Starting phenix.real_space_refine
on Mon Apr  6 15:04:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9t5w_55597/04_2026/9t5w_55597_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9t5w_55597/04_2026/9t5w_55597.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9t5w_55597/04_2026/9t5w_55597_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9t5w_55597/04_2026/9t5w_55597_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9t5w_55597/04_2026/9t5w_55597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9t5w_55597/04_2026/9t5w_55597.map"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.027
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: 7
    Type Number    sf(0)   Gaussians
     Ca      5      9.91       5
     Mn      1      7.51       5
     S      54      5.16       5
     C    6007      2.51       5
     N    1682      2.21       5
     O    1898      1.98       5
     H    9204      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18851
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 11519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 751, 11519
          Classifications: {'peptide': 751}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 715}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 7060
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 459, 7060
          Classifications: {'peptide': 459}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 434}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    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: "G"
      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: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 31
          Unusual residues: {' CA': 3, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          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: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 17
          Unusual residues: {' CA': 2, ' MN': 1, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 3.71, per 1000 atoms: 0.20
  Number of scatterers: 18851
  At special positions: 0
  Unit cell: (68.37, 152.22, 187.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      1     24.99
     Ca      5     19.99
     S      54     16.00
     O    1898      8.00
     N    1682      7.00
     C    6007      6.00
     H    9204      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  57 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  89 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 478 " - pdb=" SG  CYS A 490 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 623 " - pdb=" SG  CYS A 706 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 639 " - pdb=" SG  CYS A 696 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   3 " - pdb=" SG  CYS B  21 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  11 " - pdb=" SG  CYS B 425 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  14 " - pdb=" SG  CYS B  40 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 176 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 224 " - pdb=" SG  CYS B 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 364 " - pdb=" SG  CYS B 378 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 398 " - pdb=" SG  CYS B 423 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 427 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 437 " - pdb=" SG  CYS B 448 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 450 " - pdb=" SG  CYS B 459 " 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
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
      " BMA E   3 " - " MAN E   4 "
    ALPHA1-6
      " BMA D   3 " - " MAN D   5 "
      " BMA E   3 " - " MAN E   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A1204 " - " ASN A 677 "
      " NAG A1205 " - " ASN A 681 "
      " NAG B2004 " - " ASN B 232 "
      " NAG C   1 " - " ASN A 719 "
      " NAG D   1 " - " ASN A  70 "
      " NAG E   1 " - " ASN A 375 "
      " NAG F   1 " - " ASN B 190 "
      " NAG G   1 " - " ASN B  94 "
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 544.3 milliseconds
  

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2216

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 15 sheets defined
      19.5% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 146 through 165
    Processing helix  chain 'A' and resid 185 through 192
    Processing helix  chain 'A' and resid 194 through 200
      removed outlier: 4.054A  pdb=" N   LEU A 198 " --> pdb=" O   ASN A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 221
    Processing helix  chain 'A' and resid 224 through 228
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 3.605A  pdb=" N   GLU A 262 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
    Processing helix  chain 'A' and resid 303 through 311
    Processing helix  chain 'A' and resid 354 through 359
    Processing helix  chain 'A' and resid 409 through 413
    Processing helix  chain 'A' and resid 529 through 534
    Processing helix  chain 'A' and resid 558 through 562
    Processing helix  chain 'B' and resid 10 through 18
      removed outlier: 4.021A  pdb=" N   GLY B  18 " --> pdb=" O   CYS B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 40
      removed outlier: 3.568A  pdb=" N   ILE B  38 " --> pdb=" O   PRO B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 48
      removed outlier: 4.346A  pdb=" N   MET B  48 " --> pdb=" O   PRO B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 118
    Processing helix  chain 'B' and resid 120 through 139
      removed outlier: 3.516A  pdb=" N   GLY B 129 " --> pdb=" O   LYS B 125 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU B 137 " --> pdb=" O   ARG B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 202
      removed outlier: 3.540A  pdb=" N   GLN B 202 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 224
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 249 through 255
    Processing helix  chain 'B' and resid 273 through 277
      removed outlier: 3.755A  pdb=" N   PHE B 277 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 293
    Processing helix  chain 'B' and resid 304 through 315
      removed outlier: 3.745A  pdb=" N   GLU B 313 " --> pdb=" O   GLU B 309 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ILE B 314 " --> pdb=" O   LYS B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 341
      removed outlier: 3.626A  pdb=" N   VAL B 331 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 440
      removed outlier: 3.948A  pdb=" N   GLY B 439 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11
      removed outlier: 3.723A  pdb=" N   MET A   9 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ASP A 585 " --> pdb=" O   GLY A 575 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLY A 575 " --> pdb=" O   ASP A 585 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80
      removed outlier: 4.135A  pdb=" N   THR A  92 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   LYS A 104 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   HIS A  94 " --> pdb=" O   TYR A 102 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   TYR A 102 " --> pdb=" O   HIS A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 184
      removed outlier: 6.666A  pdb=" N   LEU A 173 " --> pdb=" O   HIS A 183 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE A 236 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 238 " --> pdb=" O   ALA A 136 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A 138 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP A 140 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   LYS A 235 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   TYR A 267 " --> pdb=" O   LYS A 235 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A 237 " --> pdb=" O   TYR A 267 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   ILE A 269 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343
    Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 396
      removed outlier: 3.731A  pdb=" N   ALA A 391 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   GLN A 401 " --> pdb=" O   GLN A 421 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   GLN A 421 " --> pdb=" O   GLN A 401 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA A 430 " --> pdb=" O   MET A 418 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ARG A 420 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   SER A 428 " --> pdb=" O   ARG A 420 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ASN A 422 " --> pdb=" O   TRP A 426 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   TRP A 426 " --> pdb=" O   ASN A 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448
      removed outlier: 6.470A  pdb=" N   HIS A 465 " --> pdb=" O   GLY A 472 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   GLY A 472 " --> pdb=" O   HIS A 465 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA A 492 " --> pdb=" O   VAL A 477 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 509 through 513
      removed outlier: 6.177A  pdb=" N   ASP A 522 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 542 through 543
      removed outlier: 3.768A  pdb=" N   GLY A 547 " --> pdb=" O   THR A 543 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 675 through 676
      removed outlier: 3.913A  pdb=" N   GLY A 634 " --> pdb=" O   LEU A 701 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 690
    Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 22
    Processing sheet with id=AB4, first strand: chain 'B' and resid 76 through 77
      removed outlier: 3.601A  pdb=" N   THR B 394 " --> pdb=" O   LYS B 357 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   SER B 362 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   ARG B 371 " --> pdb=" O   SER B 362 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 80 through 82
      removed outlier: 7.021A  pdb=" N   VAL B  81 " --> pdb=" O   GLN B 418 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER B 343 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   VAL B 345 " --> pdb=" O   ASP B 379 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   ASP B 379 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LEU B 347 " --> pdb=" O   ASP B 377 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ASP B 377 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 186 through 189
      removed outlier: 4.678A  pdb=" N   LEU B 188 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   ILE B 144 " --> pdb=" O   LEU B 188 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ILE B 105 " --> pdb=" O   ARG B 143 " (cutoff:3.500A)
      removed outlier: 8.416A  pdb=" N   GLY B 145 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   LEU B 107 " --> pdb=" O   GLY B 145 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ARG B 235 " --> pdb=" O   GLN B 295 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ILE B 297 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU B 237 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ALA B 299 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   PHE B 239 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA B 319 " --> pdb=" O   PRO B 296 " (cutoff:3.500A)

    306 hydrogen bonds defined for protein.
    810 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: 4.39

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9203
        1.03 -     1.23: 224
        1.23 -     1.43: 3891
        1.43 -     1.63: 5628
        1.63 -     1.83: 73
  Bond restraints: 19019
  Sorted by residual:
  bond pdb=" N   ILE B 455 "
       pdb=" CA  ILE B 455 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.037 1.19e-02 7.06e+03 9.72e+00
  bond pdb=" N   LYS B 457 "
       pdb=" CA  LYS B 457 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.034 1.23e-02 6.61e+03 7.58e+00
  bond pdb=" N   TYR B 454 "
       pdb=" CA  TYR B 454 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 5.97e+00
  bond pdb=" N   ARG A 487 "
       pdb=" CA  ARG A 487 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.031 1.29e-02 6.01e+03 5.82e+00
  bond pdb=" N   LEU A 480 "
       pdb=" CA  LEU A 480 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.29e-02 6.01e+03 5.81e+00
  ... (remaining 19014 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 33162
        2.02 -     4.04: 932
        4.04 -     6.06: 104
        6.06 -     8.08: 21
        8.08 -    10.10: 5
  Bond angle restraints: 34224
  Sorted by residual:
  angle pdb=" CA  TYR B  84 "
        pdb=" CB  TYR B  84 "
        pdb=" CG  TYR B  84 "
      ideal   model   delta    sigma   weight residual
     113.90  121.24   -7.34 1.80e+00 3.09e-01 1.66e+01
  angle pdb=" CA  ASN B 458 "
        pdb=" C   ASN B 458 "
        pdb=" O   ASN B 458 "
      ideal   model   delta    sigma   weight residual
     122.27  117.88    4.39 1.16e+00 7.43e-01 1.43e+01
  angle pdb=" C   PRO B 170 "
        pdb=" N   ASN B 171 "
        pdb=" CA  ASN B 171 "
      ideal   model   delta    sigma   weight residual
     121.54  128.58   -7.04 1.91e+00 2.74e-01 1.36e+01
  angle pdb=" N   GLY B 453 "
        pdb=" CA  GLY B 453 "
        pdb=" C   GLY B 453 "
      ideal   model   delta    sigma   weight residual
     114.66  110.11    4.55 1.24e+00 6.50e-01 1.35e+01
  angle pdb=" CA  ARG A 126 "
        pdb=" C   ARG A 126 "
        pdb=" O   ARG A 126 "
      ideal   model   delta    sigma   weight residual
     121.44  117.52    3.92 1.08e+00 8.57e-01 1.32e+01
  ... (remaining 34219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.05: 8392
       23.05 -    46.10: 673
       46.10 -    69.15: 172
       69.15 -    92.20: 20
       92.20 -   115.24: 34
  Dihedral angle restraints: 9291
    sinusoidal: 5319
      harmonic: 3972
  Sorted by residual:
  dihedral pdb=" CD  ARG A 482 "
           pdb=" NE  ARG A 482 "
           pdb=" CZ  ARG A 482 "
           pdb=" NH1 ARG A 482 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   70.74  -70.74     1      1.00e+01 1.00e-02 6.43e+01
  dihedral pdb=" CD  ARG A 485 "
           pdb=" NE  ARG A 485 "
           pdb=" CZ  ARG A 485 "
           pdb=" NH1 ARG A 485 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -62.98   62.98     1      1.00e+01 1.00e-02 5.24e+01
  dihedral pdb=" CA  SER A  82 "
           pdb=" C   SER A  82 "
           pdb=" N   PRO A  83 "
           pdb=" CA  PRO A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.99  -33.01     0      5.00e+00 4.00e-02 4.36e+01
  ... (remaining 9288 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1347
       0.077 -    0.154: 177
       0.154 -    0.232: 9
       0.232 -    0.309: 1
       0.309 -    0.386: 1
  Chirality restraints: 1535
  Sorted by residual:
  chirality pdb=" C1  NAG A1204 "
            pdb=" ND2 ASN A 677 "
            pdb=" C2  NAG A1204 "
            pdb=" O5  NAG A1204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.73e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 719 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" C1  NAG A1205 "
            pdb=" ND2 ASN A 681 "
            pdb=" C2  NAG A1205 "
            pdb=" O5  NAG A1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1532 not shown)

  Planarity restraints: 2892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 487 "    0.563 9.50e-02 1.11e+02   2.23e-01 3.63e+02
        pdb=" NE  ARG A 487 "    0.083 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 487 "    0.025 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 487 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 487 "   -0.030 2.00e-02 2.50e+03
        pdb="HH11 ARG A 487 "   -0.248 2.00e-02 2.50e+03
        pdb="HH12 ARG A 487 "    0.236 2.00e-02 2.50e+03
        pdb="HH21 ARG A 487 "   -0.027 2.00e-02 2.50e+03
        pdb="HH22 ARG A 487 "   -0.069 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 485 "    0.946 9.50e-02 1.11e+02   3.27e-01 2.73e+02
        pdb=" NE  ARG A 485 "   -0.094 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 485 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 485 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 485 "    0.023 2.00e-02 2.50e+03
        pdb="HH11 ARG A 485 "    0.145 2.00e-02 2.50e+03
        pdb="HH12 ARG A 485 "   -0.156 2.00e-02 2.50e+03
        pdb="HH21 ARG A 485 "   -0.027 2.00e-02 2.50e+03
        pdb="HH22 ARG A 485 "    0.113 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 482 "    1.096 9.50e-02 1.11e+02   3.66e-01 1.50e+02
        pdb=" NE  ARG A 482 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 482 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 482 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 482 "   -0.005 2.00e-02 2.50e+03
        pdb="HH11 ARG A 482 "   -0.042 2.00e-02 2.50e+03
        pdb="HH12 ARG A 482 "    0.055 2.00e-02 2.50e+03
        pdb="HH21 ARG A 482 "    0.012 2.00e-02 2.50e+03
        pdb="HH22 ARG A 482 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2889 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.36: 6193
        2.36 -     2.92: 42340
        2.92 -     3.48: 48721
        3.48 -     4.04: 66902
        4.04 -     4.60: 98309
  Nonbonded interactions: 262465
  Sorted by model distance:
  nonbonded pdb="HD11 ILE A 319 "
            pdb=" HD3 PRO B 170 "
     model   vdw
     1.797 2.440
  nonbonded pdb=" H   ASN B 207 "
            pdb="HD21 ASN B 207 "
     model   vdw
     1.811 2.100
  nonbonded pdb=" HG3 GLU A 131 "
            pdb=" HA  LYS A 315 "
     model   vdw
     1.827 2.440
  nonbonded pdb=" OE1 GLU A 314 "
            pdb=" H   GLU A 314 "
     model   vdw
     1.911 2.450
  nonbonded pdb=" H   SER A 340 "
            pdb=" HG  SER A 351 "
     model   vdw
     1.935 2.100
  ... (remaining 262460 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 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:             0.130
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.700
  Find NCS groups from input model:        0.240
  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:6.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
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      :  0.005   0.084   9852  Z= 0.237
  Angle     :  0.935  14.368  13381  Z= 0.475
  Chirality :  0.052   0.386   1535
  Planarity :  0.018   0.471   1735
  Dihedral  : 19.078 115.244   3970
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.22 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 20.60 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.23), residues: 1206
  helix: -0.28 (0.37), residues: 182
  sheet: -1.49 (0.26), residues: 366
  loop : -1.81 (0.23), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 115 
 TYR   0.015   0.001   TYR B  84 
 PHE   0.020   0.002   PHE B 404 
 TRP   0.007   0.002   TRP B 230 
 HIS   0.006   0.001   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 9815)
  covalent geometry    : angle       0.91220 (13287)
  SS BOND              : bond        0.00272 (   17)
  SS BOND              : angle       1.11696 (   34)
  hydrogen bonds       : bond        0.15739 (  306)
  hydrogen bonds       : angle       7.48410 (  810)
  link_ALPHA1-3        : bond        0.01083 (    2)
  link_ALPHA1-3        : angle       2.37723 (    6)
  link_ALPHA1-6        : bond        0.00512 (    2)
  link_ALPHA1-6        : angle       1.57375 (    6)
  link_BETA1-4         : bond        0.00461 (    8)
  link_BETA1-4         : angle       2.54205 (   24)
  link_NAG-ASN         : bond        0.01079 (    8)
  link_NAG-ASN         : angle       3.99697 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  185 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 176
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.7279 (mm) cc_final: 0.7056 (mm)
REVERT: A  580 MET cc_start: 0.7540 (mtm) cc_final: 0.7316 (mtp)
REVERT: A  585 ASP cc_start: 0.5890 (m-30) cc_final: 0.5646 (t70)
REVERT: A  602 VAL cc_start: 0.8557 (m) cc_final: 0.8160 (t)
REVERT: B   57 MET cc_start: 0.5762 (tpp) cc_final: 0.5312 (tpp)
REVERT: B  394 THR cc_start: 0.6365 (m) cc_final: 0.5996 (m)
  outliers start: 9
  outliers final: 2
  residues processed: 180
  average time/residue: 0.8837
  time to fit residues: 175.4066
Evaluate side-chains
  107 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 ASN
Chi-restraints excluded: chain B residue   94 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.2980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 332 HIS
A 600 GLN
A 694 GLN
B 177 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.137521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.087934 restraints weight = 49301.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 3.03
r_work: 0.3237 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.102   9852  Z= 0.233
  Angle     :  0.782   9.783  13381  Z= 0.388
  Chirality :  0.050   0.326   1535
  Planarity :  0.007   0.135   1735
  Dihedral  : 10.278 111.474   1720
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.72 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.24 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.23), residues: 1206
  helix:  0.51 (0.37), residues: 185
  sheet: -1.63 (0.25), residues: 375
  loop : -1.75 (0.23), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 482 
 TYR   0.015   0.002   TYR B 103 
 PHE   0.020   0.002   PHE A 611 
 TRP   0.012   0.003   TRP B  23 
 HIS   0.010   0.002   HIS A  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 9815)
  covalent geometry    : angle       0.76041 (13287)
  SS BOND              : bond        0.00281 (   17)
  SS BOND              : angle       0.80388 (   34)
  hydrogen bonds       : bond        0.03883 (  306)
  hydrogen bonds       : angle       6.16755 (  810)
  link_ALPHA1-3        : bond        0.00969 (    2)
  link_ALPHA1-3        : angle       3.12366 (    6)
  link_ALPHA1-6        : bond        0.00950 (    2)
  link_ALPHA1-6        : angle       3.26335 (    6)
  link_BETA1-4         : bond        0.00548 (    8)
  link_BETA1-4         : angle       2.09240 (   24)
  link_NAG-ASN         : bond        0.00522 (    8)
  link_NAG-ASN         : angle       3.22409 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 73
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 MET cc_start: 0.7899 (tmm) cc_final: 0.7589 (ppp)
REVERT: A  398 ASN cc_start: 0.7969 (t0) cc_final: 0.7614 (p0)
REVERT: A  660 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8594 (p)
REVERT: B   57 MET cc_start: 0.5869 (tpp) cc_final: 0.5654 (tpp)
REVERT: B  309 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7293 (mm-30)
  outliers start: 42
  outliers final: 11
  residues processed: 105
  average time/residue: 0.8272
  time to fit residues: 96.9198
Evaluate side-chains
  73 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  660 THR
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  751 PHE
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  309 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 116 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0870
   chunk 98 optimal weight:    0.6980
   chunk 12 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9990
   chunk 119 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN
A 694 GLN
A 702 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.137089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.087315 restraints weight = 49303.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 3.03
r_work: 0.3229 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   9852  Z= 0.133
  Angle     :  0.645  11.250  13381  Z= 0.310
  Chirality :  0.047   0.306   1535
  Planarity :  0.005   0.132   1735
  Dihedral  :  8.293 109.739   1718
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.39 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 22.53 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.24), residues: 1206
  helix:  0.96 (0.38), residues: 185
  sheet: -1.57 (0.25), residues: 378
  loop : -1.44 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 487 
 TYR   0.016   0.001   TYR B 103 
 PHE   0.012   0.001   PHE B  93 
 TRP   0.006   0.001   TRP A 358 
 HIS   0.003   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9815)
  covalent geometry    : angle       0.62353 (13287)
  SS BOND              : bond        0.00262 (   17)
  SS BOND              : angle       0.74282 (   34)
  hydrogen bonds       : bond        0.03609 (  306)
  hydrogen bonds       : angle       5.76416 (  810)
  link_ALPHA1-3        : bond        0.01268 (    2)
  link_ALPHA1-3        : angle       2.31810 (    6)
  link_ALPHA1-6        : bond        0.01407 (    2)
  link_ALPHA1-6        : angle       2.05463 (    6)
  link_BETA1-4         : bond        0.00388 (    8)
  link_BETA1-4         : angle       1.97743 (   24)
  link_NAG-ASN         : bond        0.00671 (    8)
  link_NAG-ASN         : angle       3.12358 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  80 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 MET cc_start: 0.8059 (tmm) cc_final: 0.7779 (ppp)
REVERT: A   81 THR cc_start: 0.8163 (m) cc_final: 0.7903 (p)
REVERT: A  660 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8588 (p)
REVERT: A  703 LEU cc_start: 0.4362 (OUTLIER) cc_final: 0.4074 (pt)
REVERT: B   57 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.5669 (tpp)
REVERT: B  309 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7421 (mm-30)
  outliers start: 22
  outliers final: 9
  residues processed: 77
  average time/residue: 0.7097
  time to fit residues: 62.3341
Evaluate side-chains
  63 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  660 THR
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  751 PHE
Chi-restraints excluded: chain B residue   57 MET
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain B residue  378 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 12 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A   2 ASN
A  36 GLN
A  94 HIS
A 332 HIS
A 694 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.135056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.084374 restraints weight = 49598.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 3.01
r_work: 0.3160 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.5936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9852  Z= 0.254
  Angle     :  0.780  13.878  13381  Z= 0.379
  Chirality :  0.050   0.251   1535
  Planarity :  0.007   0.163   1735
  Dihedral  :  8.706 117.277   1718
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.97 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.44 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.24), residues: 1206
  helix:  0.91 (0.38), residues: 191
  sheet: -1.68 (0.25), residues: 364
  loop : -1.45 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  86 
 TYR   0.013   0.002   TYR B 109 
 PHE   0.018   0.002   PHE A 121 
 TRP   0.011   0.002   TRP A 358 
 HIS   0.005   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 9815)
  covalent geometry    : angle       0.74974 (13287)
  SS BOND              : bond        0.00288 (   17)
  SS BOND              : angle       0.91100 (   34)
  hydrogen bonds       : bond        0.03512 (  306)
  hydrogen bonds       : angle       5.93160 (  810)
  link_ALPHA1-3        : bond        0.00546 (    2)
  link_ALPHA1-3        : angle       3.38496 (    6)
  link_ALPHA1-6        : bond        0.01362 (    2)
  link_ALPHA1-6        : angle       1.43107 (    6)
  link_BETA1-4         : bond        0.00569 (    8)
  link_BETA1-4         : angle       2.33408 (   24)
  link_NAG-ASN         : bond        0.01787 (    8)
  link_NAG-ASN         : angle       4.25030 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  81 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 47
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 MET cc_start: 0.8700 (mtp) cc_final: 0.8485 (mtp)
REVERT: A  440 TYR cc_start: 0.9364 (OUTLIER) cc_final: 0.8898 (t80)
REVERT: A  637 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7361 (ttm110)
REVERT: A  660 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8956 (p)
REVERT: B  267 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7734 (mp0)
REVERT: B  309 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7856 (mt-10)
REVERT: B  372 ASN cc_start: 0.7825 (m-40) cc_final: 0.7068 (p0)
REVERT: B  377 ASP cc_start: 0.6963 (p0) cc_final: 0.6670 (p0)
REVERT: B  394 THR cc_start: 0.7567 (m) cc_final: 0.7311 (m)
  outliers start: 34
  outliers final: 10
  residues processed: 78
  average time/residue: 0.8975
  time to fit residues: 77.9093
Evaluate side-chains
  57 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  660 THR
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain B residue  378 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 44 optimal weight:    0.4980
   chunk 13 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 69 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.135011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.083906 restraints weight = 49142.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 3.02
r_work: 0.3154 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.6151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   9852  Z= 0.140
  Angle     :  0.611  13.504  13381  Z= 0.298
  Chirality :  0.046   0.251   1535
  Planarity :  0.005   0.154   1735
  Dihedral  :  7.614 113.045   1718
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.06 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.73 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.24), residues: 1206
  helix:  1.07 (0.39), residues: 191
  sheet: -1.55 (0.25), residues: 366
  loop : -1.30 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 487 
 TYR   0.017   0.001   TYR A 661 
 PHE   0.014   0.001   PHE A 121 
 TRP   0.006   0.001   TRP B 230 
 HIS   0.004   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9815)
  covalent geometry    : angle       0.59055 (13287)
  SS BOND              : bond        0.00417 (   17)
  SS BOND              : angle       0.82945 (   34)
  hydrogen bonds       : bond        0.03099 (  306)
  hydrogen bonds       : angle       5.67867 (  810)
  link_ALPHA1-3        : bond        0.00915 (    2)
  link_ALPHA1-3        : angle       2.39824 (    6)
  link_ALPHA1-6        : bond        0.00705 (    2)
  link_ALPHA1-6        : angle       1.60585 (    6)
  link_BETA1-4         : bond        0.00328 (    8)
  link_BETA1-4         : angle       2.03316 (   24)
  link_NAG-ASN         : bond        0.01104 (    8)
  link_NAG-ASN         : angle       2.79531 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  65 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 42
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.8206 (tt0) cc_final: 0.7719 (tp-100)
REVERT: A  331 GLU cc_start: 0.7685 (tt0) cc_final: 0.7139 (tm-30)
REVERT: A  376 MET cc_start: 0.8619 (mtp) cc_final: 0.8418 (mtp)
REVERT: A  402 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8253 (t)
REVERT: A  440 TYR cc_start: 0.9257 (OUTLIER) cc_final: 0.8665 (t80)
REVERT: A  610 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.5943 (tm-30)
REVERT: A  637 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7278 (ttt90)
REVERT: A  660 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8717 (p)
REVERT: B   57 MET cc_start: 0.5948 (tpp) cc_final: 0.5727 (tpp)
REVERT: B  372 ASN cc_start: 0.7702 (m-40) cc_final: 0.6912 (p0)
REVERT: B  377 ASP cc_start: 0.7081 (p0) cc_final: 0.6858 (p0)
REVERT: B  394 THR cc_start: 0.7511 (m) cc_final: 0.7284 (m)
  outliers start: 23
  outliers final: 8
  residues processed: 62
  average time/residue: 0.8837
  time to fit residues: 60.9108
Evaluate side-chains
  53 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   43 GLN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain A residue  660 THR
Chi-restraints excluded: chain A residue  751 PHE
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  378 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0870
   chunk 109 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 114 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.1764

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

Flipped N/Q/H residues before XYZ refinement:
A 332 HIS
A 401 GLN
A 429 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.132630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.081199 restraints weight = 48879.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.99
r_work: 0.3098 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.6893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9852  Z= 0.209
  Angle     :  0.636   9.112  13381  Z= 0.315
  Chirality :  0.047   0.285   1535
  Planarity :  0.005   0.141   1735
  Dihedral  :  7.603 108.676   1718
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.55 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.86 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.24), residues: 1206
  helix:  1.08 (0.39), residues: 191
  sheet: -1.39 (0.26), residues: 362
  loop : -1.33 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 651 
 TYR   0.012   0.002   TYR B 308 
 PHE   0.021   0.002   PHE A 121 
 TRP   0.009   0.002   TRP B 230 
 HIS   0.005   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 9815)
  covalent geometry    : angle       0.61276 (13287)
  SS BOND              : bond        0.00336 (   17)
  SS BOND              : angle       0.88459 (   34)
  hydrogen bonds       : bond        0.03310 (  306)
  hydrogen bonds       : angle       5.60667 (  810)
  link_ALPHA1-3        : bond        0.00876 (    2)
  link_ALPHA1-3        : angle       3.13178 (    6)
  link_ALPHA1-6        : bond        0.00958 (    2)
  link_ALPHA1-6        : angle       1.63820 (    6)
  link_BETA1-4         : bond        0.00425 (    8)
  link_BETA1-4         : angle       2.33520 (   24)
  link_NAG-ASN         : bond        0.00504 (    8)
  link_NAG-ASN         : angle       2.86480 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  73 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 43
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.8246 (tt0) cc_final: 0.7934 (tp-100)
REVERT: A  138 LEU cc_start: 0.3941 (OUTLIER) cc_final: 0.3609 (mm)
REVERT: A  174 MET cc_start: 0.2347 (tmm) cc_final: 0.1508 (tmm)
REVERT: A  376 MET cc_start: 0.8481 (mtp) cc_final: 0.8236 (mtp)
REVERT: A  402 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8359 (t)
REVERT: A  440 TYR cc_start: 0.9294 (OUTLIER) cc_final: 0.8635 (t80)
REVERT: A  610 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.5893 (tm-30)
REVERT: A  637 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7318 (ttt90)
REVERT: A  660 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8769 (p)
REVERT: B   57 MET cc_start: 0.5900 (tpp) cc_final: 0.5662 (tpp)
REVERT: B  267 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8049 (mp0)
  outliers start: 30
  outliers final: 10
  residues processed: 72
  average time/residue: 0.8885
  time to fit residues: 71.1965
Evaluate side-chains
  59 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   43 GLN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain A residue  660 THR
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  378 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 32 optimal weight:    0.1980
   chunk 119 optimal weight:    7.9990
   chunk 114 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 112 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 332 HIS
A 401 GLN
A 600 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.133340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.081907 restraints weight = 48819.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.98
r_work: 0.3116 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.7064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   9852  Z= 0.137
  Angle     :  0.587   8.710  13381  Z= 0.288
  Chirality :  0.045   0.198   1535
  Planarity :  0.005   0.138   1735
  Dihedral  :  7.487 110.741   1718
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.81 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 22.24 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.24), residues: 1206
  helix:  1.22 (0.39), residues: 191
  sheet: -1.28 (0.26), residues: 362
  loop : -1.23 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 504 
 TYR   0.013   0.001   TYR A 661 
 PHE   0.015   0.001   PHE A 121 
 TRP   0.006   0.001   TRP B 230 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9815)
  covalent geometry    : angle       0.56464 (13287)
  SS BOND              : bond        0.00234 (   17)
  SS BOND              : angle       0.81613 (   34)
  hydrogen bonds       : bond        0.02987 (  306)
  hydrogen bonds       : angle       5.52097 (  810)
  link_ALPHA1-3        : bond        0.00916 (    2)
  link_ALPHA1-3        : angle       2.44475 (    6)
  link_ALPHA1-6        : bond        0.00774 (    2)
  link_ALPHA1-6        : angle       1.60746 (    6)
  link_BETA1-4         : bond        0.00282 (    8)
  link_BETA1-4         : angle       2.06145 (   24)
  link_NAG-ASN         : bond        0.00584 (    8)
  link_NAG-ASN         : angle       2.90090 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.8239 (tt0) cc_final: 0.7933 (tp-100)
REVERT: A  331 GLU cc_start: 0.7932 (tt0) cc_final: 0.7658 (tt0)
REVERT: A  418 MET cc_start: 0.9136 (ttp) cc_final: 0.8853 (ttm)
REVERT: A  440 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8493 (t80)
REVERT: A  610 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.5844 (tm-30)
REVERT: A  637 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7247 (ttm110)
REVERT: A  660 THR cc_start: 0.8920 (p) cc_final: 0.8597 (p)
REVERT: B   57 MET cc_start: 0.5974 (tpp) cc_final: 0.5691 (tpp)
REVERT: B  267 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7991 (mp0)
  outliers start: 25
  outliers final: 12
  residues processed: 66
  average time/residue: 0.9953
  time to fit residues: 72.0326
Evaluate side-chains
  58 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   43 GLN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  478 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  378 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 111 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 15 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN
A 469 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.132846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.081284 restraints weight = 48882.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.00
r_work: 0.3101 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.7305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9852  Z= 0.150
  Angle     :  0.583   7.919  13381  Z= 0.287
  Chirality :  0.045   0.222   1535
  Planarity :  0.005   0.132   1735
  Dihedral  :  7.380 109.628   1718
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.56 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.44 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.24), residues: 1206
  helix:  1.29 (0.39), residues: 191
  sheet: -1.25 (0.26), residues: 363
  loop : -1.15 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 273 
 TYR   0.013   0.001   TYR A 176 
 PHE   0.018   0.001   PHE A 121 
 TRP   0.007   0.001   TRP B 230 
 HIS   0.004   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9815)
  covalent geometry    : angle       0.56150 (13287)
  SS BOND              : bond        0.00231 (   17)
  SS BOND              : angle       0.80347 (   34)
  hydrogen bonds       : bond        0.02975 (  306)
  hydrogen bonds       : angle       5.49425 (  810)
  link_ALPHA1-3        : bond        0.00915 (    2)
  link_ALPHA1-3        : angle       2.71445 (    6)
  link_ALPHA1-6        : bond        0.00821 (    2)
  link_ALPHA1-6        : angle       1.53463 (    6)
  link_BETA1-4         : bond        0.00276 (    8)
  link_BETA1-4         : angle       2.15383 (   24)
  link_NAG-ASN         : bond        0.00833 (    8)
  link_NAG-ASN         : angle       2.66350 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  60 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 40
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.8347 (tt0) cc_final: 0.7949 (tp-100)
REVERT: A  418 MET cc_start: 0.9090 (ttp) cc_final: 0.8830 (ttm)
REVERT: A  440 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8410 (t80)
REVERT: A  610 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.5757 (tm-30)
REVERT: A  637 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7251 (ttm110)
REVERT: A  660 THR cc_start: 0.8893 (p) cc_final: 0.8544 (p)
REVERT: B   57 MET cc_start: 0.6123 (tpp) cc_final: 0.5842 (tpp)
  outliers start: 20
  outliers final: 12
  residues processed: 60
  average time/residue: 0.9447
  time to fit residues: 62.7560
Evaluate side-chains
  53 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   43 GLN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  478 CYS
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  378 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 63 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.133346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.081804 restraints weight = 48526.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.98
r_work: 0.3120 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.7393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   9852  Z= 0.128
  Angle     :  0.588  11.285  13381  Z= 0.290
  Chirality :  0.045   0.251   1535
  Planarity :  0.005   0.130   1735
  Dihedral  :  7.312 109.384   1718
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.06 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 22.34 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.24), residues: 1206
  helix:  1.35 (0.39), residues: 191
  sheet: -1.24 (0.26), residues: 366
  loop : -1.09 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 115 
 TYR   0.012   0.001   TYR A 661 
 PHE   0.016   0.001   PHE A 121 
 TRP   0.006   0.001   TRP B 230 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9815)
  covalent geometry    : angle       0.55972 (13287)
  SS BOND              : bond        0.00317 (   17)
  SS BOND              : angle       2.05529 (   34)
  hydrogen bonds       : bond        0.02930 (  306)
  hydrogen bonds       : angle       5.45256 (  810)
  link_ALPHA1-3        : bond        0.00915 (    2)
  link_ALPHA1-3        : angle       2.49280 (    6)
  link_ALPHA1-6        : bond        0.00813 (    2)
  link_ALPHA1-6        : angle       1.51773 (    6)
  link_BETA1-4         : bond        0.00249 (    8)
  link_BETA1-4         : angle       2.06232 (   24)
  link_NAG-ASN         : bond        0.00603 (    8)
  link_NAG-ASN         : angle       2.61588 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  60 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 38
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.8351 (tt0) cc_final: 0.7980 (tp-100)
REVERT: A  418 MET cc_start: 0.9122 (ttp) cc_final: 0.8857 (ttm)
REVERT: A  440 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8381 (t80)
REVERT: A  610 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.5787 (tm-30)
REVERT: A  660 THR cc_start: 0.8896 (p) cc_final: 0.8562 (p)
REVERT: B   57 MET cc_start: 0.6121 (tpp) cc_final: 0.5840 (tpp)
  outliers start: 22
  outliers final: 14
  residues processed: 60
  average time/residue: 0.8504
  time to fit residues: 57.4235
Evaluate side-chains
  51 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 35
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   43 GLN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  478 CYS
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  378 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 15 optimal weight:   30.0000
   chunk 57 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   chunk 96 optimal weight:    0.6980
   chunk 104 optimal weight:    0.0770
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.8540

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.132647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.081227 restraints weight = 48857.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.98
r_work: 0.3100 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.7586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   9852  Z= 0.157
  Angle     :  0.599  11.035  13381  Z= 0.297
  Chirality :  0.045   0.272   1535
  Planarity :  0.005   0.128   1735
  Dihedral  :  7.314 109.553   1718
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.64 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.34 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.24), residues: 1206
  helix:  1.35 (0.39), residues: 191
  sheet: -1.15 (0.26), residues: 363
  loop : -1.10 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 684 
 TYR   0.015   0.001   TYR A 176 
 PHE   0.022   0.001   PHE A 611 
 TRP   0.007   0.001   TRP B 230 
 HIS   0.004   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9815)
  covalent geometry    : angle       0.57129 (13287)
  SS BOND              : bond        0.00389 (   17)
  SS BOND              : angle       2.04065 (   34)
  hydrogen bonds       : bond        0.03042 (  306)
  hydrogen bonds       : angle       5.40690 (  810)
  link_ALPHA1-3        : bond        0.00907 (    2)
  link_ALPHA1-3        : angle       2.62438 (    6)
  link_ALPHA1-6        : bond        0.00796 (    2)
  link_ALPHA1-6        : angle       1.50923 (    6)
  link_BETA1-4         : bond        0.00253 (    8)
  link_BETA1-4         : angle       2.12600 (   24)
  link_NAG-ASN         : bond        0.00586 (    8)
  link_NAG-ASN         : angle       2.60445 (   24)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  579 is missing expected H atoms. Skipping.
Residue THR  693 is missing expected H atoms. Skipping.
Residue THR  695 is missing expected H atoms. Skipping.
Residue SER  114 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Evaluate side-chains
  57 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 37
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 MET cc_start: 0.9109 (ttp) cc_final: 0.8805 (ttm)
REVERT: A  440 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8288 (t80)
REVERT: A  610 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.5826 (tm-30)
REVERT: A  660 THR cc_start: 0.8910 (p) cc_final: 0.8584 (p)
REVERT: B   57 MET cc_start: 0.6120 (tpp) cc_final: 0.5836 (tpp)
REVERT: B  172 LYS cc_start: 0.8434 (mptt) cc_final: 0.8048 (mptt)
  outliers start: 20
  outliers final: 14
  residues processed: 56
  average time/residue: 0.9054
  time to fit residues: 56.7345
Evaluate side-chains
  53 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 37
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   43 GLN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  478 CYS
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue   94 ASN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  378 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 100 optimal weight:    0.5980
   chunk 111 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 119 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 66 optimal weight:    2.9990
   chunk 90 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 401 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.132712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.081018 restraints weight = 48866.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 3.02
r_work: 0.3097 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.7688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   9852  Z= 0.139
  Angle     :  0.586  10.244  13381  Z= 0.290
  Chirality :  0.045   0.249   1535
  Planarity :  0.004   0.127   1735
  Dihedral  :  7.262 109.193   1718
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.14 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 22.44 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.24), residues: 1206
  helix:  1.39 (0.39), residues: 191
  sheet: -1.14 (0.26), residues: 365
  loop : -1.07 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 684 
 TYR   0.012   0.001   TYR A 661 
 PHE   0.017   0.001   PHE A 121 
 TRP   0.006   0.001   TRP B 230 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9815)
  covalent geometry    : angle       0.55951 (13287)
  SS BOND              : bond        0.00376 (   17)
  SS BOND              : angle       1.87857 (   34)
  hydrogen bonds       : bond        0.02987 (  306)
  hydrogen bonds       : angle       5.37972 (  810)
  link_ALPHA1-3        : bond        0.00899 (    2)
  link_ALPHA1-3        : angle       2.50684 (    6)
  link_ALPHA1-6        : bond        0.00787 (    2)
  link_ALPHA1-6        : angle       1.48477 (    6)
  link_BETA1-4         : bond        0.00243 (    8)
  link_BETA1-4         : angle       2.06296 (   24)
  link_NAG-ASN         : bond        0.00589 (    8)
  link_NAG-ASN         : angle       2.56008 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7972.44 seconds
wall clock time: 135 minutes 29.25 seconds (8129.25 seconds total)