Starting phenix.real_space_refine
on Fri Sep 11 04:42:22 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7cmh_30406/09_2026/7cmh_30406.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cmh_30406/09_2026/7cmh_30406.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/7cmh_30406/09_2026/7cmh_30406.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cmh_30406/09_2026/7cmh_30406.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cmh_30406/09_2026/7cmh_30406.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cmh_30406/09_2026/7cmh_30406.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7cmh_30406/09_2026/7cmh_30406.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7cmh_30406/09_2026/7cmh_30406.cif"
  }
  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=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     C    4830      2.51       5
     N    1179      2.21       5
     O    1330      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7368
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3480
          Classifications: {'peptide': 458}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 25, 'TRANS': 432}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'PHE:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 60
    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 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 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 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 chiralities: 2
    Chain: "B"
      Number of atoms: 30
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 15
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 15
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 96
          Unusual residues: {'3PH': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATRP B 601 " occ=0.50
      ... (28 atoms not shown)
      pdb=" OXTBTRP B 601 " occ=0.50
  Time building chain proxies: 1.77, per 1000 atoms: 0.24
  Number of scatterers: 7368
  At special positions: 0
  Unit cell: (82.916, 84.007, 127.647, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       2     15.00
     O    1330      8.00
     N    1179      7.00
     C    4830      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 154 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  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: 0.62
  Conformation dependent library (CDL) restraints added in 387.7 milliseconds
  

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1702

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 3 sheets defined
      56.9% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 167 through 175
      removed outlier: 3.584A  pdb=" N   VAL A 173 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 200
      removed outlier: 3.747A  pdb=" N   THR A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TRP A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU A 195 " --> pdb=" O   TRP A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 208
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.916A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
      removed outlier: 3.704A  pdb=" N   LYS A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 256
      removed outlier: 3.574A  pdb=" N   SER A 254 " --> pdb=" O   ASP A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 276
      removed outlier: 3.889A  pdb=" N   THR A 276 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 301
      removed outlier: 3.548A  pdb=" N   SER A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LYS A 300 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 342
      removed outlier: 3.723A  pdb=" N   ALA A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.526A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE A 367 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.588A  pdb=" N   ILE A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 4.015A  pdb=" N   THR A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLN A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   TYR A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASN A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 459
      removed outlier: 3.701A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 516
      removed outlier: 3.974A  pdb=" N   GLU A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 534
      removed outlier: 3.501A  pdb=" N   ARG A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP A 529 " --> pdb=" O   ARG A 525 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLN A 530 " --> pdb=" O   ARG A 526 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU A 534 " --> pdb=" O   GLN A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 539
      removed outlier: 3.613A  pdb=" N   HIS A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 584
      removed outlier: 4.182A  pdb=" N   ASP A 583 " --> pdb=" O   GLN A 580 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU A 584 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 580 through 584'
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 4.006A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 54
      removed outlier: 3.860A  pdb=" N   GLY B  47 " --> pdb=" O   VAL B  43 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE B  49 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASN B  52 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 4.175A  pdb=" N   GLY B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 100
      removed outlier: 3.657A  pdb=" N   ILE B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY B  83 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU B  96 " --> pdb=" O   CYS B  92 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 111
      removed outlier: 3.734A  pdb=" N   VAL B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 129
      removed outlier: 3.922A  pdb=" N   PHE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU B 123 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B 128 " --> pdb=" O   TRP B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 147
      removed outlier: 3.634A  pdb=" N   GLN B 135 " --> pdb=" O   TYR B 131 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL B 137 " --> pdb=" O   THR B 133 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE B 138 " --> pdb=" O   ASN B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 178
      removed outlier: 3.708A  pdb=" N   CYS B 168 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TRP B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 186
    Processing helix  chain 'B' and resid 186 through 210
      removed outlier: 3.542A  pdb=" N   PHE B 190 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN B 208 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 234
    Processing helix  chain 'B' and resid 235 through 240
      removed outlier: 3.547A  pdb=" N   GLN B 240 " --> pdb=" O   LEU B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 258
      removed outlier: 3.920A  pdb=" N   GLU B 257 " --> pdb=" O   VAL B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 289
      removed outlier: 3.954A  pdb=" N   ILE B 271 " --> pdb=" O   ARG B 267 " (cutoff:3.500A)
      Proline residue:  B 274  - end of helix
      removed outlier: 3.521A  pdb=" N   TYR B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL B 288 " --> pdb=" O   ASN B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 301 through 309
      removed outlier: 3.732A  pdb=" N   LYS B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 336
      removed outlier: 4.050A  pdb=" N   ILE B 317 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      Proline residue:  B 319  - end of helix
      removed outlier: 3.762A  pdb=" N   VAL B 322 " --> pdb=" O   MET B 318 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   SER B 325 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL B 330 " --> pdb=" O   THR B 326 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER B 333 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   THR B 336 " --> pdb=" O   GLY B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 346
      removed outlier: 3.660A  pdb=" N   ALA B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA B 345 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG B 346 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 369
      removed outlier: 3.689A  pdb=" N   LEU B 368 " --> pdb=" O   PRO B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 380
      removed outlier: 3.709A  pdb=" N   ILE B 373 " --> pdb=" O   LEU B 369 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   THR B 375 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   MET B 378 " --> pdb=" O   SER B 374 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL B 380 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 412
      removed outlier: 4.025A  pdb=" N   ASN B 389 " --> pdb=" O   TYR B 385 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR B 390 " --> pdb=" O   THR B 386 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE B 394 " --> pdb=" O   TYR B 390 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE B 398 " --> pdb=" O   ILE B 394 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   THR B 402 " --> pdb=" O   PHE B 398 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   VAL B 403 " --> pdb=" O   TYR B 399 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ARG B 410 " --> pdb=" O   GLN B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 445
      removed outlier: 4.169A  pdb=" N   TYR B 430 " --> pdb=" O   PHE B 426 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL B 439 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   PHE B 440 " --> pdb=" O   PHE B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 457
      removed outlier: 3.551A  pdb=" N   CYS B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY B 452 " --> pdb=" O   VAL B 448 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ILE B 455 " --> pdb=" O   ILE B 451 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   MET B 456 " --> pdb=" O   GLY B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 465
      removed outlier: 3.690A  pdb=" N   VAL B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE B 464 " --> pdb=" O   VAL B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 491
      removed outlier: 3.707A  pdb=" N   ASP B 478 " --> pdb=" O   LYS B 474 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   PHE B 479 " --> pdb=" O   CYS B 475 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE B 480 " --> pdb=" O   PHE B 476 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL B 486 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227
      removed outlier: 7.090A  pdb=" N   CYS A 432 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   VAL A 466 " --> pdb=" O   CYS A 432 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.536A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262
      removed outlier: 7.224A  pdb=" N   ARG A 304 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   LEU A 262 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ILE A 306 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 8.457A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   GLY A 380 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   VAL A 348 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 544
      removed outlier: 5.988A  pdb=" N   ARG A 626 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   LEU A 596 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU A 610 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    804 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: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2161
        1.34 -     1.45: 1262
        1.45 -     1.57: 4079
        1.57 -     1.69: 2
        1.69 -     1.81: 41
  Bond restraints: 7545
  Sorted by residual:
  bond pdb=" C31 3PH B 603 "
       pdb=" O31 3PH B 603 "
    ideal  model  delta    sigma   weight residual
    1.325  1.452 -0.127 2.00e-02 2.50e+03 4.03e+01
  bond pdb=" C21 3PH B 603 "
       pdb=" O21 3PH B 603 "
    ideal  model  delta    sigma   weight residual
    1.328  1.455 -0.127 2.00e-02 2.50e+03 4.01e+01
  bond pdb=" C31 3PH B 602 "
       pdb=" O31 3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.325  1.451 -0.126 2.00e-02 2.50e+03 3.95e+01
  bond pdb=" C21 3PH B 602 "
       pdb=" O21 3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.328  1.452 -0.124 2.00e-02 2.50e+03 3.81e+01
  bond pdb=" O11 3PH B 602 "
       pdb=" P   3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.703  1.608  0.095 2.00e-02 2.50e+03 2.25e+01
  ... (remaining 7540 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 9720
        2.09 -     4.17: 435
        4.17 -     6.26: 66
        6.26 -     8.35: 32
        8.35 -    10.43: 6
  Bond angle restraints: 10259
  Sorted by residual:
  angle pdb=" C   GLY A 175 "
        pdb=" N   SER A 176 "
        pdb=" CA  SER A 176 "
      ideal   model   delta    sigma   weight residual
     122.83  129.01   -6.18 1.08e+00 8.57e-01 3.28e+01
  angle pdb=" N   ASN B 176 "
        pdb=" CA  ASN B 176 "
        pdb=" C   ASN B 176 "
      ideal   model   delta    sigma   weight residual
     111.28  116.28   -5.00 1.09e+00 8.42e-01 2.10e+01
  angle pdb=" N   SER B  61 "
        pdb=" CA  SER B  61 "
        pdb=" C   SER B  61 "
      ideal   model   delta    sigma   weight residual
     113.25  118.96   -5.71 1.30e+00 5.92e-01 1.93e+01
  angle pdb=" N   SER B 178 "
        pdb=" CA  SER B 178 "
        pdb=" C   SER B 178 "
      ideal   model   delta    sigma   weight residual
     110.28  116.55   -6.27 1.48e+00 4.57e-01 1.80e+01
  angle pdb=" CA  SER A 176 "
        pdb=" C   SER A 176 "
        pdb=" N   PRO A 177 "
      ideal   model   delta    sigma   weight residual
     118.09  121.55   -3.46 8.20e-01 1.49e+00 1.78e+01
  ... (remaining 10254 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 3811
       16.95 -    33.89: 420
       33.89 -    50.84: 105
       50.84 -    67.78: 11
       67.78 -    84.73: 8
  Dihedral angle restraints: 4355
    sinusoidal: 1701
      harmonic: 2654
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 154 "
           pdb=" CB  CYS B 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -37.22  -48.78     1      1.00e+01 1.00e-02 3.27e+01
  dihedral pdb=" CA  SER A 176 "
           pdb=" C   SER A 176 "
           pdb=" N   PRO A 177 "
           pdb=" CA  PRO A 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.48   26.52     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" CA  THR B 381 "
           pdb=" C   THR B 381 "
           pdb=" N   SER B 382 "
           pdb=" CA  SER B 382 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.16  -24.84     0      5.00e+00 4.00e-02 2.47e+01
  ... (remaining 4352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1088
       0.089 -    0.178: 103
       0.178 -    0.267: 8
       0.267 -    0.356: 1
       0.356 -    0.445: 1
  Chirality restraints: 1201
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.96   -0.44 2.00e-01 2.50e+01 4.95e+00
  chirality pdb=" CB  VAL B 492 "
            pdb=" CA  VAL B 492 "
            pdb=" CG1 VAL B 492 "
            pdb=" CG2 VAL B 492 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 425 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 1198 not shown)

  Planarity restraints: 1265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 228 "   -0.054 5.00e-02 4.00e+02   8.10e-02 1.05e+01
        pdb=" N   PRO B 229 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO B 229 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 229 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 131 "   -0.041 5.00e-02 4.00e+02   6.04e-02 5.84e+00
        pdb=" N   PRO B 132 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 132 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 132 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 460 "   -0.040 5.00e-02 4.00e+02   5.97e-02 5.69e+00
        pdb=" N   PRO B 461 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 461 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 461 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1262 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1084
        2.75 -     3.29: 6682
        3.29 -     3.83: 11635
        3.83 -     4.36: 13972
        4.36 -     4.90: 23671
  Nonbonded interactions: 57044
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 243 "
            pdb=" CE3ATRP B 601 "
     model   vdw
     2.214 3.340
  nonbonded pdb=" OD1 ASN B 134 "
            pdb=" N  ATRP B 601 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   PHE B  59 "
            pdb=" OH  TYR B 145 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   VAL B 129 "
            pdb=" OG1 THR B 133 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   PHE B 243 "
            pdb=" N  BTRP B 601 "
     model   vdw
     2.279 3.120
  ... (remaining 57039 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.290
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
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      :  0.006   0.127   7554  Z= 0.302
  Angle     :  1.075  10.434  10285  Z= 0.561
  Chirality :  0.056   0.445   1201
  Planarity :  0.007   0.081   1261
  Dihedral  : 15.202  84.727   2650
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  8.56 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 10.08 %
    Favored  : 88.74 %
  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: -5.98 (0.17), residues: 923
  helix: -4.53 (0.10), residues: 463
  sheet: -1.57 (0.58), residues: 70
  loop : -3.54 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 304 
 TYR   0.034   0.002   TYR B 145 
 PHE   0.018   0.002   PHE B 335 
 TRP   0.010   0.001   TRP B 124 
 HIS   0.006   0.002   HIS B 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00631 /  0.30 ( 7545)
  covalent geometry    : angle       1.06019 /  0.56 (10259)
  SS BOND              : bond        0.00322 /  0.17 (    1)
  SS BOND              : angle       3.87621 /  1.79 (    2)
  hydrogen bonds       : bond        0.33611 / 21.22 (  278)
  hydrogen bonds       : angle      10.92540 /  7.48 (  804)
  link_BETA1-4         : bond        0.00807 /  0.38 (    4)
  link_BETA1-4         : angle       3.44235 /  1.87 (   12)
  link_NAG-ASN         : bond        0.00417 /  0.22 (    4)
  link_NAG-ASN         : angle       3.99761 /  2.17 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 191
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.8554 (tp) cc_final: 0.8234 (tp)
REVERT: A  383 SER cc_start: 0.8874 (m) cc_final: 0.8385 (m)
REVERT: A  430 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8128 (mtm180)
REVERT: B  204 MET cc_start: 0.8038 (mmt) cc_final: 0.7653 (mmm)
REVERT: B  257 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5924 (tm-30)
REVERT: B  263 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8102 (ptpp)
REVERT: B  443 TRP cc_start: 0.5862 (t-100) cc_final: 0.5494 (t60)
REVERT: B  479 PHE cc_start: 0.7763 (t80) cc_final: 0.7520 (t80)
  outliers start: 9
  outliers final: 2
  residues processed: 197
  average time/residue: 0.0879
  time to fit residues: 23.3981
Evaluate side-chains
  143 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  263 LYS
Chi-restraints excluded: chain B residue  363 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 235 GLN
A 296 GLN
A 317 ASN
A 353 ASN
A 560 GLN
A 601 GLN
A 620 HIS
B 284 ASN
B 331 ASN
B 349 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.133345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.108810 restraints weight = 12081.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.89
r_work: 0.3185 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7554  Z= 0.143
  Angle     :  0.704   9.226  10285  Z= 0.348
  Chirality :  0.044   0.276   1201
  Planarity :  0.006   0.058   1261
  Dihedral  :  8.230  60.294   1067
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.93 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.15 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.10 (0.22), residues: 923
  helix: -2.67 (0.18), residues: 489
  sheet: -0.63 (0.66), residues: 57
  loop : -2.99 (0.26), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 440 
 TYR   0.013   0.001   TYR B 495 
 PHE   0.010   0.001   PHE A 627 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.003   0.001   HIS A 543 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 7545)
  covalent geometry    : angle       0.69277 /  0.35 (10259)
  SS BOND              : bond        0.00114 /  0.06 (    1)
  SS BOND              : angle       2.95465 /  1.35 (    2)
  hydrogen bonds       : bond        0.05685 /  3.60 (  278)
  hydrogen bonds       : angle       5.31657 /  3.64 (  804)
  link_BETA1-4         : bond        0.00309 /  0.14 (    4)
  link_BETA1-4         : angle       1.90103 /  1.04 (   12)
  link_NAG-ASN         : bond        0.00324 /  0.15 (    4)
  link_NAG-ASN         : angle       3.02207 /  1.70 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.8607 (tp) cc_final: 0.8318 (tp)
REVERT: A  430 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8410 (mtm180)
REVERT: A  451 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9205 (tt)
REVERT: B  111 LYS cc_start: 0.8231 (tptm) cc_final: 0.7588 (ttpp)
REVERT: B  257 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5684 (tm-30)
REVERT: B  469 TRP cc_start: 0.5909 (t-100) cc_final: 0.5109 (t-100)
  outliers start: 17
  outliers final: 8
  residues processed: 165
  average time/residue: 0.0746
  time to fit residues: 17.4052
Evaluate side-chains
  141 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  601 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  308 GLU
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  490 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0070
   chunk 46 optimal weight:    0.0980
   chunk 82 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 217 GLN
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 396 ASN
** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 ASN
B 349 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.132939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.108185 restraints weight = 12064.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.88
r_work: 0.3159 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7554  Z= 0.132
  Angle     :  0.640   9.398  10285  Z= 0.314
  Chirality :  0.042   0.265   1201
  Planarity :  0.005   0.051   1261
  Dihedral  :  7.487  60.678   1060
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.48 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.76 %
    Favored  : 77.09 %
  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: -3.04 (0.25), residues: 923
  helix: -1.61 (0.21), residues: 489
  sheet: -0.55 (0.68), residues: 57
  loop : -2.72 (0.27), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 418 
 TYR   0.010   0.001   TYR A 313 
 PHE   0.012   0.001   PHE A 627 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 471 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 7545)
  covalent geometry    : angle       0.62978 /  0.31 (10259)
  SS BOND              : bond        0.00493 /  0.26 (    1)
  SS BOND              : angle       2.16097 /  1.01 (    2)
  hydrogen bonds       : bond        0.04614 /  2.91 (  278)
  hydrogen bonds       : angle       4.70942 /  3.25 (  804)
  link_BETA1-4         : bond        0.00506 /  0.24 (    4)
  link_BETA1-4         : angle       1.94358 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00439 /  0.23 (    4)
  link_NAG-ASN         : angle       2.72560 /  1.56 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  183 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7122 (mtm110)
REVERT: A  344 ASP cc_start: 0.8065 (t70) cc_final: 0.7552 (t0)
REVERT: A  440 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7704 (mmt90)
REVERT: A  508 MET cc_start: 0.7443 (ttm) cc_final: 0.7169 (ttm)
REVERT: A  595 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7814 (p0)
REVERT: B  111 LYS cc_start: 0.8289 (tptm) cc_final: 0.7654 (ttpp)
REVERT: B  260 ASP cc_start: 0.8255 (t70) cc_final: 0.6975 (m-30)
REVERT: B  469 TRP cc_start: 0.5845 (t-100) cc_final: 0.5054 (t-100)
  outliers start: 23
  outliers final: 14
  residues processed: 151
  average time/residue: 0.0756
  time to fit residues: 15.8502
Evaluate side-chains
  143 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  308 GLU
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  490 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 35 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 63 optimal weight:    8.9990
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 GLN
A 601 GLN
B 208 GLN
B 284 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.133076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.108268 restraints weight = 12107.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.88
r_work: 0.3166 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
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   0.032   7554  Z= 0.119
  Angle     :  0.622   9.179  10285  Z= 0.300
  Chirality :  0.042   0.243   1201
  Planarity :  0.004   0.048   1261
  Dihedral  :  6.962  59.337   1057
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.26 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.68 %
    Favored  : 75.65 %
  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: -2.26 (0.26), residues: 923
  helix: -0.88 (0.23), residues: 484
  sheet: -0.44 (0.68), residues: 57
  loop : -2.43 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 418 
 TYR   0.013   0.001   TYR A 251 
 PHE   0.018   0.001   PHE A 346 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 471 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 7545)
  covalent geometry    : angle       0.61254 /  0.30 (10259)
  SS BOND              : bond        0.00038 /  0.02 (    1)
  SS BOND              : angle       2.16483 /  1.00 (    2)
  hydrogen bonds       : bond        0.03963 /  2.50 (  278)
  hydrogen bonds       : angle       4.39111 /  3.03 (  804)
  link_BETA1-4         : bond        0.00396 /  0.18 (    4)
  link_BETA1-4         : angle       1.89118 /  1.04 (   12)
  link_NAG-ASN         : bond        0.00295 /  0.15 (    4)
  link_NAG-ASN         : angle       2.49396 /  1.43 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  179 TRP cc_start: 0.8096 (m100) cc_final: 0.7604 (m100)
REVERT: A  183 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7158 (mtm110)
REVERT: A  344 ASP cc_start: 0.7968 (t70) cc_final: 0.7468 (t0)
REVERT: A  430 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8333 (mtm180)
REVERT: A  440 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7771 (mmt90)
REVERT: A  508 MET cc_start: 0.7496 (ttm) cc_final: 0.7166 (ttm)
REVERT: B  111 LYS cc_start: 0.8247 (tptm) cc_final: 0.7568 (ttpp)
REVERT: B  458 THR cc_start: 0.8869 (p) cc_final: 0.8581 (t)
REVERT: B  469 TRP cc_start: 0.5754 (t-100) cc_final: 0.4979 (t-100)
  outliers start: 28
  outliers final: 13
  residues processed: 155
  average time/residue: 0.0806
  time to fit residues: 17.2727
Evaluate side-chains
  143 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  483 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 GLN
B 284 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.130268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.105182 restraints weight = 12369.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.89
r_work: 0.3113 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7554  Z= 0.188
  Angle     :  0.672   9.567  10285  Z= 0.325
  Chirality :  0.044   0.212   1201
  Planarity :  0.005   0.051   1261
  Dihedral  :  7.038  61.063   1057
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.13 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 20.68 %
    Favored  : 74.61 %
  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: -1.91 (0.27), residues: 923
  helix: -0.66 (0.23), residues: 489
  sheet: -0.36 (0.69), residues: 57
  loop : -2.17 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 418 
 TYR   0.016   0.002   TYR B 495 
 PHE   0.018   0.001   PHE A 346 
 TRP   0.014   0.001   TRP B 124 
 HIS   0.006   0.001   HIS B 471 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.19 ( 7545)
  covalent geometry    : angle       0.66370 /  0.32 (10259)
  SS BOND              : bond        0.01384 /  0.73 (    1)
  SS BOND              : angle       2.17943 /  1.04 (    2)
  hydrogen bonds       : bond        0.04210 /  2.65 (  278)
  hydrogen bonds       : angle       4.35480 /  3.01 (  804)
  link_BETA1-4         : bond        0.00388 /  0.19 (    4)
  link_BETA1-4         : angle       2.01072 /  1.09 (   12)
  link_NAG-ASN         : bond        0.00157 /  0.08 (    4)
  link_NAG-ASN         : angle       2.47099 /  1.43 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 136
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  344 ASP cc_start: 0.8053 (t70) cc_final: 0.7547 (t0)
REVERT: A  508 MET cc_start: 0.7456 (ttm) cc_final: 0.7186 (ttm)
REVERT: A  595 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7790 (p0)
REVERT: B  111 LYS cc_start: 0.8271 (tptm) cc_final: 0.7632 (ttpp)
REVERT: B  458 THR cc_start: 0.8882 (p) cc_final: 0.8638 (t)
REVERT: B  469 TRP cc_start: 0.5779 (t-100) cc_final: 0.4977 (t-100)
  outliers start: 36
  outliers final: 22
  residues processed: 158
  average time/residue: 0.0757
  time to fit residues: 16.8211
Evaluate side-chains
  146 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  601 GLN
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  448 VAL
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  483 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    0.2980
   chunk 49 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0770
   chunk 34 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.132682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.107874 restraints weight = 11706.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.82
r_work: 0.3153 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7554  Z= 0.114
  Angle     :  0.616   9.267  10285  Z= 0.296
  Chirality :  0.042   0.228   1201
  Planarity :  0.004   0.047   1261
  Dihedral  :  6.807  59.670   1057
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.58 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 22.51 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.57 (0.27), residues: 923
  helix: -0.40 (0.24), residues: 495
  sheet: -0.26 (0.68), residues: 57
  loop : -2.00 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 440 
 TYR   0.008   0.001   TYR A 313 
 PHE   0.011   0.001   PHE B 306 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.11 ( 7545)
  covalent geometry    : angle       0.60741 /  0.29 (10259)
  SS BOND              : bond        0.00698 /  0.37 (    1)
  SS BOND              : angle       1.88104 /  0.90 (    2)
  hydrogen bonds       : bond        0.03714 /  2.34 (  278)
  hydrogen bonds       : angle       4.16824 /  2.88 (  804)
  link_BETA1-4         : bond        0.00394 /  0.18 (    4)
  link_BETA1-4         : angle       1.93841 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00259 /  0.13 (    4)
  link_NAG-ASN         : angle       2.30658 /  1.33 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  344 ASP cc_start: 0.8016 (t70) cc_final: 0.7492 (t0)
REVERT: A  430 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8307 (mtm180)
REVERT: A  595 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7768 (p0)
REVERT: B  111 LYS cc_start: 0.8233 (tptm) cc_final: 0.7578 (ttpp)
REVERT: B  406 GLN cc_start: 0.9286 (tm-30) cc_final: 0.9000 (tm-30)
REVERT: B  458 THR cc_start: 0.8882 (p) cc_final: 0.8660 (t)
REVERT: B  469 TRP cc_start: 0.5735 (t-100) cc_final: 0.4862 (t-100)
  outliers start: 29
  outliers final: 21
  residues processed: 153
  average time/residue: 0.0755
  time to fit residues: 16.4050
Evaluate side-chains
  143 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  308 GLU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  483 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 86 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.0386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.131307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.106303 restraints weight = 12220.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.86
r_work: 0.3128 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7554  Z= 0.147
  Angle     :  0.649   9.437  10285  Z= 0.313
  Chirality :  0.043   0.233   1201
  Planarity :  0.004   0.049   1261
  Dihedral  :  6.744  59.782   1057
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.69 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 23.43 %
    Favored  : 72.77 %
  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: -1.43 (0.27), residues: 923
  helix: -0.25 (0.24), residues: 498
  sheet: -0.31 (0.68), residues: 57
  loop : -1.96 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 418 
 TYR   0.010   0.001   TYR A 313 
 PHE   0.025   0.001   PHE A 346 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.004   0.001   HIS B 471 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 7545)
  covalent geometry    : angle       0.64044 /  0.31 (10259)
  SS BOND              : bond        0.00823 /  0.43 (    1)
  SS BOND              : angle       2.69990 /  1.23 (    2)
  hydrogen bonds       : bond        0.03814 /  2.38 (  278)
  hydrogen bonds       : angle       4.16365 /  2.88 (  804)
  link_BETA1-4         : bond        0.00384 /  0.18 (    4)
  link_BETA1-4         : angle       1.99091 /  1.08 (   12)
  link_NAG-ASN         : bond        0.00168 /  0.08 (    4)
  link_NAG-ASN         : angle       2.26501 /  1.31 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  344 ASP cc_start: 0.8014 (t70) cc_final: 0.7506 (t0)
REVERT: A  440 ARG cc_start: 0.8224 (mmt90) cc_final: 0.7995 (mmt90)
REVERT: A  595 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7754 (p0)
REVERT: B  111 LYS cc_start: 0.8297 (tptm) cc_final: 0.7626 (ttpp)
REVERT: B  406 GLN cc_start: 0.9274 (tm-30) cc_final: 0.9027 (tm-30)
REVERT: B  469 TRP cc_start: 0.5822 (t-100) cc_final: 0.4911 (t-100)
  outliers start: 29
  outliers final: 25
  residues processed: 147
  average time/residue: 0.0736
  time to fit residues: 15.3405
Evaluate side-chains
  147 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  308 GLU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  448 VAL
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  483 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0170
   chunk 52 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.7824

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 266 HIS
B 284 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.132574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.107548 restraints weight = 12004.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.85
r_work: 0.3138 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7554  Z= 0.127
  Angle     :  0.628   9.254  10285  Z= 0.302
  Chirality :  0.042   0.220   1201
  Planarity :  0.004   0.047   1261
  Dihedral  :  6.631  58.904   1057
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.15 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 23.95 %
    Favored  : 72.25 %
  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: -1.22 (0.28), residues: 923
  helix: -0.04 (0.24), residues: 499
  sheet: -0.27 (0.67), residues: 57
  loop : -1.93 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 339 
 TYR   0.009   0.001   TYR A 313 
 PHE   0.017   0.001   PHE A 346 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 471 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 7545)
  covalent geometry    : angle       0.61923 /  0.30 (10259)
  SS BOND              : bond        0.00077 /  0.04 (    1)
  SS BOND              : angle       2.45284 /  1.12 (    2)
  hydrogen bonds       : bond        0.03622 /  2.26 (  278)
  hydrogen bonds       : angle       4.09371 /  2.83 (  804)
  link_BETA1-4         : bond        0.00400 /  0.18 (    4)
  link_BETA1-4         : angle       1.97011 /  1.07 (   12)
  link_NAG-ASN         : bond        0.00218 /  0.11 (    4)
  link_NAG-ASN         : angle       2.23397 /  1.29 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  344 ASP cc_start: 0.7973 (t70) cc_final: 0.7483 (t0)
REVERT: A  440 ARG cc_start: 0.8237 (mmt90) cc_final: 0.8006 (mmt90)
REVERT: A  595 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7834 (p0)
REVERT: B  111 LYS cc_start: 0.8284 (tptm) cc_final: 0.7587 (ttpp)
REVERT: B  406 GLN cc_start: 0.9260 (tm-30) cc_final: 0.9044 (tm-30)
  outliers start: 29
  outliers final: 24
  residues processed: 149
  average time/residue: 0.0753
  time to fit residues: 15.9007
Evaluate side-chains
  147 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  308 GLU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  448 VAL
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  483 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0020
   chunk 36 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0770
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.4950

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.133952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.109124 restraints weight = 11779.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.82
r_work: 0.3165 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7554  Z= 0.113
  Angle     :  0.618   8.965  10285  Z= 0.296
  Chirality :  0.041   0.221   1201
  Planarity :  0.004   0.048   1261
  Dihedral  :  6.459  56.892   1057
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.48 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 24.61 %
    Favored  : 71.73 %
  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: -1.02 (0.28), residues: 923
  helix:  0.22 (0.24), residues: 495
  sheet: -0.30 (0.68), residues: 52
  loop : -1.94 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 339 
 TYR   0.007   0.001   TYR A 554 
 PHE   0.014   0.001   PHE A 346 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.11 ( 7545)
  covalent geometry    : angle       0.60992 /  0.29 (10259)
  SS BOND              : bond        0.00283 /  0.15 (    1)
  SS BOND              : angle       2.07888 /  0.95 (    2)
  hydrogen bonds       : bond        0.03415 /  2.13 (  278)
  hydrogen bonds       : angle       4.00278 /  2.77 (  804)
  link_BETA1-4         : bond        0.00400 /  0.18 (    4)
  link_BETA1-4         : angle       1.92949 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00258 /  0.13 (    4)
  link_NAG-ASN         : angle       2.16973 /  1.26 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  344 ASP cc_start: 0.7972 (t70) cc_final: 0.7413 (t0)
REVERT: A  440 ARG cc_start: 0.8245 (mmt90) cc_final: 0.8020 (mmt90)
REVERT: A  595 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7874 (p0)
REVERT: B  111 LYS cc_start: 0.8262 (tptm) cc_final: 0.7590 (ttpp)
REVERT: B  406 GLN cc_start: 0.9217 (tm-30) cc_final: 0.9006 (tm-30)
  outliers start: 28
  outliers final: 20
  residues processed: 152
  average time/residue: 0.0808
  time to fit residues: 17.0919
Evaluate side-chains
  150 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  448 VAL
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  480 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    0.0670
   chunk 69 optimal weight:    0.1980
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0370
   chunk 72 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.4196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.134828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.109724 restraints weight = 12007.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.87
r_work: 0.3181 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7554  Z= 0.110
  Angle     :  0.624  10.334  10285  Z= 0.296
  Chirality :  0.041   0.218   1201
  Planarity :  0.004   0.061   1261
  Dihedral  :  6.425  56.787   1057
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.93 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 26.31 %
    Favored  : 71.20 %
  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: -0.97 (0.28), residues: 923
  helix:  0.25 (0.24), residues: 499
  sheet: -0.13 (0.70), residues: 57
  loop : -1.98 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 339 
 TYR   0.010   0.001   TYR B 253 
 PHE   0.013   0.001   PHE A 346 
 TRP   0.017   0.001   TRP A 179 
 HIS   0.002   0.001   HIS B 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 ( 7545)
  covalent geometry    : angle       0.61626 /  0.29 (10259)
  SS BOND              : bond        0.00295 /  0.16 (    1)
  SS BOND              : angle       1.85408 /  0.86 (    2)
  hydrogen bonds       : bond        0.03268 /  2.05 (  278)
  hydrogen bonds       : angle       3.96253 /  2.76 (  804)
  link_BETA1-4         : bond        0.00405 /  0.18 (    4)
  link_BETA1-4         : angle       1.90881 /  1.05 (   12)
  link_NAG-ASN         : bond        0.00254 /  0.12 (    4)
  link_NAG-ASN         : angle       2.11916 /  1.23 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  183 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.7778 (mtm-85)
REVERT: A  344 ASP cc_start: 0.7966 (t70) cc_final: 0.7453 (t0)
REVERT: A  440 ARG cc_start: 0.8254 (mmt90) cc_final: 0.8032 (mmt90)
REVERT: A  595 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7848 (p0)
REVERT: B  111 LYS cc_start: 0.8258 (tptm) cc_final: 0.7662 (ttpp)
REVERT: B  406 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8972 (tm-30)
REVERT: B  497 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7636 (tm-30)
  outliers start: 19
  outliers final: 17
  residues processed: 144
  average time/residue: 0.0801
  time to fit residues: 16.2952
Evaluate side-chains
  144 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  448 VAL
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  480 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 7 optimal weight:    0.1980
   chunk 30 optimal weight:    0.0170
   chunk 82 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0770
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.3576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.135952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.111145 restraints weight = 11658.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.82
r_work: 0.3173 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7554  Z= 0.105
  Angle     :  0.612   9.872  10285  Z= 0.291
  Chirality :  0.041   0.220   1201
  Planarity :  0.004   0.051   1261
  Dihedral  :  6.267  56.711   1057
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.83 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 26.18 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.84 (0.28), residues: 923
  helix:  0.38 (0.24), residues: 501
  sheet: -0.05 (0.69), residues: 57
  loop : -1.96 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 418 
 TYR   0.008   0.001   TYR A 313 
 PHE   0.012   0.001   PHE B 306 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.10 ( 7545)
  covalent geometry    : angle       0.60470 /  0.29 (10259)
  SS BOND              : bond        0.00197 /  0.10 (    1)
  SS BOND              : angle       1.48817 /  0.69 (    2)
  hydrogen bonds       : bond        0.03159 /  1.98 (  278)
  hydrogen bonds       : angle       3.90685 /  2.71 (  804)
  link_BETA1-4         : bond        0.00431 /  0.20 (    4)
  link_BETA1-4         : angle       1.87541 /  1.03 (   12)
  link_NAG-ASN         : bond        0.00265 /  0.13 (    4)
  link_NAG-ASN         : angle       2.10732 /  1.23 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1833.84 seconds
wall clock time: 32 minutes 9.10 seconds (1929.10 seconds total)