00
  bond pdb=" N   PHE B 134 "
       pdb=" CA  PHE B 134 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.69e+00
  ... (remaining 6295 not shown)

  Histogram of bond angle deviations from ideal:
      100.00 -   106.80: 145
      106.80 -   113.60: 3359
      113.60 -   120.40: 2505
      120.40 -   127.20: 2473
      127.20 -   133.99: 54
  Bond angle restraints: 8536
  Sorted by residual:
  angle pdb=" CA  GLU A 239 "
        pdb=" C   GLU A 239 "
        pdb=" O   GLU A 239 "
      ideal   model   delta    sigma   weight residual
     120.55  117.31    3.24 1.06e+00 8.90e-01 9.33e+00
  angle pdb=" O   ILE B 133 "
        pdb=" C   ILE B 133 "
        pdb=" N   PHE B 134 "
      ideal   model   delta    sigma   weight residual
     121.87  124.67   -2.80 9.70e-01 1.06e+00 8.31e+00
  angle pdb=" CA  GLU B 239 "
        pdb=" C   GLU B 239 "
        pdb=" O   GLU B 239 "
      ideal   model   delta    sigma   weight residual
     120.42  117.44    2.98 1.06e+00 8.90e-01 7.92e+00
  angle pdb=" C   ARG A 451 "
        pdb=" N   ASP A 452 "
        pdb=" CA  ASP A 452 "
      ideal   model   delta    sigma   weight residual
     121.54  126.33   -4.79 1.91e+00 2.74e-01 6.28e+00
  angle pdb=" CA  ASN B 136 "
        pdb=" C   ASN B 136 "
        pdb=" O   ASN B 136 "
      ideal   model   delta    sigma   weight residual
     120.55  117.92    2.63 1.06e+00 8.90e-01 6.17e+00
  ... (remaining 8531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 3335
       17.41 -    34.82: 179
       34.82 -    52.23: 37
       52.23 -    69.64: 3
       69.64 -    87.05: 6
  Dihedral angle restraints: 3560
    sinusoidal: 1337
      harmonic: 2223
  Sorted by residual:
  dihedral pdb=" CA  PHE B 129 "
           pdb=" C   PHE B 129 "
           pdb=" N   ASP B 130 "
           pdb=" CA  ASP B 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.91   19.09     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  PHE A 129 "
           pdb=" C   PHE A 129 "
           pdb=" N   ASP A 130 "
           pdb=" CA  ASP A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.91   19.09     0      5.00e+00 4.00e-02 1.46e+01
  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  163.95   16.05     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 3557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 596
       0.031 -    0.062: 307
       0.062 -    0.093: 71
       0.093 -    0.124: 15
       0.124 -    0.155: 2
  Chirality restraints: 991
  Sorted by residual:
  chirality pdb=" CA  GLU A 239 "
            pdb=" N   GLU A 239 "
            pdb=" C   GLU A 239 "
            pdb=" CB  GLU A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CA  ILE B 133 "
            pdb=" N   ILE B 133 "
            pdb=" C   ILE B 133 "
            pdb=" CB  ILE B 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" CA  ASP A 229 "
            pdb=" N   ASP A 229 "
            pdb=" C   ASP A 229 "
            pdb=" CB  ASP A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.33e-01
  ... (remaining 988 not shown)

  Planarity restraints: 1030
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 139 "    0.036 5.00e-02 4.00e+02   5.41e-02 4.69e+00
        pdb=" N   PRO B 140 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 140 "    0.027 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   LEU A 139 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A 140 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 140 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 140 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 131 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   PRO B 131 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   PRO B 131 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLU B 132 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1027 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1681
        2.80 -     3.32: 6544
        3.32 -     3.85: 9741
        3.85 -     4.37: 11818
        4.37 -     4.90: 18863
  Nonbonded interactions: 48647
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 382 "
            pdb=" OG1 THR B 386 "
     model   vdw
     2.269 2.440
  nonbonded pdb=" O   GLY A 477 "
            pdb=" OG1 THR A 480 "
     model   vdw
     2.281 2.440
  nonbonded pdb=" OG  SER A 455 "
            pdb=" OE1 GLN A 459 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" O   TYR A 350 "
            pdb=" NZ  LYS A 358 "
     model   vdw
     2.292 2.520
  nonbonded pdb=" O   TYR B 350 "
            pdb=" NZ  LYS B 358 "
     model   vdw
     2.293 2.520
  ... (remaining 48642 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 489))
}

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      46      5.16       5
     C    4137      2.51       5
     N     933      2.21       5
     O    1015      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 group one per residue
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:             1.100
  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:          3.620
  Check model and map are aligned:         0.090
  Process input model:                     20.250
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Set scattering table:                    0.060
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
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   0.039   6300  Z= 0.133
  Angle     :  0.523   6.361   8536  Z= 0.292
  Chirality :  0.037   0.155    991
  Planarity :  0.003   0.054   1030
  Dihedral  : 11.752  87.051   2122
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer Outliers :  1.68 %
  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:  0.09 (0.32), residues: 747
  helix:  0.77 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.47 (0.45), residues: 231

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 1
  residues processed: 186
  average time/residue: 0.1783
  time to fit residues: 43.6803
Evaluate side-chains
  126 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.768 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0620
  time to fit residues: 1.1667
-------------------------------------------------------------------------------
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:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 69 optimal weight:    0.1980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6300  Z= 0.254
  Angle     :  0.784  10.723   8536  Z= 0.386
  Chirality :  0.044   0.183    991
  Planarity :  0.005   0.053   1030
  Dihedral  :  4.601  18.203    801
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer Outliers :  2.45 %
  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: -0.35 (0.32), residues: 747
  helix:  0.39 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.77 (0.49), residues: 205

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 9
  residues processed: 143
  average time/residue: 0.1444
  time to fit residues: 28.6185
Evaluate side-chains
  126 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.714 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0582
  time to fit residues: 1.9038
-------------------------------------------------------------------------------
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:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0980
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
B 369 ASN
B 390 HIS
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 432 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6300  Z= 0.197
  Angle     :  0.701   9.869   8536  Z= 0.350
  Chirality :  0.042   0.173    991
  Planarity :  0.004   0.056   1030
  Dihedral  :  4.636  18.995    801
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer Outliers :  2.30 %
  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: -0.57 (0.31), residues: 747
  helix:  0.23 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.82 (0.48), residues: 209

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 6
  residues processed: 141
  average time/residue: 0.1663
  time to fit residues: 32.9743
Evaluate side-chains
  124 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.761 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0834
  time to fit residues: 2.0061
-------------------------------------------------------------------------------
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:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 389 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6300  Z= 0.185
  Angle     :  0.686  11.477   8536  Z= 0.339
  Chirality :  0.041   0.143    991
  Planarity :  0.004   0.058   1030
  Dihedral  :  4.619  18.253    801
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer Outliers :  2.14 %
  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: -0.70 (0.32), residues: 747
  helix:  0.15 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.98 (0.49), residues: 203

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 9
  residues processed: 136
  average time/residue: 0.1445
  time to fit residues: 27.3674
Evaluate side-chains
  128 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.693 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0650
  time to fit residues: 1.9922
-------------------------------------------------------------------------------
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:    0.0570
   chunk 41 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.9500

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6300  Z= 0.186
  Angle     :  0.690  12.056   8536  Z= 0.342
  Chirality :  0.042   0.167    991
  Planarity :  0.004   0.056   1030
  Dihedral  :  4.646  18.301    801
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer Outliers :  1.68 %
  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 (0.32), residues: 747
  helix:  0.21 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -1.96 (0.51), residues: 194

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 2
  residues processed: 136
  average time/residue: 0.1514
  time to fit residues: 28.5569
Evaluate side-chains
  115 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.715 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0782
  time to fit residues: 1.2270
-------------------------------------------------------------------------------
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:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0980
   chunk 43 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 38 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   overall best weight:    1.2188

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6300  Z= 0.200
  Angle     :  0.701  12.325   8536  Z= 0.347
  Chirality :  0.043   0.200    991
  Planarity :  0.004   0.056   1030
  Dihedral  :  4.679  18.395    801
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer Outliers :  2.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.32), residues: 747
  helix:  0.13 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -2.06 (0.51), residues: 191

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 3
  residues processed: 130
  average time/residue: 0.1436
  time to fit residues: 26.3335
Evaluate side-chains
  114 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.631 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0571
  time to fit residues: 1.1401
-------------------------------------------------------------------------------
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:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6300  Z= 0.193
  Angle     :  0.714  10.820   8536  Z= 0.354
  Chirality :  0.044   0.226    991
  Planarity :  0.004   0.055   1030
  Dihedral  :  4.685  18.345    801
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer Outliers :  1.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.32), residues: 747
  helix:  0.11 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.92 (0.52), residues: 192

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 3
  residues processed: 124
  average time/residue: 0.1472
  time to fit residues: 25.5415
Evaluate side-chains
  109 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.655 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0611
  time to fit residues: 1.2618
-------------------------------------------------------------------------------
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:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.064   6300  Z= 0.268
  Angle     :  0.747  10.417   8536  Z= 0.374
  Chirality :  0.046   0.340    991
  Planarity :  0.004   0.051   1030
  Dihedral  :  4.869  19.255    801
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer Outliers :  1.38 %
  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: -0.79 (0.32), residues: 747
  helix:  0.12 (0.22), residues: 559
  sheet:  None (None), residues: 0
  loop : -2.30 (0.51), residues: 188

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 4
  residues processed: 112
  average time/residue: 0.1558
  time to fit residues: 24.3022
Evaluate side-chains
  106 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.783 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0620
  time to fit residues: 1.4251
-------------------------------------------------------------------------------
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:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 64 optimal weight:    0.3980
   chunk 68 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.077   6300  Z= 0.226
  Angle     :  0.815  18.421   8536  Z= 0.388
  Chirality :  0.046   0.219    991
  Planarity :  0.004   0.051   1030
  Dihedral  :  4.894  18.419    801
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer Outliers :  1.38 %
  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: -0.62 (0.33), residues: 747
  helix:  0.20 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -1.93 (0.52), residues: 198

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 4
  residues processed: 112
  average time/residue: 0.1578
  time to fit residues: 24.5939
Evaluate side-chains
  108 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.703 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0577
  time to fit residues: 1.4063
-------------------------------------------------------------------------------
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:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.4320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6300  Z= 0.214
  Angle     :  0.796  14.143   8536  Z= 0.387
  Chirality :  0.046   0.313    991
  Planarity :  0.004   0.050   1030
  Dihedral  :  4.840  19.807    801
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  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: -0.53 (0.33), residues: 747
  helix:  0.25 (0.22), residues: 557
  sheet:  None (None), residues: 0
  loop : -1.97 (0.53), residues: 190

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1516
  time to fit residues: 23.5534
Evaluate side-chains
  105 residues out of total 653 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.737 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9447
-------------------------------------------------------------------------------
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:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 7 optimal weight:    0.2980
   chunk 11 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** 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 = 0.4042 r_free = 0.4042 target = 0.093631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.085220 restraints weight = 30333.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.086553 restraints weight = 19412.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.087414 restraints weight = 14514.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.4405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6300  Z= 0.205
  Angle     :  0.791  12.517   8536  Z= 0.379
  Chirality :  0.045   0.297    991
  Planarity :  0.005   0.050   1030
  Dihedral  :  4.896  18.891    801
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 17.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  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: -0.62 (0.33), residues: 747
  helix:  0.23 (0.23), residues: 561
  sheet:  None (None), residues: 0
  loop : -2.19 (0.52), residues: 186

===============================================================================
Job complete
usr+sys time: 1322.70 seconds
wall clock time: 25 minutes 4.76 seconds (1504.76 seconds total)