Starting phenix.real_space_refine
on Fri Jul 25 14:00:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cmh_30406/07_2025/7cmh_30406.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cmh_30406/07_2025/7cmh_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cmh_30406/07_2025/7cmh_30406.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cmh_30406/07_2025/7cmh_30406.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cmh_30406/07_2025/7cmh_30406.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cmh_30406/07_2025/7cmh_30406.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4}
          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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 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: 4.77, per 1000 atoms: 0.65
  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: 1.95
  Conformation dependent library (CDL) restraints added in 836.8 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: 0.69
  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: 1.80

  Time building geometry restraints manager: 2.29 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 -    21.77: 4137
       21.77 -    43.54: 342
       43.54 -    65.31: 42
       65.31 -    87.09: 12
       87.09 -   108.86: 8
  Dihedral angle restraints: 4541
    sinusoidal: 1887
      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 4538 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:             1.050
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.710
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
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  : 16.328 108.858   2836
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 9.49
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.010   0.001   TRP B 124 
 HIS   0.006   0.002   HIS B 358 
 PHE   0.018   0.002   PHE B 335 
 TYR   0.034   0.002   TYR B 145 
 ARG   0.004   0.000   ARG A 304 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00417 (    4)
  link_NAG-ASN         : angle       3.99761 (   12)
  link_BETA1-4         : bond        0.00807 (    4)
  link_BETA1-4         : angle       3.44235 (   12)
  hydrogen bonds       : bond        0.33611 (  278)
  hydrogen bonds       : angle      10.92540 (  804)
  SS BOND              : bond        0.00322 (    1)
  SS BOND              : angle       3.87621 (    2)
  covalent geometry    : bond        0.00631 ( 7545)
  covalent geometry    : angle       1.06019 (10259)

*********************** 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  : 0.855 
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: 0.5925 (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: 0.7519 (t80)
  outliers start: 9
  outliers final: 2
  residues processed: 197
  average time/residue: 0.2048
  time to fit residues: 53.9966
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  : 0.858 
-------------------------------------------------------------------------------
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 76 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0050
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
** 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
B 284 ASN
B 331 ASN
B 349 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.132280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.108106 restraints weight = 11543.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.80
r_work: 0.3165 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    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 = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7554  Z= 0.152
  Angle     :  0.722   9.248  10285  Z= 0.355
  Chirality :  0.045   0.295   1201
  Planarity :  0.006   0.059   1261
  Dihedral  : 11.819  94.140   1253
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.37 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.02 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.22), residues: 923
  helix: -2.64 (0.18), residues: 491
  sheet: -0.64 (0.66), residues: 57
  loop : -2.99 (0.26), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 124 
 HIS   0.003   0.001   HIS A 539 
 PHE   0.010   0.001   PHE A 627 
 TYR   0.014   0.002   TYR B 495 
 ARG   0.006   0.001   ARG A 440 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00292 (    4)
  link_NAG-ASN         : angle       3.13295 (   12)
  link_BETA1-4         : bond        0.00262 (    4)
  link_BETA1-4         : angle       2.27190 (   12)
  hydrogen bonds       : bond        0.05759 (  278)
  hydrogen bonds       : angle       5.31014 (  804)
  SS BOND              : bond        0.00430 (    1)
  SS BOND              : angle       2.81591 (    2)
  covalent geometry    : bond        0.00338 ( 7545)
  covalent geometry    : angle       0.70976 (10259)

*********************** 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
  174 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.8606 (tp) cc_final: 0.8303 (tp)
REVERT: A  383 SER cc_start: 0.9072 (m) cc_final: 0.8870 (p)
REVERT: A  430 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8415 (mtm180)
REVERT: A  451 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9211 (tt)
REVERT: B   46 CYS cc_start: 0.8799 (m) cc_final: 0.8570 (m)
REVERT: B  111 LYS cc_start: 0.8241 (tptm) cc_final: 0.7580 (ttpp)
REVERT: B  257 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5668 (tm-30)
REVERT: B  469 TRP cc_start: 0.5907 (t-100) cc_final: 0.5106 (t-100)
  outliers start: 17
  outliers final: 7
  residues processed: 163
  average time/residue: 0.1734
  time to fit residues: 39.3703
Evaluate side-chains
  138 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 7 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 57 optimal weight:    0.1980
   chunk 43 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 GLN
A 396 ASN
** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 GLN
B 284 ASN
B 349 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.134577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.109768 restraints weight = 11936.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.90
r_work: 0.3180 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
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= 0.116
  Angle     :  0.637   9.052  10285  Z= 0.310
  Chirality :  0.043   0.295   1201
  Planarity :  0.005   0.050   1261
  Dihedral  : 10.655  84.164   1246
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.37 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.24 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.25), residues: 923
  helix: -1.56 (0.22), residues: 490
  sheet: -0.57 (0.68), residues: 57
  loop : -2.67 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 358 
 PHE   0.011   0.001   PHE A 627 
 TYR   0.009   0.001   TYR A 554 
 ARG   0.003   0.000   ARG A 440 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00545 (    4)
  link_NAG-ASN         : angle       2.86793 (   12)
  link_BETA1-4         : bond        0.00422 (    4)
  link_BETA1-4         : angle       2.30741 (   12)
  hydrogen bonds       : bond        0.04545 (  278)
  hydrogen bonds       : angle       4.63749 (  804)
  SS BOND              : bond        0.00491 (    1)
  SS BOND              : angle       2.16426 (    2)
  covalent geometry    : bond        0.00254 ( 7545)
  covalent geometry    : angle       0.62432 (10259)

*********************** 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
  169 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A  344 ASP cc_start: 0.8044 (t70) cc_final: 0.7517 (t0)
REVERT: A  451 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9142 (tt)
REVERT: A  508 MET cc_start: 0.7437 (ttm) cc_final: 0.7167 (ttm)
REVERT: A  595 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7813 (p0)
REVERT: B   46 CYS cc_start: 0.8740 (m) cc_final: 0.8534 (m)
REVERT: B  111 LYS cc_start: 0.8276 (tptm) cc_final: 0.7628 (ttpp)
REVERT: B  469 TRP cc_start: 0.5818 (t-100) cc_final: 0.5063 (t-100)
  outliers start: 25
  outliers final: 13
  residues processed: 153
  average time/residue: 0.1737
  time to fit residues: 36.8325
Evaluate side-chains
  144 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
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  231 LEU
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain B residue  308 GLU
Chi-restraints excluded: chain B residue  407 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 56 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0970
   chunk 50 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 ASN ** 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 = 0.3608 r_free = 0.3608 target = 0.133454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.108298 restraints weight = 12620.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.97
r_work: 0.3159 rms_B_bonded: 3.57 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 = 0.46   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 = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2666

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= 0.126
  Angle     :  0.633   9.360  10285  Z= 0.303
  Chirality :  0.043   0.256   1201
  Planarity :  0.004   0.049   1261
  Dihedral  :  9.549  70.817   1243
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.04 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.29 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.26), residues: 923
  helix: -0.85 (0.23), residues: 485
  sheet: -0.44 (0.68), residues: 57
  loop : -2.36 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 179 
 HIS   0.003   0.001   HIS B 471 
 PHE   0.017   0.001   PHE A 346 
 TYR   0.014   0.001   TYR A 251 
 ARG   0.002   0.000   ARG A 430 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    4)
  link_NAG-ASN         : angle       2.69661 (   12)
  link_BETA1-4         : bond        0.00404 (    4)
  link_BETA1-4         : angle       2.26264 (   12)
  hydrogen bonds       : bond        0.03980 (  278)
  hydrogen bonds       : angle       4.33282 (  804)
  SS BOND              : bond        0.02428 (    1)
  SS BOND              : angle       1.86781 (    2)
  covalent geometry    : bond        0.00292 ( 7545)
  covalent geometry    : angle       0.62155 (10259)

*********************** 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
  166 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A  183 ARG cc_start: 0.8247 (ttm110) cc_final: 0.7184 (mtm110)
REVERT: A  344 ASP cc_start: 0.7965 (t70) cc_final: 0.7470 (t0)
REVERT: A  440 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7787 (mmt90)
REVERT: A  451 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9125 (tt)
REVERT: A  508 MET cc_start: 0.7444 (ttm) cc_final: 0.7090 (ttm)
REVERT: B   46 CYS cc_start: 0.8750 (m) cc_final: 0.8495 (m)
REVERT: B  111 LYS cc_start: 0.8248 (tptm) cc_final: 0.7567 (ttpp)
REVERT: B  458 THR cc_start: 0.8876 (p) cc_final: 0.8595 (t)
REVERT: B  469 TRP cc_start: 0.5775 (t-100) cc_final: 0.4989 (t-100)
  outliers start: 29
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1859
  time to fit residues: 38.8758
Evaluate side-chains
  144 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
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  451 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   49 ILE
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  477 SER
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 36 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0670
   chunk 68 optimal weight:    0.0470
   chunk 26 optimal weight:    0.4980
   chunk 50 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 34 optimal weight:    0.3980
   chunk 75 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.3016

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.136401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.111546 restraints weight = 11677.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.85
r_work: 0.3202 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3198
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3198
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2941

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= 0.103
  Angle     :  0.599   7.908  10285  Z= 0.286
  Chirality :  0.042   0.264   1201
  Planarity :  0.004   0.047   1261
  Dihedral  :  8.685  61.242   1243
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.15 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.55 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.27), residues: 923
  helix: -0.44 (0.24), residues: 492
  sheet: -0.25 (0.69), residues: 57
  loop : -2.08 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 358 
 PHE   0.013   0.001   PHE A 346 
 TYR   0.008   0.001   TYR A 251 
 ARG   0.005   0.000   ARG A 430 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00370 (    4)
  link_NAG-ASN         : angle       2.64836 (   12)
  link_BETA1-4         : bond        0.00458 (    4)
  link_BETA1-4         : angle       2.33971 (   12)
  hydrogen bonds       : bond        0.03447 (  278)
  hydrogen bonds       : angle       4.05314 (  804)
  SS BOND              : bond        0.00662 (    1)
  SS BOND              : angle       1.92015 (    2)
  covalent geometry    : bond        0.00227 ( 7545)
  covalent geometry    : angle       0.58666 (10259)

*********************** 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
  175 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  210 ARG cc_start: 0.4964 (mmt180) cc_final: 0.4178 (mmt90)
REVERT: A  344 ASP cc_start: 0.7955 (t70) cc_final: 0.7449 (t0)
REVERT: A  440 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7737 (mmt90)
REVERT: A  451 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8966 (tt)
REVERT: A  595 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7758 (p0)
REVERT: B  111 LYS cc_start: 0.8198 (tptm) cc_final: 0.7537 (ttpp)
REVERT: B  458 THR cc_start: 0.8804 (p) cc_final: 0.8561 (t)
  outliers start: 29
  outliers final: 15
  residues processed: 164
  average time/residue: 0.2368
  time to fit residues: 55.2490
Evaluate side-chains
  144 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 LEU
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  412 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  316 TRP
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0770
   chunk 67 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0050
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.5152

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

Flipped N/Q/H residues before XYZ refinement:
A 235 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 = 0.3634 r_free = 0.3634 target = 0.135723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110780 restraints weight = 11796.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.86
r_work: 0.3189 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3121

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= 0.110
  Angle     :  0.608   8.073  10285  Z= 0.290
  Chirality :  0.042   0.276   1201
  Planarity :  0.004   0.046   1261
  Dihedral  :  8.301  61.229   1243
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.39 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 21.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.27), residues: 923
  helix: -0.16 (0.24), residues: 492
  sheet: -0.12 (0.70), residues: 57
  loop : -2.00 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 471 
 PHE   0.012   0.001   PHE A 346 
 TYR   0.009   0.001   TYR A 313 
 ARG   0.003   0.000   ARG A 430 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00289 (    4)
  link_NAG-ASN         : angle       2.71856 (   12)
  link_BETA1-4         : bond        0.00414 (    4)
  link_BETA1-4         : angle       2.32711 (   12)
  hydrogen bonds       : bond        0.03374 (  278)
  hydrogen bonds       : angle       3.96250 (  804)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       1.49344 (    2)
  covalent geometry    : bond        0.00252 ( 7545)
  covalent geometry    : angle       0.59560 (10259)

*********************** 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
  166 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A  210 ARG cc_start: 0.5101 (mmt180) cc_final: 0.4275 (mmt90)
REVERT: A  344 ASP cc_start: 0.8020 (t70) cc_final: 0.7481 (t0)
REVERT: A  440 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7797 (mmt90)
REVERT: A  451 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8924 (tt)
REVERT: A  508 MET cc_start: 0.7391 (ttm) cc_final: 0.7080 (ttm)
REVERT: A  520 LEU cc_start: 0.9096 (tp) cc_final: 0.8862 (tt)
REVERT: A  595 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7766 (p0)
REVERT: B  111 LYS cc_start: 0.8224 (tptm) cc_final: 0.7620 (ttpp)
REVERT: B  406 GLN cc_start: 0.9260 (tm-30) cc_final: 0.8965 (tm-30)
  outliers start: 34
  outliers final: 21
  residues processed: 156
  average time/residue: 0.1681
  time to fit residues: 37.0774
Evaluate side-chains
  147 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
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  412 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  559 ASP
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  288 VAL
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 73 optimal weight:    0.0770
   chunk 72 optimal weight:    0.0670
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0050
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    0.3980
   overall best weight:    0.2290

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3653 r_free = 0.3653 target = 0.137193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.112240 restraints weight = 11998.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.89
r_work: 0.3210 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3326

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= 0.102
  Angle     :  0.604   7.323  10285  Z= 0.284
  Chirality :  0.042   0.304   1201
  Planarity :  0.004   0.048   1261
  Dihedral  :  7.897  60.411   1243
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 22.51 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.28), residues: 923
  helix:  0.16 (0.24), residues: 488
  sheet: -0.07 (0.71), residues: 52
  loop : -1.94 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 124 
 HIS   0.002   0.000   HIS B 358 
 PHE   0.024   0.001   PHE A 346 
 TYR   0.007   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A 430 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00340 (    4)
  link_NAG-ASN         : angle       2.80567 (   12)
  link_BETA1-4         : bond        0.00442 (    4)
  link_BETA1-4         : angle       2.35042 (   12)
  hydrogen bonds       : bond        0.03172 (  278)
  hydrogen bonds       : angle       3.86578 (  804)
  SS BOND              : bond        0.00360 (    1)
  SS BOND              : angle       1.32952 (    2)
  covalent geometry    : bond        0.00228 ( 7545)
  covalent geometry    : angle       0.59095 (10259)

*********************** 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
  169 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A  210 ARG cc_start: 0.4887 (mmt180) cc_final: 0.4052 (mmt90)
REVERT: A  344 ASP cc_start: 0.8052 (t70) cc_final: 0.7533 (t0)
REVERT: A  440 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7760 (mmt90)
REVERT: A  451 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8900 (tt)
REVERT: A  508 MET cc_start: 0.7445 (ttm) cc_final: 0.7165 (ttm)
REVERT: A  520 LEU cc_start: 0.9080 (tp) cc_final: 0.8855 (tt)
REVERT: A  595 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7726 (p0)
REVERT: B  111 LYS cc_start: 0.8209 (tptm) cc_final: 0.7578 (ttpp)
REVERT: B  178 SER cc_start: 0.8371 (t) cc_final: 0.7968 (m)
REVERT: B  263 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7171 (tttt)
REVERT: B  406 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8877 (tm-30)
  outliers start: 33
  outliers final: 21
  residues processed: 159
  average time/residue: 0.2423
  time to fit residues: 54.8474
Evaluate side-chains
  150 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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  412 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  559 ASP
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  263 LYS
Chi-restraints excluded: chain B residue  288 VAL
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  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 54 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0060
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3628 r_free = 0.3628 target = 0.135211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.110255 restraints weight = 11688.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.82
r_work: 0.3184 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
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= 0.118
  Angle     :  0.616   8.140  10285  Z= 0.292
  Chirality :  0.043   0.328   1201
  Planarity :  0.004   0.048   1261
  Dihedral  :  7.658  61.224   1243
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.72 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.51 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.28), residues: 923
  helix:  0.31 (0.24), residues: 487
  sheet: -0.00 (0.71), residues: 57
  loop : -1.83 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 471 
 PHE   0.012   0.001   PHE A 346 
 TYR   0.011   0.001   TYR A 313 
 ARG   0.003   0.000   ARG A 430 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    4)
  link_NAG-ASN         : angle       2.93801 (   12)
  link_BETA1-4         : bond        0.00392 (    4)
  link_BETA1-4         : angle       2.32396 (   12)
  hydrogen bonds       : bond        0.03325 (  278)
  hydrogen bonds       : angle       3.86459 (  804)
  SS BOND              : bond        0.00288 (    1)
  SS BOND              : angle       1.83123 (    2)
  covalent geometry    : bond        0.00278 ( 7545)
  covalent geometry    : angle       0.60326 (10259)

*********************** 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
  159 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A  344 ASP cc_start: 0.8043 (t70) cc_final: 0.7547 (t0)
REVERT: A  451 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8913 (tt)
REVERT: A  508 MET cc_start: 0.7471 (ttm) cc_final: 0.7197 (ttm)
REVERT: A  595 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7757 (p0)
REVERT: B  111 LYS cc_start: 0.8195 (tptm) cc_final: 0.7611 (ttpp)
REVERT: B  263 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.7187 (tttt)
REVERT: B  406 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8892 (tm-30)
REVERT: B  481 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7169 (pt0)
  outliers start: 31
  outliers final: 20
  residues processed: 149
  average time/residue: 0.1746
  time to fit residues: 36.7403
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  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  559 ASP
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  263 LYS
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  316 TRP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3614 r_free = 0.3614 target = 0.134115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.109168 restraints weight = 11887.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.83
r_work: 0.3168 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7554  Z= 0.131
  Angle     :  0.645   9.260  10285  Z= 0.306
  Chirality :  0.043   0.334   1201
  Planarity :  0.004   0.073   1261
  Dihedral  :  7.649  61.901   1243
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.50 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.56 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.28), residues: 923
  helix:  0.43 (0.25), residues: 483
  sheet: -0.21 (0.70), residues: 58
  loop : -1.78 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 471 
 PHE   0.010   0.001   PHE A 542 
 TYR   0.010   0.001   TYR A 313 
 ARG   0.017   0.001   ARG B 339 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    4)
  link_NAG-ASN         : angle       2.97391 (   12)
  link_BETA1-4         : bond        0.00419 (    4)
  link_BETA1-4         : angle       2.33240 (   12)
  hydrogen bonds       : bond        0.03407 (  278)
  hydrogen bonds       : angle       3.90649 (  804)
  SS BOND              : bond        0.00361 (    1)
  SS BOND              : angle       2.01232 (    2)
  covalent geometry    : bond        0.00313 ( 7545)
  covalent geometry    : angle       0.63232 (10259)

*********************** 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
  156 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 ARG cc_start: 0.5724 (mmm160) cc_final: 0.4772 (mmt90)
REVERT: A  344 ASP cc_start: 0.8036 (t70) cc_final: 0.7557 (t0)
REVERT: A  508 MET cc_start: 0.7509 (ttm) cc_final: 0.7244 (ttm)
REVERT: A  595 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7766 (p0)
REVERT: B  263 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.7178 (tttt)
REVERT: B  406 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8900 (tm-30)
REVERT: B  497 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7652 (tm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 149
  average time/residue: 0.1796
  time to fit residues: 37.6004
Evaluate side-chains
  150 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  335 LEU
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  559 ASP
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  263 LYS
Chi-restraints excluded: chain B residue  288 VAL
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  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 25 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0270
   chunk 35 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0670
   chunk 57 optimal weight:    0.1980
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 620 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.136584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.111583 restraints weight = 11853.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.83
r_work: 0.3195 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3483

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= 0.108
  Angle     :  0.631   8.343  10285  Z= 0.297
  Chirality :  0.042   0.334   1201
  Planarity :  0.004   0.059   1261
  Dihedral  :  7.537  61.789   1243
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.93 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 24.35 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.28), residues: 923
  helix:  0.57 (0.25), residues: 484
  sheet: -0.24 (0.69), residues: 58
  loop : -1.78 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 358 
 PHE   0.010   0.001   PHE B 306 
 TYR   0.008   0.001   TYR A 313 
 ARG   0.011   0.001   ARG B 339 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00301 (    4)
  link_NAG-ASN         : angle       2.97949 (   12)
  link_BETA1-4         : bond        0.00427 (    4)
  link_BETA1-4         : angle       2.30505 (   12)
  hydrogen bonds       : bond        0.03211 (  278)
  hydrogen bonds       : angle       3.85518 (  804)
  SS BOND              : bond        0.00333 (    1)
  SS BOND              : angle       1.78758 (    2)
  covalent geometry    : bond        0.00246 ( 7545)
  covalent geometry    : angle       0.61835 (10259)

********************** 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
  155 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A  210 ARG cc_start: 0.5822 (mmm160) cc_final: 0.4859 (mmt90)
REVERT: A  344 ASP cc_start: 0.8084 (t70) cc_final: 0.7630 (t0)
REVERT: A  508 MET cc_start: 0.7502 (ttm) cc_final: 0.7284 (ttm)
REVERT: A  595 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7768 (p0)
REVERT: B  263 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7203 (tttt)
REVERT: B  406 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8868 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 151
  average time/residue: 0.1733
  time to fit residues: 36.4760
Evaluate side-chains
  143 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  335 LEU
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  559 ASP
Chi-restraints excluded: chain A residue  595 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  263 LYS
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  316 TRP
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0870
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0670
   chunk 50 optimal weight:    0.6980
   chunk 57 optimal weight:    0.4980
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3649 r_free = 0.3649 target = 0.137117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.112128 restraints weight = 11785.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.82
r_work: 0.3207 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3622

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= 0.106
  Angle     :  0.622   8.240  10285  Z= 0.293
  Chirality :  0.042   0.344   1201
  Planarity :  0.004   0.050   1261
  Dihedral  :  7.398  61.714   1243
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.28 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.35 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.28), residues: 923
  helix:  0.67 (0.25), residues: 484
  sheet: -0.20 (0.68), residues: 58
  loop : -1.75 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 179 
 HIS   0.002   0.001   HIS B 358 
 PHE   0.030   0.001   PHE B 436 
 TYR   0.009   0.001   TYR A 313 
 ARG   0.004   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00288 (    4)
  link_NAG-ASN         : angle       3.01144 (   12)
  link_BETA1-4         : bond        0.00411 (    4)
  link_BETA1-4         : angle       2.23994 (   12)
  hydrogen bonds       : bond        0.03114 (  278)
  hydrogen bonds       : angle       3.80883 (  804)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       1.58903 (    2)
  covalent geometry    : bond        0.00243 ( 7545)
  covalent geometry    : angle       0.60939 (10259)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4014.38 seconds
wall clock time: 71 minutes 54.84 seconds (4314.84 seconds total)