Starting phenix.real_space_refine
on Tue Mar  3 18:43:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dsq_30841/03_2026/7dsq_30841_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dsq_30841/03_2026/7dsq_30841.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dsq_30841/03_2026/7dsq_30841_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dsq_30841/03_2026/7dsq_30841_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dsq_30841/03_2026/7dsq_30841.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dsq_30841/03_2026/7dsq_30841.map"
  }
  resolution = 3.4
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     I       2     10.91       5
     P       1      5.49       5
     S      27      5.16       5
     C    4917      2.51       5
     N    1189      2.21       5
     O    1371      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7507
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3661
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 22, 'TRANS': 447}
    Chain: "B"
      Number of atoms: 3586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3586
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 24, 'TRANS': 439}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Classifications: {'peptide': 1}
    Chain: "B"
      Number of atoms: 133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 133
          Unusual residues: {'3PH': 1, 'Y01': 2}
          Classifications: {'undetermined': 3, 'water': 15}
          Link IDs: {None: 17}
  Time building chain proxies: 1.88, per 1000 atoms: 0.25
  Number of scatterers: 7507
  At special positions: 0
  Unit cell: (81.525, 85.873, 126.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     I       2     52.95
     S      27     16.00
     P       1     15.00
     O    1371      8.00
     N    1189      7.00
     C    4917      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " distance=1.68

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 273.4 milliseconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      57.8% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
      removed outlier: 3.610A  pdb=" N   LEU A 170 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 207
      removed outlier: 3.845A  pdb=" N   ARG A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A 195 " --> pdb=" O   TRP A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.671A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.191A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.814A  pdb=" N   LEU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LYS A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLY A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 241 through 247'
    Processing helix  chain 'A' and resid 248 through 256
    Processing helix  chain 'A' and resid 272 through 274
      No H-bonds generated for 'chain 'A' and resid 272 through 274'
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 3.915A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 3.564A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.597A  pdb=" N   SER A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 428
      removed outlier: 3.549A  pdb=" N   SER A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 459
      removed outlier: 3.706A  pdb=" N   PHE A 459 " --> pdb=" O   GLN A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 520 through 532
      removed outlier: 3.909A  pdb=" N   ARG A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
      removed outlier: 3.802A  pdb=" N   HIS A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.652A  pdb=" N   ALA B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ILE B  58 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   THR B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 78
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 4.404A  pdb=" N   ALA B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLY B  93 " --> pdb=" O   TRP B  89 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE B  95 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER B  96 " --> pdb=" O   CYS B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 125
      removed outlier: 3.863A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY B 125 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 139
      removed outlier: 4.042A  pdb=" N   LYS B 132 " --> pdb=" O   PRO B 128 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B 138 " --> pdb=" O   TRP B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 145
      removed outlier: 3.505A  pdb=" N   SER B 144 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 140 through 145'
    Processing helix  chain 'B' and resid 145 through 157
    Processing helix  chain 'B' and resid 158 through 161
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.691A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL B 174 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 182 " --> pdb=" O   CYS B 178 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 219
      removed outlier: 3.540A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLN B 197 " --> pdb=" O   ALA B 193 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLN B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 253
      removed outlier: 3.952A  pdb=" N   ALA B 246 " --> pdb=" O   ASN B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 297
      removed outlier: 3.706A  pdb=" N   LEU B 274 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
      Proline residue:  B 275  - end of helix
      removed outlier: 3.693A  pdb=" N   ILE B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
      removed outlier: 3.548A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE B 297 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.735A  pdb=" N   VAL B 329 " --> pdb=" O   TRP B 325 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL B 339 " --> pdb=" O   CYS B 335 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASN B 340 " --> pdb=" O   PHE B 336 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE B 344 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR B 345 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER B 354 " --> pdb=" O   PHE B 350 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLU B 356 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
      removed outlier: 3.685A  pdb=" N   PHE B 379 " --> pdb=" O   PRO B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 389
      No H-bonds generated for 'chain 'B' and resid 387 through 389'
    Processing helix  chain 'B' and resid 393 through 395
      No H-bonds generated for 'chain 'B' and resid 393 through 395'
    Processing helix  chain 'B' and resid 396 through 422
      removed outlier: 3.793A  pdb=" N   HIS B 420 " --> pdb=" O   ILE B 416 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG B 421 " --> pdb=" O   TRP B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 452
      removed outlier: 3.505A  pdb=" N   PHE B 439 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 467
      removed outlier: 3.520A  pdb=" N   CYS B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE B 460 " --> pdb=" O   VAL B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 476
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.529A  pdb=" N   GLN B 487 " --> pdb=" O   LYS B 483 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227
    Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262
      removed outlier: 5.944A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   LEU A 262 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   GLY A 380 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   VAL A 348 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 268
      removed outlier: 6.771A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.546A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA6, first strand: chain 'A' and resid 593 through 594

    336 hydrogen bonds defined for protein.
    975 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: 1.03

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.18 -     1.37: 2569
        1.37 -     1.57: 5047
        1.57 -     1.76: 20
        1.76 -     1.95: 40
        1.95 -     2.14: 2
  Bond restraints: 7678
  Sorted by residual:
  bond pdb=" CAI Y01 B 602 "
       pdb=" CAZ Y01 B 602 "
    ideal  model  delta    sigma   weight residual
    1.332  1.551 -0.219 2.00e-02 2.50e+03 1.20e+02
  bond pdb=" CAI Y01 B 603 "
       pdb=" CAZ Y01 B 603 "
    ideal  model  delta    sigma   weight residual
    1.332  1.550 -0.218 2.00e-02 2.50e+03 1.19e+02
  bond pdb=" CBG Y01 B 602 "
       pdb=" CBI Y01 B 602 "
    ideal  model  delta    sigma   weight residual
    1.537  1.386  0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CAI Y01 B 603 "
       pdb=" CAK Y01 B 603 "
    ideal  model  delta    sigma   weight residual
    1.492  1.637 -0.145 2.00e-02 2.50e+03 5.23e+01
  bond pdb=" CBG Y01 B 603 "
       pdb=" CBI Y01 B 603 "
    ideal  model  delta    sigma   weight residual
    1.537  1.397  0.140 2.00e-02 2.50e+03 4.87e+01
  ... (remaining 7673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 9912
        2.31 -     4.62: 434
        4.62 -     6.93: 72
        6.93 -     9.24: 29
        9.24 -    11.55: 9
  Bond angle restraints: 10456
  Sorted by residual:
  angle pdb=" N   LYS B 453 "
        pdb=" CA  LYS B 453 "
        pdb=" C   LYS B 453 "
      ideal   model   delta    sigma   weight residual
     114.62  108.18    6.44 1.14e+00 7.69e-01 3.20e+01
  angle pdb=" N   ASN B 230 "
        pdb=" CA  ASN B 230 "
        pdb=" C   ASN B 230 "
      ideal   model   delta    sigma   weight residual
     109.31  117.18   -7.87 1.42e+00 4.96e-01 3.07e+01
  angle pdb=" C   PHE B 233 "
        pdb=" N   GLU B 234 "
        pdb=" CA  GLU B 234 "
      ideal   model   delta    sigma   weight residual
     121.54  131.90  -10.36 1.91e+00 2.74e-01 2.94e+01
  angle pdb=" C   ASN B 226 "
        pdb=" N   LEU B 227 "
        pdb=" CA  LEU B 227 "
      ideal   model   delta    sigma   weight residual
     121.54  131.10   -9.56 1.91e+00 2.74e-01 2.51e+01
  angle pdb=" C   PRO B 373 "
        pdb=" N   VAL B 374 "
        pdb=" CA  VAL B 374 "
      ideal   model   delta    sigma   weight residual
     120.33  123.94   -3.61 8.00e-01 1.56e+00 2.03e+01
  ... (remaining 10451 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.67: 4526
       35.67 -    71.34: 127
       71.34 -   107.01: 20
      107.01 -   142.68: 31
      142.68 -   178.35: 7
  Dihedral angle restraints: 4711
    sinusoidal: 2032
      harmonic: 2679
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 164 "
           pdb=" CB  CYS B 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.33   70.33     1      1.00e+01 1.00e-02 6.37e+01
  dihedral pdb=" CA  GLY B 235 "
           pdb=" C   GLY B 235 "
           pdb=" N   THR B 236 "
           pdb=" CA  THR B 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.30  -25.70     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  SER A 409 "
           pdb=" C   SER A 409 "
           pdb=" N   GLY A 410 "
           pdb=" CA  GLY A 410 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.38   25.62     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 4708 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.183: 1222
       1.183 -    2.367: 0
       2.367 -    3.550: 0
       3.550 -    4.733: 0
       4.733 -    5.917: 10
  Chirality restraints: 1232
  Sorted by residual:
  chirality pdb=" CBI Y01 B 603 "
            pdb=" CAU Y01 B 603 "
            pdb=" CBE Y01 B 603 "
            pdb=" CBG Y01 B 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94   -2.98    5.92 2.00e-01 2.50e+01 8.75e+02
  chirality pdb=" CBI Y01 B 602 "
            pdb=" CAU Y01 B 602 "
            pdb=" CBE Y01 B 602 "
            pdb=" CBG Y01 B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94   -2.96    5.89 2.00e-01 2.50e+01 8.69e+02
  chirality pdb=" CBH Y01 B 602 "
            pdb=" CAT Y01 B 602 "
            pdb=" CAZ Y01 B 602 "
            pdb=" CBF Y01 B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85    2.65   -5.50 2.00e-01 2.50e+01 7.57e+02
  ... (remaining 1229 not shown)

  Planarity restraints: 1283
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 164 "    0.052 5.00e-02 4.00e+02   7.98e-02 1.02e+01
        pdb=" N   PRO B 165 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO B 165 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 165 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 166 "    0.051 5.00e-02 4.00e+02   7.74e-02 9.58e+00
        pdb=" N   PRO B 167 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO B 167 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 167 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 618 "   -0.049 5.00e-02 4.00e+02   7.46e-02 8.90e+00
        pdb=" N   PRO A 619 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 619 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 619 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1280 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.83: 2374
        2.83 -     3.36: 6826
        3.36 -     3.89: 12288
        3.89 -     4.43: 14509
        4.43 -     4.96: 25146
  Nonbonded interactions: 61143
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG1 THR B  62 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG1 THR A 460 "
            pdb=" OH  TYR A 554 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   HOH B 706 "
            pdb=" O   HOH B 707 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   LEU B 371 "
            pdb=" O   HOH B 701 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER B 308 "
            pdb=" OD2 ASP B 314 "
     model   vdw
     2.321 3.040
  ... (remaining 61138 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.220
  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:             0.020
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.570
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
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      :  0.011   0.354   7687  Z= 0.542
  Angle     :  1.244  17.773  10482  Z= 0.645
  Chirality :  0.489   5.917   1232
  Planarity :  0.008   0.080   1279
  Dihedral  : 22.623 178.347   2986
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  :  8.82 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  7.99 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.52 (0.20), residues: 930
  helix: -2.77 (0.16), residues: 476
  sheet: -0.76 (0.63), residues: 62
  loop : -3.61 (0.23), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 556 
 TYR   0.028   0.003   TYR B 259 
 PHE   0.021   0.003   PHE B 351 
 TRP   0.010   0.002   TRP A 220 
 HIS   0.006   0.001   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.01046 ( 7678)
  covalent geometry    : angle       1.19430 (10456)
  SS BOND              : bond        0.35359 (    1)
  SS BOND              : angle       6.74025 (    2)
  hydrogen bonds       : bond        0.19511 (  336)
  hydrogen bonds       : angle       6.73477 (  975)
  link_BETA1-4         : bond        0.02346 (    4)
  link_BETA1-4         : angle       7.04705 (   12)
  link_NAG-ASN         : bond        0.00203 (    4)
  link_NAG-ASN         : angle       7.14172 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 157
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 LEU cc_start: 0.7942 (mm) cc_final: 0.7550 (pp)
REVERT: A  191 TRP cc_start: 0.8301 (m100) cc_final: 0.8075 (m100)
REVERT: A  332 LYS cc_start: 0.8851 (tttp) cc_final: 0.8456 (tmmt)
REVERT: A  365 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8697 (tp-100)
REVERT: B   77 LYS cc_start: 0.7742 (tttm) cc_final: 0.7516 (ttmt)
REVERT: B  120 MET cc_start: 0.8117 (ttm) cc_final: 0.7858 (mtp)
REVERT: B  137 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9015 (pt)
REVERT: B  386 LEU cc_start: 0.9068 (mm) cc_final: 0.8843 (mm)
REVERT: B  412 ILE cc_start: 0.8882 (mm) cc_final: 0.8636 (mm)
REVERT: B  417 TRP cc_start: 0.7350 (t-100) cc_final: 0.7075 (t-100)
REVERT: B  477 TRP cc_start: 0.8751 (t60) cc_final: 0.8414 (t60)
REVERT: B  478 TRP cc_start: 0.8613 (t60) cc_final: 0.8357 (t60)
  outliers start: 7
  outliers final: 3
  residues processed: 161
  average time/residue: 0.0893
  time to fit residues: 19.2894
Evaluate side-chains
  124 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  370 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0370
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9662

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 275 GLN
A 353 ASN
A 396 ASN
A 539 HIS
A 561 ASN
B 273 ASN
B 501 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.114156 restraints weight = 7834.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.23
r_work: 0.3178 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7687  Z= 0.154
  Angle     :  1.283  33.557  10482  Z= 0.501
  Chirality :  0.109   1.791   1232
  Planarity :  0.006   0.051   1279
  Dihedral  : 23.209 178.279   1352
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  7.31 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.69 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.25), residues: 930
  helix: -0.92 (0.22), residues: 492
  sheet: -0.84 (0.60), residues: 67
  loop : -2.98 (0.27), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 440 
 TYR   0.021   0.001   TYR B 259 
 PHE   0.014   0.001   PHE B 252 
 TRP   0.009   0.001   TRP B  89 
 HIS   0.004   0.001   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7678)
  covalent geometry    : angle       1.26037 (10456)
  SS BOND              : bond        0.00760 (    1)
  SS BOND              : angle       4.44846 (    2)
  hydrogen bonds       : bond        0.04986 (  336)
  hydrogen bonds       : angle       4.46229 (  975)
  link_BETA1-4         : bond        0.01294 (    4)
  link_BETA1-4         : angle       3.96285 (   12)
  link_NAG-ASN         : bond        0.00352 (    4)
  link_NAG-ASN         : angle       5.93128 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.8422 (m100) cc_final: 0.8215 (m100)
REVERT: A  332 LYS cc_start: 0.8945 (tttp) cc_final: 0.8532 (tmmt)
REVERT: A  365 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8592 (tp-100)
REVERT: A  529 ASP cc_start: 0.8419 (t0) cc_final: 0.8162 (t0)
REVERT: B  120 MET cc_start: 0.8561 (ttm) cc_final: 0.8359 (mtp)
REVERT: B  365 MET cc_start: 0.9036 (mtt) cc_final: 0.8776 (mtt)
REVERT: B  386 LEU cc_start: 0.9021 (mm) cc_final: 0.8701 (mm)
REVERT: B  412 ILE cc_start: 0.8738 (mm) cc_final: 0.8527 (mm)
REVERT: B  477 TRP cc_start: 0.8751 (t60) cc_final: 0.8524 (t60)
REVERT: B  478 TRP cc_start: 0.8658 (t60) cc_final: 0.8307 (t60)
  outliers start: 18
  outliers final: 12
  residues processed: 138
  average time/residue: 0.0802
  time to fit residues: 15.0801
Evaluate side-chains
  125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  492 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0980
   chunk 34 optimal weight:    0.0770
   chunk 19 optimal weight:    6.9990
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
B 304 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.146467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.115255 restraints weight = 7880.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.20
r_work: 0.3194 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7687  Z= 0.126
  Angle     :  1.238  32.158  10482  Z= 0.473
  Chirality :  0.109   1.827   1232
  Planarity :  0.005   0.044   1279
  Dihedral  : 22.997 178.863   1349
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.20 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.97 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.27), residues: 930
  helix:  0.04 (0.23), residues: 493
  sheet: -0.81 (0.59), residues: 69
  loop : -2.66 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 195 
 TYR   0.020   0.001   TYR A 469 
 PHE   0.020   0.001   PHE B 474 
 TRP   0.020   0.001   TRP B 417 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7678)
  covalent geometry    : angle       1.21764 (10456)
  SS BOND              : bond        0.00883 (    1)
  SS BOND              : angle       4.36948 (    2)
  hydrogen bonds       : bond        0.04037 (  336)
  hydrogen bonds       : angle       4.03037 (  975)
  link_BETA1-4         : bond        0.01315 (    4)
  link_BETA1-4         : angle       3.76699 (   12)
  link_NAG-ASN         : bond        0.00317 (    4)
  link_NAG-ASN         : angle       5.47210 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 LEU cc_start: 0.8124 (mt) cc_final: 0.7751 (pp)
REVERT: A  191 TRP cc_start: 0.8567 (m100) cc_final: 0.8337 (m100)
REVERT: A  332 LYS cc_start: 0.8974 (tttp) cc_final: 0.8621 (ttpt)
REVERT: A  365 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8608 (tt0)
REVERT: A  440 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8252 (mmm-85)
REVERT: A  529 ASP cc_start: 0.8718 (t0) cc_final: 0.8516 (t0)
REVERT: B  103 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7248 (t80)
REVERT: B  120 MET cc_start: 0.8684 (ttm) cc_final: 0.8448 (mtp)
REVERT: B  304 GLN cc_start: 0.5787 (tp40) cc_final: 0.5531 (tp-100)
REVERT: B  365 MET cc_start: 0.9072 (mtt) cc_final: 0.8796 (mtt)
REVERT: B  386 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8702 (mm)
REVERT: B  478 TRP cc_start: 0.8691 (t60) cc_final: 0.8272 (t60)
  outliers start: 16
  outliers final: 10
  residues processed: 130
  average time/residue: 0.0726
  time to fit residues: 13.5128
Evaluate side-chains
  122 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  420 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 59 optimal weight:    0.4980
   chunk 74 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0980
   chunk 82 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.146759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.115452 restraints weight = 7843.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.19
r_work: 0.3198 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7687  Z= 0.121
  Angle     :  1.222  32.950  10482  Z= 0.465
  Chirality :  0.108   1.813   1232
  Planarity :  0.004   0.041   1279
  Dihedral  : 22.889 176.900   1349
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.85 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.01 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.28), residues: 930
  helix:  0.52 (0.24), residues: 493
  sheet: -0.57 (0.60), residues: 69
  loop : -2.46 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 421 
 TYR   0.026   0.001   TYR A 469 
 PHE   0.030   0.001   PHE B  95 
 TRP   0.009   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7678)
  covalent geometry    : angle       1.20338 (10456)
  SS BOND              : bond        0.00867 (    1)
  SS BOND              : angle       4.44419 (    2)
  hydrogen bonds       : bond        0.03624 (  336)
  hydrogen bonds       : angle       3.84777 (  975)
  link_BETA1-4         : bond        0.01231 (    4)
  link_BETA1-4         : angle       3.55338 (   12)
  link_NAG-ASN         : bond        0.00287 (    4)
  link_NAG-ASN         : angle       5.19359 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 LEU cc_start: 0.8115 (mt) cc_final: 0.7752 (pp)
REVERT: A  191 TRP cc_start: 0.8601 (m100) cc_final: 0.8366 (m100)
REVERT: A  332 LYS cc_start: 0.8989 (tttp) cc_final: 0.8668 (ttpt)
REVERT: A  365 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8583 (tt0)
REVERT: A  440 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.8284 (mmm-85)
REVERT: B  309 GLU cc_start: 0.8090 (mp0) cc_final: 0.7757 (mp0)
REVERT: B  333 LEU cc_start: 0.8814 (mt) cc_final: 0.8471 (mt)
REVERT: B  365 MET cc_start: 0.9099 (mtt) cc_final: 0.8859 (mtm)
REVERT: B  386 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8675 (mm)
REVERT: B  451 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6209 (m-80)
REVERT: B  478 TRP cc_start: 0.8682 (t60) cc_final: 0.8241 (t60)
  outliers start: 17
  outliers final: 10
  residues processed: 131
  average time/residue: 0.0732
  time to fit residues: 13.7598
Evaluate side-chains
  123 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  451 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
B 420 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.146086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.115261 restraints weight = 7607.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.14
r_work: 0.3197 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7687  Z= 0.128
  Angle     :  1.224  33.242  10482  Z= 0.465
  Chirality :  0.108   1.817   1232
  Planarity :  0.004   0.040   1279
  Dihedral  : 22.861 177.171   1349
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.89 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.28), residues: 930
  helix:  0.87 (0.24), residues: 486
  sheet: -0.46 (0.61), residues: 69
  loop : -2.28 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 421 
 TYR   0.028   0.001   TYR A 469 
 PHE   0.026   0.002   PHE B  95 
 TRP   0.007   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7678)
  covalent geometry    : angle       1.20619 (10456)
  SS BOND              : bond        0.00884 (    1)
  SS BOND              : angle       4.55647 (    2)
  hydrogen bonds       : bond        0.03689 (  336)
  hydrogen bonds       : angle       3.80584 (  975)
  link_BETA1-4         : bond        0.01225 (    4)
  link_BETA1-4         : angle       3.50391 (   12)
  link_NAG-ASN         : bond        0.00272 (    4)
  link_NAG-ASN         : angle       4.99256 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  171 LEU cc_start: 0.8123 (mt) cc_final: 0.7759 (pp)
REVERT: A  191 TRP cc_start: 0.8569 (m100) cc_final: 0.8325 (m100)
REVERT: A  332 LYS cc_start: 0.8986 (tttp) cc_final: 0.8678 (ttpt)
REVERT: A  365 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8575 (tt0)
REVERT: A  440 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8330 (mmm-85)
REVERT: B  103 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7142 (t80)
REVERT: B  218 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: B  304 GLN cc_start: 0.5818 (tp40) cc_final: 0.5540 (tp-100)
REVERT: B  309 GLU cc_start: 0.8110 (mp0) cc_final: 0.7873 (mp0)
REVERT: B  333 LEU cc_start: 0.8801 (mt) cc_final: 0.8584 (mt)
REVERT: B  386 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8664 (mm)
REVERT: B  418 LEU cc_start: 0.8593 (tt) cc_final: 0.8319 (tt)
REVERT: B  451 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6271 (m-80)
REVERT: B  478 TRP cc_start: 0.8631 (t60) cc_final: 0.8196 (t60)
  outliers start: 21
  outliers final: 13
  residues processed: 128
  average time/residue: 0.0790
  time to fit residues: 14.1554
Evaluate side-chains
  129 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  440 ILE
Chi-restraints excluded: chain B residue  451 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 80 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   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 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.146080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.115373 restraints weight = 7341.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.12
r_work: 0.3202 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7687  Z= 0.124
  Angle     :  1.216  33.407  10482  Z= 0.462
  Chirality :  0.108   1.814   1232
  Planarity :  0.004   0.039   1279
  Dihedral  : 22.834 178.520   1349
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.27 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.28), residues: 930
  helix:  1.09 (0.24), residues: 485
  sheet: -0.46 (0.61), residues: 69
  loop : -2.14 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 440 
 TYR   0.029   0.001   TYR A 469 
 PHE   0.024   0.001   PHE B  95 
 TRP   0.010   0.001   TRP B 417 
 HIS   0.001   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7678)
  covalent geometry    : angle       1.19992 (10456)
  SS BOND              : bond        0.00764 (    1)
  SS BOND              : angle       4.03693 (    2)
  hydrogen bonds       : bond        0.03632 (  336)
  hydrogen bonds       : angle       3.79228 (  975)
  link_BETA1-4         : bond        0.01224 (    4)
  link_BETA1-4         : angle       3.42664 (   12)
  link_NAG-ASN         : bond        0.00267 (    4)
  link_NAG-ASN         : angle       4.77511 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  171 LEU cc_start: 0.8106 (mt) cc_final: 0.7741 (pp)
REVERT: A  186 LEU cc_start: 0.8656 (mm) cc_final: 0.8431 (mt)
REVERT: A  191 TRP cc_start: 0.8499 (m100) cc_final: 0.8256 (m100)
REVERT: A  332 LYS cc_start: 0.8997 (tttp) cc_final: 0.8693 (ttpt)
REVERT: A  365 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8574 (tt0)
REVERT: B  103 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.6975 (t80)
REVERT: B  218 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7897 (tm-30)
REVERT: B  309 GLU cc_start: 0.8054 (mp0) cc_final: 0.7795 (mp0)
REVERT: B  333 LEU cc_start: 0.8812 (mt) cc_final: 0.8473 (mt)
REVERT: B  386 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8679 (mm)
REVERT: B  415 MET cc_start: 0.7426 (tmm) cc_final: 0.7103 (ttt)
REVERT: B  451 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6220 (m-80)
REVERT: B  478 TRP cc_start: 0.8626 (t60) cc_final: 0.8170 (t60)
REVERT: B  497 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8216 (mm-40)
  outliers start: 17
  outliers final: 12
  residues processed: 126
  average time/residue: 0.0760
  time to fit residues: 13.5291
Evaluate side-chains
  126 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  451 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 56 optimal weight:    0.4980
   chunk 58 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 601 GLN
B 404 ASN
B 501 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.145832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.115661 restraints weight = 7111.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.06
r_work: 0.3204 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7687  Z= 0.131
  Angle     :  1.215  33.336  10482  Z= 0.462
  Chirality :  0.108   1.815   1232
  Planarity :  0.004   0.040   1279
  Dihedral  : 22.849 179.210   1349
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.53 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.29), residues: 930
  helix:  1.26 (0.25), residues: 485
  sheet: -0.41 (0.61), residues: 69
  loop : -2.10 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 440 
 TYR   0.030   0.001   TYR A 469 
 PHE   0.023   0.001   PHE B  95 
 TRP   0.007   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7678)
  covalent geometry    : angle       1.20012 (10456)
  SS BOND              : bond        0.00930 (    1)
  SS BOND              : angle       4.34952 (    2)
  hydrogen bonds       : bond        0.03664 (  336)
  hydrogen bonds       : angle       3.80460 (  975)
  link_BETA1-4         : bond        0.01217 (    4)
  link_BETA1-4         : angle       3.36540 (   12)
  link_NAG-ASN         : bond        0.00264 (    4)
  link_NAG-ASN         : angle       4.58826 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  171 LEU cc_start: 0.8109 (mt) cc_final: 0.7747 (pp)
REVERT: A  186 LEU cc_start: 0.8650 (mm) cc_final: 0.8419 (mt)
REVERT: A  191 TRP cc_start: 0.8490 (m100) cc_final: 0.8186 (m100)
REVERT: A  316 GLU cc_start: 0.8441 (tp30) cc_final: 0.8198 (tm-30)
REVERT: A  332 LYS cc_start: 0.8993 (tttp) cc_final: 0.8697 (ttpt)
REVERT: A  365 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8551 (tt0)
REVERT: B  103 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7060 (t80)
REVERT: B  218 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: B  309 GLU cc_start: 0.8118 (mp0) cc_final: 0.7884 (mp0)
REVERT: B  333 LEU cc_start: 0.8810 (mt) cc_final: 0.8476 (mt)
REVERT: B  386 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8711 (mm)
REVERT: B  417 TRP cc_start: 0.7695 (t60) cc_final: 0.7337 (t60)
REVERT: B  451 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6236 (m-80)
REVERT: B  478 TRP cc_start: 0.8602 (t60) cc_final: 0.8195 (t60)
  outliers start: 17
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0702
  time to fit residues: 12.1167
Evaluate side-chains
  127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  451 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 24 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.146399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.116231 restraints weight = 7182.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.09
r_work: 0.3215 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7687  Z= 0.122
  Angle     :  1.203  32.666  10482  Z= 0.457
  Chirality :  0.109   1.812   1232
  Planarity :  0.004   0.040   1279
  Dihedral  : 22.896 179.380   1349
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.04 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.29), residues: 930
  helix:  1.45 (0.25), residues: 485
  sheet: -0.39 (0.61), residues: 69
  loop : -2.08 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 440 
 TYR   0.029   0.001   TYR A 469 
 PHE   0.023   0.001   PHE B  95 
 TRP   0.006   0.001   TRP B  89 
 HIS   0.001   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7678)
  covalent geometry    : angle       1.18971 (10456)
  SS BOND              : bond        0.00823 (    1)
  SS BOND              : angle       4.14855 (    2)
  hydrogen bonds       : bond        0.03511 (  336)
  hydrogen bonds       : angle       3.74236 (  975)
  link_BETA1-4         : bond        0.01158 (    4)
  link_BETA1-4         : angle       3.23784 (   12)
  link_NAG-ASN         : bond        0.00266 (    4)
  link_NAG-ASN         : angle       4.25972 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  171 LEU cc_start: 0.8084 (mt) cc_final: 0.7707 (pp)
REVERT: A  186 LEU cc_start: 0.8620 (mm) cc_final: 0.8415 (mt)
REVERT: A  191 TRP cc_start: 0.8453 (m100) cc_final: 0.8147 (m100)
REVERT: A  316 GLU cc_start: 0.8532 (tp30) cc_final: 0.8264 (tm-30)
REVERT: A  332 LYS cc_start: 0.8982 (tttp) cc_final: 0.8707 (ttpt)
REVERT: A  365 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8558 (tt0)
REVERT: B  103 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7007 (t80)
REVERT: B  218 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7906 (tm-30)
REVERT: B  309 GLU cc_start: 0.8047 (mp0) cc_final: 0.7841 (mp0)
REVERT: B  333 LEU cc_start: 0.8800 (mt) cc_final: 0.8471 (mt)
REVERT: B  386 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8703 (mm)
REVERT: B  417 TRP cc_start: 0.7724 (t60) cc_final: 0.7291 (t60)
REVERT: B  451 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.6221 (m-80)
REVERT: B  478 TRP cc_start: 0.8606 (t60) cc_final: 0.8200 (t60)
REVERT: B  497 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8018 (mm-40)
  outliers start: 16
  outliers final: 13
  residues processed: 127
  average time/residue: 0.0769
  time to fit residues: 13.9732
Evaluate side-chains
  127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  451 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
B 501 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.141503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.111575 restraints weight = 7685.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.10
r_work: 0.3151 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7687  Z= 0.202
  Angle     :  1.244  32.688  10482  Z= 0.483
  Chirality :  0.110   1.799   1232
  Planarity :  0.004   0.040   1279
  Dihedral  : 23.090 179.286   1349
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.04 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.29), residues: 930
  helix:  1.25 (0.24), residues: 486
  sheet: -0.28 (0.61), residues: 67
  loop : -2.01 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 440 
 TYR   0.029   0.002   TYR A 469 
 PHE   0.023   0.002   PHE B  95 
 TRP   0.008   0.001   TRP A 431 
 HIS   0.004   0.001   HIS A 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 7678)
  covalent geometry    : angle       1.23078 (10456)
  SS BOND              : bond        0.00961 (    1)
  SS BOND              : angle       4.53620 (    2)
  hydrogen bonds       : bond        0.04522 (  336)
  hydrogen bonds       : angle       4.02756 (  975)
  link_BETA1-4         : bond        0.01162 (    4)
  link_BETA1-4         : angle       3.25255 (   12)
  link_NAG-ASN         : bond        0.00310 (    4)
  link_NAG-ASN         : angle       4.17043 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.8490 (m100) cc_final: 0.8172 (m100)
REVERT: A  332 LYS cc_start: 0.8995 (tttp) cc_final: 0.8605 (ttpt)
REVERT: A  365 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8619 (tt0)
REVERT: B  103 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7249 (t80)
REVERT: B  218 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8051 (tm-30)
REVERT: B  309 GLU cc_start: 0.8057 (mp0) cc_final: 0.7791 (mp0)
REVERT: B  386 LEU cc_start: 0.9113 (mm) cc_final: 0.8780 (mm)
REVERT: B  417 TRP cc_start: 0.7857 (t60) cc_final: 0.7240 (t60)
REVERT: B  451 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6224 (m-80)
REVERT: B  478 TRP cc_start: 0.8630 (t60) cc_final: 0.8218 (t60)
REVERT: B  497 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8001 (mm-40)
  outliers start: 16
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0722
  time to fit residues: 12.3323
Evaluate side-chains
  122 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  451 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0040
   chunk 80 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0570
   chunk 76 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.5510

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.144631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114420 restraints weight = 7961.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.19
r_work: 0.3188 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7687  Z= 0.121
  Angle     :  1.210  31.888  10482  Z= 0.463
  Chirality :  0.109   1.803   1232
  Planarity :  0.004   0.039   1279
  Dihedral  : 22.908 177.105   1349
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.29 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.29), residues: 930
  helix:  1.53 (0.25), residues: 485
  sheet: -0.37 (0.61), residues: 69
  loop : -2.00 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 440 
 TYR   0.030   0.001   TYR A 469 
 PHE   0.034   0.002   PHE B 403 
 TRP   0.008   0.001   TRP B 405 
 HIS   0.001   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7678)
  covalent geometry    : angle       1.19803 (10456)
  SS BOND              : bond        0.00777 (    1)
  SS BOND              : angle       4.18008 (    2)
  hydrogen bonds       : bond        0.03591 (  336)
  hydrogen bonds       : angle       3.78042 (  975)
  link_BETA1-4         : bond        0.01025 (    4)
  link_BETA1-4         : angle       3.08370 (   12)
  link_NAG-ASN         : bond        0.00255 (    4)
  link_NAG-ASN         : angle       3.84937 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  186 LEU cc_start: 0.8649 (mm) cc_final: 0.8395 (mt)
REVERT: A  191 TRP cc_start: 0.8453 (m100) cc_final: 0.8135 (m100)
REVERT: A  365 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8558 (tt0)
REVERT: B  103 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6986 (t80)
REVERT: B  218 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: B  386 LEU cc_start: 0.8975 (mm) cc_final: 0.8689 (mm)
REVERT: B  417 TRP cc_start: 0.7792 (t60) cc_final: 0.7051 (t60)
REVERT: B  451 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6160 (m-80)
REVERT: B  478 TRP cc_start: 0.8573 (t60) cc_final: 0.8129 (t60)
REVERT: B  497 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7974 (mm-40)
  outliers start: 15
  outliers final: 12
  residues processed: 121
  average time/residue: 0.0681
  time to fit residues: 12.0286
Evaluate side-chains
  118 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  451 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0570
   chunk 11 optimal weight:    0.0470
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.145582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.115015 restraints weight = 8117.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.19
r_work: 0.3178 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7687  Z= 0.122
  Angle     :  1.206  31.690  10482  Z= 0.462
  Chirality :  0.110   1.820   1232
  Planarity :  0.004   0.040   1279
  Dihedral  : 22.791 177.935   1349
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.42 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.29), residues: 930
  helix:  1.64 (0.25), residues: 484
  sheet: -0.32 (0.61), residues: 69
  loop : -2.03 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 440 
 TYR   0.029   0.001   TYR A 469 
 PHE   0.021   0.001   PHE B  95 
 TRP   0.007   0.001   TRP B  89 
 HIS   0.001   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7678)
  covalent geometry    : angle       1.19568 (10456)
  SS BOND              : bond        0.00819 (    1)
  SS BOND              : angle       4.01675 (    2)
  hydrogen bonds       : bond        0.03467 (  336)
  hydrogen bonds       : angle       3.71417 (  975)
  link_BETA1-4         : bond        0.01000 (    4)
  link_BETA1-4         : angle       2.95130 (   12)
  link_NAG-ASN         : bond        0.00266 (    4)
  link_NAG-ASN         : angle       3.58564 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1906.58 seconds
wall clock time: 33 minutes 14.04 seconds (1994.04 seconds total)