Starting phenix.real_space_refine
on Mon May 12 19:35:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fjf_50502/05_2025/9fjf_50502.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fjf_50502/05_2025/9fjf_50502.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fjf_50502/05_2025/9fjf_50502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fjf_50502/05_2025/9fjf_50502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fjf_50502/05_2025/9fjf_50502.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fjf_50502/05_2025/9fjf_50502.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.008 sd=   1.041
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: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    5922      2.51       5
     N    1519      2.21       5
     O    1824      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9307
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 3166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 3166
          Classifications: {'peptide': 391}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 370}
    Chain: "B"
      Number of atoms: 3854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 487, 3854
          Classifications: {'peptide': 487}
          Link IDs: {'PTRANS': 33, 'TRANS': 453}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 1014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1014
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
    Chain: "D"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 888
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 5, 'TRANS': 110}
          Chain breaks: 1
    Chain: "E"
      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: "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: "H"
      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: "I"
      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: "J"
      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: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 68
          Unusual residues: {'MES': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 78
          Unusual residues: {'MES': 3, 'NAG': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
    Chain: "B"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "D"
      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: 5.96, per 1000 atoms: 0.64
  Number of scatterers: 9307
  At special positions: 0
  Unit cell: (89.725, 114.7, 135.975, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1824      8.00
     N    1519      7.00
     C    5922      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 329 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 318 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  95 " 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 I   3 " - " MAN I   4 "
    ALPHA1-6
      " BMA I   3 " - " MAN I   5 "
    BETA1-4
      " 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 H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A  45 "
      " NAG A 502 " - " ASN A 224 "
      " NAG A 503 " - " ASN A 304 "
      " NAG A 504 " - " ASN A 105 "
      " NAG B 501 " - " ASN B  59 "
      " NAG B 502 " - " ASN B 146 "
      " NAG B 503 " - " ASN B 270 "
      " NAG E   1 " - " ASN A  68 "
      " NAG F   1 " - " ASN A 206 "
      " NAG G   1 " - " ASN A 249 "
      " NAG H   1 " - " ASN A 325 "
      " NAG I   1 " - " ASN A 412 "
      " NAG J   1 " - " ASN B  19 "
  Time building additional restraints: 2.49
  Conformation dependent library (CDL) restraints added in 992.6 milliseconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2082

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 14 sheets defined
      20.3% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 55
      removed outlier: 3.619A  pdb=" N   LYS A  55 " --> pdb=" O   ASP A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 77
      removed outlier: 4.058A  pdb=" N   LEU A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ARG A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 72 through 77'
    Processing helix  chain 'A' and resid 127 through 130
    Processing helix  chain 'A' and resid 137 through 149
      removed outlier: 3.824A  pdb=" N   LEU A 141 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER A 147 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLN A 148 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 163
      removed outlier: 3.943A  pdb=" N   LYS A 161 " --> pdb=" O   GLU A 157 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA A 162 " --> pdb=" O   ALA A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 179
    Processing helix  chain 'A' and resid 183 through 190
      removed outlier: 3.904A  pdb=" N   VAL A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 331
    Processing helix  chain 'A' and resid 339 through 343
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 4.077A  pdb=" N   VAL A 350 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ILE A 353 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 429
      removed outlier: 3.867A  pdb=" N   SER A 427 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   MET A 428 " --> pdb=" O   ARG A 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 94
      removed outlier: 3.562A  pdb=" N   ALA B  90 " --> pdb=" O   THR B  86 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 109
      removed outlier: 3.655A  pdb=" N   TYR B 108 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 157
      removed outlier: 3.507A  pdb=" N   THR B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS B 157 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 165
      removed outlier: 3.758A  pdb=" N   LEU B 165 " --> pdb=" O   ILE B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 168
      No H-bonds generated for 'chain 'B' and resid 166 through 168'
    Processing helix  chain 'B' and resid 203 through 210
    Processing helix  chain 'B' and resid 211 through 221
      removed outlier: 3.637A  pdb=" N   LYS B 215 " --> pdb=" O   ARG B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 224
      No H-bonds generated for 'chain 'B' and resid 222 through 224'
    Processing helix  chain 'B' and resid 254 through 263
      removed outlier: 3.846A  pdb=" N   ASP B 258 " --> pdb=" O   GLU B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 271
      removed outlier: 3.561A  pdb=" N   ALA B 269 " --> pdb=" O   GLY B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 296
      removed outlier: 3.630A  pdb=" N   ALA B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LYS B 293 " --> pdb=" O   PRO B 289 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL B 294 " --> pdb=" O   HIS B 290 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   VAL B 295 " --> pdb=" O   TRP B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 331
      removed outlier: 4.346A  pdb=" N   HIS B 328 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   ARG B 329 " --> pdb=" O   GLY B 325 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LEU B 330 " --> pdb=" O   GLU B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 371
      removed outlier: 3.786A  pdb=" N   MET B 361 " --> pdb=" O   TRP B 357 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   GLN B 362 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   TYR B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER B 364 " --> pdb=" O   GLY B 360 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B 371 " --> pdb=" O   ILE B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 374
      No H-bonds generated for 'chain 'B' and resid 372 through 374'
    Processing helix  chain 'B' and resid 414 through 427
      removed outlier: 4.325A  pdb=" N   TYR B 418 " --> pdb=" O   GLN B 414 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   PHE B 423 " --> pdb=" O   HIS B 419 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   PHE B 426 " --> pdb=" O   HIS B 422 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE B 427 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.505A  pdb=" N   TYR C  31 " --> pdb=" O   THR C  28 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86
      removed outlier: 3.805A  pdb=" N   PHE A  66 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TYR A  61 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER A 414 " --> pdb=" O   TYR A  61 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A  67 " --> pdb=" O   VAL A 408 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   VAL A 408 " --> pdb=" O   PHE A  67 " (cutoff:3.500A)
      removed outlier: 11.924A  pdb=" N   VAL A  69 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   PHE A 406 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET A 404 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ILE A 385 " --> pdb=" O   VAL A 408 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   TYR A 410 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   PHE A 383 " --> pdb=" O   TYR A 410 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   ASN A 412 " --> pdb=" O   LYS A 381 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LYS A 381 " --> pdb=" O   ASN A 412 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   SER A 414 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ALA A 379 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   LYS A 378 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA A 380 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   PHE A 366 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   LYS A 296 " --> pdb=" O   PHE A 281 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   PHE A 281 " --> pdb=" O   LYS A 296 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 215
      removed outlier: 3.800A  pdb=" N   TYR A 213 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 111 " --> pdb=" O   TYR A 213 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   THR A 108 " --> pdb=" O   PHE A 102 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   PHE A 102 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   SER A 110 " --> pdb=" O   ILE A 100 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   ILE A 100 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   VAL A  60 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TYR A  61 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER A 414 " --> pdb=" O   TYR A  61 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A  67 " --> pdb=" O   VAL A 408 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   VAL A 408 " --> pdb=" O   PHE A  67 " (cutoff:3.500A)
      removed outlier: 11.924A  pdb=" N   VAL A  69 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   PHE A 406 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET A 404 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ILE A 385 " --> pdb=" O   VAL A 408 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   TYR A 410 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   PHE A 383 " --> pdb=" O   TYR A 410 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   ASN A 412 " --> pdb=" O   LYS A 381 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LYS A 381 " --> pdb=" O   ASN A 412 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   SER A 414 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ALA A 379 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 135
    Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181
    Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 19
      removed outlier: 3.529A  pdb=" N   CYS B  18 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LEU B 385 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 55
      removed outlier: 3.629A  pdb=" N   TRP B 494 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B 449 " --> pdb=" O   VAL B 457 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL B 459 " --> pdb=" O   VAL B 447 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL B 447 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLN B 432 " --> pdb=" O   MET B 450 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 437
      removed outlier: 3.832A  pdb=" N   LYS B 473 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU B  69 " --> pdb=" O   LYS B 473 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 177
      removed outlier: 3.911A  pdb=" N   SER B 177 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE B 118 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 308 through 311
    Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.912A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47
      removed outlier: 3.828A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 126 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   VAL C 126 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 50
      removed outlier: 3.602A  pdb=" N   CYS C  50 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   TYR C  59 " --> pdb=" O   CYS C  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 23
      removed outlier: 3.926A  pdb=" N   THR D  68 " --> pdb=" O   GLN D  81 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 59
      removed outlier: 3.578A  pdb=" N   ASN D  58 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   TYR D  50 " --> pdb=" O   ASN D  58 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL D  48 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    600 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: 2.53

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1930
        1.33 -     1.45: 2447
        1.45 -     1.58: 5085
        1.58 -     1.70: 0
        1.70 -     1.83: 63
  Bond restraints: 9525
  Sorted by residual:
  bond pdb=" C   HIS A 357 "
       pdb=" N   PRO A 358 "
    ideal  model  delta    sigma   weight residual
    1.328  1.406 -0.077 1.26e-02 6.30e+03 3.76e+01
  bond pdb=" N   VAL A 229 "
       pdb=" CA  VAL A 229 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.036 9.00e-03 1.23e+04 1.56e+01
  bond pdb=" N   SER B 400 "
       pdb=" CA  SER B 400 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.036 9.20e-03 1.18e+04 1.51e+01
  bond pdb=" N   VAL C 128 "
       pdb=" CA  VAL C 128 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 9.00e-03 1.23e+04 1.50e+01
  bond pdb=" CA  PRO A  56 "
       pdb=" C   PRO A  56 "
    ideal  model  delta    sigma   weight residual
    1.514  1.536 -0.021 5.50e-03 3.31e+04 1.49e+01
  ... (remaining 9520 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 11127
        1.49 -     2.98: 1493
        2.98 -     4.47: 303
        4.47 -     5.96: 31
        5.96 -     7.45: 3
  Bond angle restraints: 12957
  Sorted by residual:
  angle pdb=" N   ARG C 100 "
        pdb=" CA  ARG C 100 "
        pdb=" C   ARG C 100 "
      ideal   model   delta    sigma   weight residual
     112.88  107.75    5.13 1.29e+00 6.01e-01 1.58e+01
  angle pdb=" CA  VAL A 112 "
        pdb=" C   VAL A 112 "
        pdb=" O   VAL A 112 "
      ideal   model   delta    sigma   weight residual
     121.63  117.78    3.85 9.90e-01 1.02e+00 1.52e+01
  angle pdb=" N   PRO B 150 "
        pdb=" CA  PRO B 150 "
        pdb=" C   PRO B 150 "
      ideal   model   delta    sigma   weight residual
     111.13  116.89   -5.76 1.49e+00 4.50e-01 1.49e+01
  angle pdb=" N   HIS B 274 "
        pdb=" CA  HIS B 274 "
        pdb=" C   HIS B 274 "
      ideal   model   delta    sigma   weight residual
     114.39  108.80    5.59 1.45e+00 4.76e-01 1.48e+01
  angle pdb=" CA  GLU A 354 "
        pdb=" C   GLU A 354 "
        pdb=" O   GLU A 354 "
      ideal   model   delta    sigma   weight residual
     121.94  117.53    4.41 1.15e+00 7.56e-01 1.47e+01
  ... (remaining 12952 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.68: 5416
       21.68 -    43.35: 385
       43.35 -    65.03: 88
       65.03 -    86.70: 17
       86.70 -   108.38: 9
  Dihedral angle restraints: 5915
    sinusoidal: 2658
      harmonic: 3257
  Sorted by residual:
  dihedral pdb=" CB  CYS A 274 "
           pdb=" SG  CYS A 274 "
           pdb=" SG  CYS A 329 "
           pdb=" CB  CYS A 329 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.61   76.61     1      1.00e+01 1.00e-02 7.38e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  95 "
           pdb=" CB  CYS D  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -120.33   34.33     1      1.00e+01 1.00e-02 1.67e+01
  dihedral pdb=" O4  BMA I   3 "
           pdb=" C4  BMA I   3 "
           pdb=" C5  BMA I   3 "
           pdb=" O5  BMA I   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -179.67  108.38     1      3.00e+01 1.11e-03 1.40e+01
  ... (remaining 5912 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 1271
       0.108 -    0.217: 182
       0.217 -    0.325: 11
       0.325 -    0.433: 1
       0.433 -    0.541: 3
  Chirality restraints: 1468
  Sorted by residual:
  chirality pdb=" C1  MAN I   5 "
            pdb=" O6  BMA I   3 "
            pdb=" C2  MAN I   5 "
            pdb=" O5  MAN I   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.94    0.46 2.00e-02 2.50e+03 5.25e+02
  chirality pdb=" C1  NAG G   2 "
            pdb=" O4  NAG G   1 "
            pdb=" C2  NAG G   2 "
            pdb=" O5  NAG G   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-02 2.50e+03 2.08e+02
  chirality pdb=" C1  MAN I   4 "
            pdb=" O3  BMA I   3 "
            pdb=" C2  MAN I   4 "
            pdb=" O5  MAN I   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.17    0.23 2.00e-02 2.50e+03 1.28e+02
  ... (remaining 1465 not shown)

  Planarity restraints: 1638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG J   2 "   -0.284 2.00e-02 2.50e+03   2.43e-01 7.41e+02
        pdb=" C7  NAG J   2 "    0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG J   2 "   -0.163 2.00e-02 2.50e+03
        pdb=" N2  NAG J   2 "    0.427 2.00e-02 2.50e+03
        pdb=" O7  NAG J   2 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG I   2 "   -0.280 2.00e-02 2.50e+03   2.37e-01 7.02e+02
        pdb=" C7  NAG I   2 "    0.071 2.00e-02 2.50e+03
        pdb=" C8  NAG I   2 "   -0.176 2.00e-02 2.50e+03
        pdb=" N2  NAG I   2 "    0.407 2.00e-02 2.50e+03
        pdb=" O7  NAG I   2 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG I   1 "   -0.271 2.00e-02 2.50e+03   2.33e-01 6.79e+02
        pdb=" C7  NAG I   1 "    0.059 2.00e-02 2.50e+03
        pdb=" C8  NAG I   1 "    0.012 2.00e-02 2.50e+03
        pdb=" N2  NAG I   1 "    0.395 2.00e-02 2.50e+03
        pdb=" O7  NAG I   1 "   -0.196 2.00e-02 2.50e+03
  ... (remaining 1635 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1673
        2.78 -     3.31: 7955
        3.31 -     3.84: 12841
        3.84 -     4.37: 14329
        4.37 -     4.90: 26055
  Nonbonded interactions: 62853
  Sorted by model distance:
  nonbonded pdb=" O   MET B 123 "
            pdb=" OH  TYR B 135 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" NH2 ARG B  47 "
            pdb=" OG  SER D  56 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O3  NAG A 501 "
            pdb=" O7  NAG A 501 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OE1 GLU B  41 "
            pdb=" O   HOH B 601 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" NE2 GLN D   1 "
            pdb=" O   GLN D   3 "
     model   vdw
     2.315 3.120
  ... (remaining 62848 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 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'J'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.700
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
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      :  0.009   0.077   9553  Z= 0.617
  Angle     :  1.080  10.851  13036  Z= 0.730
  Chirality :  0.074   0.541   1468
  Planarity :  0.015   0.243   1625
  Dihedral  : 15.892 108.379   3818
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 14.36 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.24), residues: 1112
  helix: -1.01 (0.40), residues: 146
  sheet: -0.33 (0.32), residues: 271
  loop : -1.92 (0.22), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 116 
 HIS   0.005   0.001   HIS B  60 
 PHE   0.013   0.001   PHE A 269 
 TYR   0.025   0.001   TYR C 105 
 ARG   0.004   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00825 (   13)
  link_NAG-ASN         : angle       4.05045 (   39)
  link_ALPHA1-6        : bond        0.00085 (    1)
  link_ALPHA1-6        : angle       3.89702 (    3)
  link_BETA1-4         : bond        0.00901 (    8)
  link_BETA1-4         : angle       2.19252 (   24)
  link_ALPHA1-3        : bond        0.01169 (    1)
  link_ALPHA1-3        : angle       2.23106 (    3)
  hydrogen bonds       : bond        0.24728 (  221)
  hydrogen bonds       : angle       7.15292 (  600)
  SS BOND              : bond        0.00387 (    5)
  SS BOND              : angle       0.99859 (   10)
  covalent geometry    : bond        0.00856 ( 9525)
  covalent geometry    : angle       1.05352 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7940 (mt) cc_final: 0.7528 (mt)
REVERT: A  100 ILE cc_start: 0.8155 (mm) cc_final: 0.7928 (mm)
REVERT: B  408 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7933 (mtpp)
REVERT: C   83 MET cc_start: 0.6419 (mmm) cc_final: 0.6062 (mmm)
REVERT: C   95 TYR cc_start: 0.7630 (m-80) cc_final: 0.7094 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 117
  average time/residue: 0.2041
  time to fit residues: 33.4831
Evaluate side-chains
  97 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 164 GLN
A 357 HIS
B 226 GLN
B 442 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.176005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.148447 restraints weight = 11314.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.145806 restraints weight = 22563.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.132030 restraints weight = 22867.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9553  Z= 0.184
  Angle     :  0.736  17.397  13036  Z= 0.363
  Chirality :  0.047   0.262   1468
  Planarity :  0.005   0.080   1625
  Dihedral  :  9.709  72.140   1751
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 14.46 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.24), residues: 1112
  helix: -0.64 (0.39), residues: 153
  sheet: -0.23 (0.31), residues: 276
  loop : -2.02 (0.22), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 494 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.015   0.002   PHE B  81 
 TYR   0.018   0.002   TYR A 410 
 ARG   0.003   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00943 (   13)
  link_NAG-ASN         : angle       4.77671 (   39)
  link_ALPHA1-6        : bond        0.00854 (    1)
  link_ALPHA1-6        : angle       1.39492 (    3)
  link_BETA1-4         : bond        0.00792 (    8)
  link_BETA1-4         : angle       2.32633 (   24)
  link_ALPHA1-3        : bond        0.01596 (    1)
  link_ALPHA1-3        : angle       1.80550 (    3)
  hydrogen bonds       : bond        0.06683 (  221)
  hydrogen bonds       : angle       5.37410 (  600)
  SS BOND              : bond        0.00433 (    5)
  SS BOND              : angle       0.76366 (   10)
  covalent geometry    : bond        0.00403 ( 9525)
  covalent geometry    : angle       0.68155 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6861 (tt0)
REVERT: A   76 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7042 (mm)
REVERT: A  267 TYR cc_start: 0.8790 (m-80) cc_final: 0.8569 (m-80)
REVERT: B  104 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9060 (tt)
REVERT: B  303 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7126 (tptp)
REVERT: C  102 GLN cc_start: 0.8898 (mp10) cc_final: 0.8545 (mm-40)
  outliers start: 32
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1887
  time to fit residues: 33.2967
Evaluate side-chains
  111 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  441 LYS
Chi-restraints excluded: chain B residue  442 ASN
Chi-restraints excluded: chain B residue  467 ASP
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   69 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 108 optimal weight:    5.9990
   chunk 86 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 89 optimal weight:    9.9990
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.175682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.151764 restraints weight = 11401.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.131648 restraints weight = 24451.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.126999 restraints weight = 16909.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9553  Z= 0.152
  Angle     :  0.639  11.866  13036  Z= 0.321
  Chirality :  0.045   0.238   1468
  Planarity :  0.005   0.073   1625
  Dihedral  :  8.629  63.226   1751
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.08 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.23), residues: 1112
  helix: -0.45 (0.40), residues: 152
  sheet: -0.22 (0.31), residues: 267
  loop : -2.10 (0.21), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 179 
 HIS   0.003   0.001   HIS B 255 
 PHE   0.011   0.001   PHE B 259 
 TYR   0.017   0.001   TYR A 410 
 ARG   0.003   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00843 (   13)
  link_NAG-ASN         : angle       3.61926 (   39)
  link_ALPHA1-6        : bond        0.00890 (    1)
  link_ALPHA1-6        : angle       1.31500 (    3)
  link_BETA1-4         : bond        0.00599 (    8)
  link_BETA1-4         : angle       1.97309 (   24)
  link_ALPHA1-3        : bond        0.01321 (    1)
  link_ALPHA1-3        : angle       1.28680 (    3)
  hydrogen bonds       : bond        0.05943 (  221)
  hydrogen bonds       : angle       5.06101 (  600)
  SS BOND              : bond        0.00363 (    5)
  SS BOND              : angle       0.69175 (   10)
  covalent geometry    : bond        0.00329 ( 9525)
  covalent geometry    : angle       0.60222 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6594 (tt0)
REVERT: A   76 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7014 (mm)
REVERT: A  267 TYR cc_start: 0.8765 (m-80) cc_final: 0.8525 (m-80)
REVERT: A  372 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6902 (mt)
REVERT: B  104 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9050 (tt)
REVERT: B  166 GLN cc_start: 0.8511 (tp40) cc_final: 0.7669 (tt0)
REVERT: B  303 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7113 (tptp)
REVERT: B  310 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8401 (m)
REVERT: C  102 GLN cc_start: 0.8826 (mp10) cc_final: 0.8538 (mm-40)
  outliers start: 24
  outliers final: 13
  residues processed: 116
  average time/residue: 0.1842
  time to fit residues: 31.4745
Evaluate side-chains
  108 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  467 ASP
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   69 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 98 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 86 optimal weight:    0.4980
   chunk 88 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0030
   chunk 101 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
A 357 HIS
B 442 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.178385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.154597 restraints weight = 11254.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.151247 restraints weight = 23197.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.131675 restraints weight = 27107.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9553  Z= 0.113
  Angle     :  0.562   9.031  13036  Z= 0.282
  Chirality :  0.043   0.224   1468
  Planarity :  0.004   0.059   1625
  Dihedral  :  7.332  54.203   1748
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.39 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.23), residues: 1112
  helix: -0.15 (0.41), residues: 154
  sheet: -0.29 (0.30), residues: 275
  loop : -2.11 (0.22), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 494 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.009   0.001   PHE B 411 
 TYR   0.016   0.001   TYR A 410 
 ARG   0.002   0.000   ARG B  47 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00591 (   13)
  link_NAG-ASN         : angle       2.92110 (   39)
  link_ALPHA1-6        : bond        0.00752 (    1)
  link_ALPHA1-6        : angle       1.39654 (    3)
  link_BETA1-4         : bond        0.00558 (    8)
  link_BETA1-4         : angle       1.65819 (   24)
  link_ALPHA1-3        : bond        0.01305 (    1)
  link_ALPHA1-3        : angle       1.33933 (    3)
  hydrogen bonds       : bond        0.04277 (  221)
  hydrogen bonds       : angle       4.75079 (  600)
  SS BOND              : bond        0.00273 (    5)
  SS BOND              : angle       0.60253 (   10)
  covalent geometry    : bond        0.00235 ( 9525)
  covalent geometry    : angle       0.53516 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6679 (tt0)
REVERT: A   76 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7141 (mm)
REVERT: A  115 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7379 (mtpt)
REVERT: A  267 TYR cc_start: 0.8728 (m-80) cc_final: 0.8489 (m-80)
REVERT: A  372 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6948 (mt)
REVERT: B  166 GLN cc_start: 0.8233 (tp40) cc_final: 0.7643 (tt0)
REVERT: C  102 GLN cc_start: 0.8853 (mp10) cc_final: 0.8585 (mm-40)
  outliers start: 28
  outliers final: 14
  residues processed: 114
  average time/residue: 0.1767
  time to fit residues: 30.2627
Evaluate side-chains
  105 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  442 ASN
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   69 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0070
   chunk 46 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   chunk 102 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 87 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0570
   chunk 104 optimal weight:   20.0000
   chunk 106 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.3716

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

Flipped N/Q/H residues before XYZ refinement:
A 357 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.179086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.152635 restraints weight = 11290.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.138624 restraints weight = 23865.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.133539 restraints weight = 16838.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9553  Z= 0.106
  Angle     :  0.543   8.258  13036  Z= 0.271
  Chirality :  0.042   0.221   1468
  Planarity :  0.004   0.059   1625
  Dihedral  :  7.039  53.908   1748
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.12 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.24), residues: 1112
  helix: -0.02 (0.41), residues: 155
  sheet: -0.37 (0.30), residues: 280
  loop : -2.05 (0.22), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 179 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.011   0.001   PHE B 411 
 TYR   0.015   0.001   TYR A 410 
 ARG   0.002   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00604 (   13)
  link_NAG-ASN         : angle       2.78479 (   39)
  link_ALPHA1-6        : bond        0.00649 (    1)
  link_ALPHA1-6        : angle       1.45156 (    3)
  link_BETA1-4         : bond        0.00551 (    8)
  link_BETA1-4         : angle       1.50203 (   24)
  link_ALPHA1-3        : bond        0.01315 (    1)
  link_ALPHA1-3        : angle       1.31233 (    3)
  hydrogen bonds       : bond        0.04001 (  221)
  hydrogen bonds       : angle       4.61933 (  600)
  SS BOND              : bond        0.00246 (    5)
  SS BOND              : angle       0.56098 (   10)
  covalent geometry    : bond        0.00217 ( 9525)
  covalent geometry    : angle       0.51740 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6667 (tt0)
REVERT: A   76 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7009 (mm)
REVERT: A  115 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7438 (mtpt)
REVERT: A  372 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6944 (mt)
REVERT: B  166 GLN cc_start: 0.8249 (tp40) cc_final: 0.7688 (tt0)
REVERT: B  443 ASP cc_start: 0.8338 (t0) cc_final: 0.7906 (t0)
REVERT: C  102 GLN cc_start: 0.8907 (mp10) cc_final: 0.8669 (mm-40)
  outliers start: 21
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1733
  time to fit residues: 28.1892
Evaluate side-chains
  103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   69 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 67 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 36 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0970
   chunk 39 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 357 HIS
B  60 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.177929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.153637 restraints weight = 11300.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.150312 restraints weight = 20065.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.132783 restraints weight = 24931.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9553  Z= 0.115
  Angle     :  0.549   7.409  13036  Z= 0.276
  Chirality :  0.043   0.205   1468
  Planarity :  0.004   0.056   1625
  Dihedral  :  6.745  58.547   1748
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.53 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.24), residues: 1112
  helix:  0.07 (0.41), residues: 154
  sheet: -0.33 (0.30), residues: 280
  loop : -2.04 (0.22), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 179 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE A 256 
 TYR   0.015   0.001   TYR A 410 
 ARG   0.002   0.000   ARG B  47 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00564 (   13)
  link_NAG-ASN         : angle       2.74139 (   39)
  link_ALPHA1-6        : bond        0.00576 (    1)
  link_ALPHA1-6        : angle       1.58918 (    3)
  link_BETA1-4         : bond        0.00537 (    8)
  link_BETA1-4         : angle       1.43932 (   24)
  link_ALPHA1-3        : bond        0.01218 (    1)
  link_ALPHA1-3        : angle       1.08816 (    3)
  hydrogen bonds       : bond        0.04346 (  221)
  hydrogen bonds       : angle       4.49927 (  600)
  SS BOND              : bond        0.00280 (    5)
  SS BOND              : angle       0.60221 (   10)
  covalent geometry    : bond        0.00243 ( 9525)
  covalent geometry    : angle       0.52538 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6792 (tt0)
REVERT: A   76 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7156 (mm)
REVERT: A  372 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6905 (mt)
REVERT: B  123 MET cc_start: 0.6374 (mtp) cc_final: 0.6031 (mtp)
REVERT: B  333 ASN cc_start: 0.7387 (m110) cc_final: 0.6806 (m-40)
REVERT: B  443 ASP cc_start: 0.8261 (t0) cc_final: 0.7867 (t0)
REVERT: C  102 GLN cc_start: 0.8871 (mp10) cc_final: 0.8650 (mm-40)
  outliers start: 25
  outliers final: 15
  residues processed: 105
  average time/residue: 0.1793
  time to fit residues: 28.0165
Evaluate side-chains
  99 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  467 ASP
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   51 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 1 optimal weight:    0.1980
   chunk 61 optimal weight:    0.5980
   chunk 96 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.177464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.134508 restraints weight = 11378.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.132016 restraints weight = 15149.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.131865 restraints weight = 12602.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9553  Z= 0.120
  Angle     :  0.550   7.270  13036  Z= 0.277
  Chirality :  0.043   0.202   1468
  Planarity :  0.004   0.055   1625
  Dihedral  :  6.655  59.408   1748
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.25 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.24), residues: 1112
  helix:  0.01 (0.40), residues: 154
  sheet: -0.36 (0.30), residues: 286
  loop : -2.08 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 179 
 HIS   0.003   0.001   HIS B  60 
 PHE   0.020   0.001   PHE A 256 
 TYR   0.016   0.001   TYR A 410 
 ARG   0.003   0.000   ARG B  47 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00561 (   13)
  link_NAG-ASN         : angle       2.70038 (   39)
  link_ALPHA1-6        : bond        0.00519 (    1)
  link_ALPHA1-6        : angle       1.48258 (    3)
  link_BETA1-4         : bond        0.00506 (    8)
  link_BETA1-4         : angle       1.48441 (   24)
  link_ALPHA1-3        : bond        0.01412 (    1)
  link_ALPHA1-3        : angle       1.15917 (    3)
  hydrogen bonds       : bond        0.04496 (  221)
  hydrogen bonds       : angle       4.46852 (  600)
  SS BOND              : bond        0.00280 (    5)
  SS BOND              : angle       0.59553 (   10)
  covalent geometry    : bond        0.00261 ( 9525)
  covalent geometry    : angle       0.52635 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6836 (tt0)
REVERT: A   76 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7207 (mm)
REVERT: A  372 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6946 (mt)
REVERT: B  333 ASN cc_start: 0.7420 (m110) cc_final: 0.6846 (m-40)
REVERT: B  443 ASP cc_start: 0.8174 (t0) cc_final: 0.7710 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 100
  average time/residue: 0.1805
  time to fit residues: 27.0150
Evaluate side-chains
  100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  126 CYS
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   51 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0270
   chunk 102 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 72 optimal weight:    9.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.6238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.177395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.149772 restraints weight = 11433.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.136342 restraints weight = 23009.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.130392 restraints weight = 16067.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9553  Z= 0.119
  Angle     :  0.551   6.985  13036  Z= 0.277
  Chirality :  0.042   0.195   1468
  Planarity :  0.004   0.053   1625
  Dihedral  :  6.582  59.849   1748
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.46 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.24), residues: 1112
  helix:  0.00 (0.40), residues: 154
  sheet: -0.36 (0.30), residues: 286
  loop : -2.11 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 179 
 HIS   0.003   0.001   HIS B  60 
 PHE   0.018   0.001   PHE A 256 
 TYR   0.015   0.001   TYR A 410 
 ARG   0.001   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00551 (   13)
  link_NAG-ASN         : angle       2.64908 (   39)
  link_ALPHA1-6        : bond        0.00502 (    1)
  link_ALPHA1-6        : angle       1.45018 (    3)
  link_BETA1-4         : bond        0.00509 (    8)
  link_BETA1-4         : angle       1.46826 (   24)
  link_ALPHA1-3        : bond        0.01355 (    1)
  link_ALPHA1-3        : angle       1.02360 (    3)
  hydrogen bonds       : bond        0.04414 (  221)
  hydrogen bonds       : angle       4.44380 (  600)
  SS BOND              : bond        0.00295 (    5)
  SS BOND              : angle       0.58441 (   10)
  covalent geometry    : bond        0.00260 ( 9525)
  covalent geometry    : angle       0.52810 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6733 (tt0)
REVERT: A   76 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6978 (mm)
REVERT: A  230 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7330 (tp30)
REVERT: B  303 LYS cc_start: 0.7572 (tptp) cc_final: 0.7282 (pttt)
REVERT: B  333 ASN cc_start: 0.7474 (m110) cc_final: 0.6927 (m-40)
REVERT: B  443 ASP cc_start: 0.8327 (t0) cc_final: 0.7898 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 104
  average time/residue: 0.1793
  time to fit residues: 27.7627
Evaluate side-chains
  101 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  126 CYS
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   51 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   chunk 57 optimal weight:    0.0020
   chunk 99 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.177794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.156072 restraints weight = 11245.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.133242 restraints weight = 21454.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.128747 restraints weight = 20955.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9553  Z= 0.112
  Angle     :  0.537   6.782  13036  Z= 0.271
  Chirality :  0.042   0.193   1468
  Planarity :  0.004   0.054   1625
  Dihedral  :  6.463  59.243   1748
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.36 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.24), residues: 1112
  helix:  0.05 (0.40), residues: 154
  sheet: -0.33 (0.30), residues: 286
  loop : -2.11 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 179 
 HIS   0.003   0.001   HIS B  60 
 PHE   0.022   0.001   PHE A 256 
 TYR   0.015   0.001   TYR A 410 
 ARG   0.001   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00534 (   13)
  link_NAG-ASN         : angle       2.55119 (   39)
  link_ALPHA1-6        : bond        0.00490 (    1)
  link_ALPHA1-6        : angle       1.42980 (    3)
  link_BETA1-4         : bond        0.00502 (    8)
  link_BETA1-4         : angle       1.42992 (   24)
  link_ALPHA1-3        : bond        0.01328 (    1)
  link_ALPHA1-3        : angle       0.97849 (    3)
  hydrogen bonds       : bond        0.04237 (  221)
  hydrogen bonds       : angle       4.41853 (  600)
  SS BOND              : bond        0.00274 (    5)
  SS BOND              : angle       0.59087 (   10)
  covalent geometry    : bond        0.00243 ( 9525)
  covalent geometry    : angle       0.51578 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7075 (mm)
REVERT: A  230 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7357 (tp30)
REVERT: B   44 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6274 (ttm170)
REVERT: B  333 ASN cc_start: 0.7450 (m110) cc_final: 0.6919 (m-40)
  outliers start: 21
  outliers final: 17
  residues processed: 98
  average time/residue: 0.2012
  time to fit residues: 29.7063
Evaluate side-chains
  101 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  126 CYS
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   82 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 107 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.175945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.151310 restraints weight = 11409.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.148652 restraints weight = 23278.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.131646 restraints weight = 25068.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9553  Z= 0.134
  Angle     :  0.571   6.954  13036  Z= 0.290
  Chirality :  0.043   0.187   1468
  Planarity :  0.004   0.053   1625
  Dihedral  :  6.532  59.728   1748
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.98 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.23), residues: 1112
  helix: -0.06 (0.40), residues: 154
  sheet: -0.49 (0.30), residues: 290
  loop : -2.10 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 179 
 HIS   0.003   0.001   HIS B  60 
 PHE   0.015   0.001   PHE B 411 
 TYR   0.016   0.001   TYR A 410 
 ARG   0.002   0.000   ARG B 359 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00575 (   13)
  link_NAG-ASN         : angle       2.70646 (   39)
  link_ALPHA1-6        : bond        0.00581 (    1)
  link_ALPHA1-6        : angle       1.41144 (    3)
  link_BETA1-4         : bond        0.00528 (    8)
  link_BETA1-4         : angle       1.52236 (   24)
  link_ALPHA1-3        : bond        0.01326 (    1)
  link_ALPHA1-3        : angle       0.99590 (    3)
  hydrogen bonds       : bond        0.04924 (  221)
  hydrogen bonds       : angle       4.46566 (  600)
  SS BOND              : bond        0.00331 (    5)
  SS BOND              : angle       0.64462 (   10)
  covalent geometry    : bond        0.00299 ( 9525)
  covalent geometry    : angle       0.54815 (12957)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7076 (mm)
REVERT: A  230 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7265 (tp30)
REVERT: B   44 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.6359 (ttm170)
REVERT: B  333 ASN cc_start: 0.7550 (m110) cc_final: 0.7037 (m-40)
REVERT: B  443 ASP cc_start: 0.8305 (t0) cc_final: 0.7861 (t0)
  outliers start: 19
  outliers final: 17
  residues processed: 103
  average time/residue: 0.1809
  time to fit residues: 27.9382
Evaluate side-chains
  103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  126 CYS
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   82 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0060
   chunk 88 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0770
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.3952

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

Flipped N/Q/H residues before XYZ refinement:
C 102 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.178569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.152623 restraints weight = 11275.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.135309 restraints weight = 22547.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.131482 restraints weight = 16136.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9553  Z= 0.102
  Angle     :  0.522   6.513  13036  Z= 0.264
  Chirality :  0.042   0.190   1468
  Planarity :  0.004   0.052   1625
  Dihedral  :  6.307  59.510   1748
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.29 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.24), residues: 1112
  helix:  0.15 (0.41), residues: 154
  sheet: -0.40 (0.29), residues: 298
  loop : -2.07 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 179 
 HIS   0.003   0.001   HIS B  60 
 PHE   0.010   0.001   PHE B 411 
 TYR   0.014   0.001   TYR A 410 
 ARG   0.001   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00494 (   13)
  link_NAG-ASN         : angle       2.37549 (   39)
  link_ALPHA1-6        : bond        0.00519 (    1)
  link_ALPHA1-6        : angle       1.39734 (    3)
  link_BETA1-4         : bond        0.00498 (    8)
  link_BETA1-4         : angle       1.39052 (   24)
  link_ALPHA1-3        : bond        0.01315 (    1)
  link_ALPHA1-3        : angle       0.93140 (    3)
  hydrogen bonds       : bond        0.03825 (  221)
  hydrogen bonds       : angle       4.36930 (  600)
  SS BOND              : bond        0.00255 (    5)
  SS BOND              : angle       0.58322 (   10)
  covalent geometry    : bond        0.00213 ( 9525)
  covalent geometry    : angle       0.50285 (12957)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2922.18 seconds
wall clock time: 52 minutes 4.54 seconds (3124.54 seconds total)