Starting phenix.real_space_refine
on Thu Jul  2 22:14:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdd_37132/07_2026/8kdd_37132.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdd_37132/07_2026/8kdd_37132.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdd_37132/07_2026/8kdd_37132.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdd_37132/07_2026/8kdd_37132.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdd_37132/07_2026/8kdd_37132.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdd_37132/07_2026/8kdd_37132.cif"
  }
  resolution = 3.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      2      4.86       5
     C    6872      2.51       5
     N    1734      2.21       5
     O    1978      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10626
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3513
          Classifications: {'peptide': 455}
          Link IDs: {'PTRANS': 23, 'TRANS': 431}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1686
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 205}
    Chain: "H"
      Number of atoms: 1689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1689
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          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: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'VRW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.91, per 1000 atoms: 0.18
  Number of scatterers: 10626
  At special positions: 0
  Unit cell: (79.794, 139.64, 150.381, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      40     16.00
     O    1978      8.00
     N    1734      7.00
     C    6872      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.17
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.10
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.08
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 202 " distance=2.08

  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
    NAG-ASN
      " NAG A 701 " - " ASN A 381 "
      " NAG A 702 " - " ASN A 506 "
      " NAG A 703 " - " ASN A 365 "
      " NAG A 704 " - " ASN A 424 "
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 280.5 milliseconds
  

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2516

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 12 sheets defined
      47.0% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 174
    Processing helix  chain 'A' and resid 175 through 206
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 4.276A  pdb=" N   GLY A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 255
      removed outlier: 3.705A  pdb=" N   GLY A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG A 247 " --> pdb=" O   GLY A 243 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   ASP A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   TYR A 250 " --> pdb=" O   GLY A 246 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 286 through 300
    Processing helix  chain 'A' and resid 322 through 341
      removed outlier: 3.633A  pdb=" N   VAL A 326 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   GLU A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 355 through 371
    Processing helix  chain 'A' and resid 384 through 395
      removed outlier: 4.218A  pdb=" N   SER A 394 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASN A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 427
    Processing helix  chain 'A' and resid 440 through 444
    Processing helix  chain 'A' and resid 449 through 458
      removed outlier: 3.557A  pdb=" N   MET A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
    Processing helix  chain 'A' and resid 504 through 507
    Processing helix  chain 'A' and resid 508 through 514
      removed outlier: 4.031A  pdb=" N   GLU A 514 " --> pdb=" O   LYS A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 533
    Processing helix  chain 'A' and resid 533 through 539
    Processing helix  chain 'A' and resid 584 through 588
      removed outlier: 4.208A  pdb=" N   SER A 588 " --> pdb=" O   ALA A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 614
      No H-bonds generated for 'chain 'A' and resid 612 through 614'
    Processing helix  chain 'B' and resid 51 through 65
      removed outlier: 3.791A  pdb=" N   THR B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLY B  65 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 71 through 80
      removed outlier: 3.845A  pdb=" N   VAL B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 4.050A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 125
      removed outlier: 3.929A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.652A  pdb=" N   ILE B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.938A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS B 178 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 221
    Processing helix  chain 'B' and resid 239 through 252
      removed outlier: 4.055A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 255
      No H-bonds generated for 'chain 'B' and resid 253 through 255'
    Processing helix  chain 'B' and resid 258 through 267
      removed outlier: 5.698A  pdb=" N   GLU B 265 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 280
      Proline residue:  B 275  - end of helix
      removed outlier: 3.548A  pdb=" N   ILE B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 298
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 310 through 321
      removed outlier: 3.652A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY B 321 " --> pdb=" O   ASN B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 324
      No H-bonds generated for 'chain 'B' and resid 322 through 324'
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.619A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 393 through 399
      removed outlier: 3.796A  pdb=" N   ILE B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 422
      removed outlier: 4.137A  pdb=" N   ASN B 404 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 454
      removed outlier: 3.577A  pdb=" N   ALA B 448 " --> pdb=" O   LEU B 444 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   THR B 454 " --> pdb=" O   SER B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 466
      removed outlier: 3.536A  pdb=" N   LEU B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 3.802A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 4.123A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.951A  pdb=" N   LEU L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 129 through 133
    Processing helix  chain 'L' and resid 189 through 194
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.737A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.578A  pdb=" N   LYS H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 136 through 140
      removed outlier: 3.933A  pdb=" N   ASN H 140 " --> pdb=" O   ALA H 137 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 194 through 198
      removed outlier: 3.606A  pdb=" N   GLU H 198 " --> pdb=" O   TRP H 195 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401
      removed outlier: 6.681A  pdb=" N   LEU A 376 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   THR A 401 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ALA A 378 " --> pdb=" O   THR A 401 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   GLY A 379 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL A 347 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE A 466 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 540 through 544
      removed outlier: 4.103A  pdb=" N   SER A 552 " --> pdb=" O   PHE A 544 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LEU A 623 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574
      removed outlier: 6.291A  pdb=" N   GLY A 573 " --> pdb=" O   ILE L 100 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.629A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.637A  pdb=" N   VAL L 139 " --> pdb=" O   PHE L 124 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 159 through 161
      removed outlier: 4.407A  pdb=" N   TRP L 154 " --> pdb=" O   ARG L 161 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA9, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.447A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   MET H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   GLU H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.447A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   TYR H 109 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 127 through 131
      removed outlier: 5.326A  pdb=" N   THR H 144 " --> pdb=" O   VAL H 190 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL H 190 " --> pdb=" O   THR H 144 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   GLY H 146 " --> pdb=" O   VAL H 188 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   VAL H 188 " --> pdb=" O   GLY H 146 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   LEU H 148 " --> pdb=" O   SER H 186 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   SER H 186 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   LYS H 150 " --> pdb=" O   LEU H 184 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LEU H 184 " --> pdb=" O   LYS H 150 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   SER H 185 " --> pdb=" O   PRO H 174 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   SER H 187 " --> pdb=" O   THR H 172 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   THR H 172 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   THR H 189 " --> pdb=" O   VAL H 170 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL H 170 " --> pdb=" O   THR H 189 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 201 through 205
      removed outlier: 3.589A  pdb=" N   LYS H 215 " --> pdb=" O   CYS H 202 " (cutoff:3.500A)

    540 hydrogen bonds defined for protein.
    1455 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1710
        1.31 -     1.44: 3021
        1.44 -     1.57: 6098
        1.57 -     1.71: 5
        1.71 -     1.84: 60
  Bond restraints: 10894
  Sorted by residual:
  bond pdb=" CG  HIS L  97 "
       pdb=" CD2 HIS L  97 "
    ideal  model  delta    sigma   weight residual
    1.354  1.267  0.087 1.10e-02 8.26e+03 6.22e+01
  bond pdb=" CB  HIS H  35 "
       pdb=" CG  HIS H  35 "
    ideal  model  delta    sigma   weight residual
    1.497  1.396  0.101 1.40e-02 5.10e+03 5.23e+01
  bond pdb=" CB  HIS L  97 "
       pdb=" CG  HIS L  97 "
    ideal  model  delta    sigma   weight residual
    1.497  1.402  0.095 1.40e-02 5.10e+03 4.58e+01
  bond pdb=" C   VAL A 256 "
       pdb=" O   VAL A 256 "
    ideal  model  delta    sigma   weight residual
    1.234  1.174  0.060 9.50e-03 1.11e+04 3.95e+01
  bond pdb=" ND1 HIS H  35 "
       pdb=" CE1 HIS H  35 "
    ideal  model  delta    sigma   weight residual
    1.321  1.372 -0.051 1.00e-02 1.00e+04 2.65e+01
  ... (remaining 10889 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.99: 13298
        2.99 -     5.98: 1417
        5.98 -     8.97: 118
        8.97 -    11.96: 13
       11.96 -    14.95: 2
  Bond angle restraints: 14848
  Sorted by residual:
  angle pdb=" C   GLN A 579 "
        pdb=" CA  GLN A 579 "
        pdb=" CB  GLN A 579 "
      ideal   model   delta    sigma   weight residual
     111.70  123.06  -11.36 1.52e+00 4.33e-01 5.58e+01
  angle pdb=" N   HIS A 619 "
        pdb=" CA  HIS A 619 "
        pdb=" CB  HIS A 619 "
      ideal   model   delta    sigma   weight residual
     113.65  102.73   10.92 1.47e+00 4.63e-01 5.52e+01
  angle pdb=" CA  THR A 415 "
        pdb=" CB  THR A 415 "
        pdb=" OG1 THR A 415 "
      ideal   model   delta    sigma   weight residual
     109.60   98.62   10.98 1.50e+00 4.44e-01 5.36e+01
  angle pdb=" CA  VAL B 374 "
        pdb=" C   VAL B 374 "
        pdb=" N   PRO B 375 "
      ideal   model   delta    sigma   weight residual
     120.83  124.96   -4.13 5.90e-01 2.87e+00 4.91e+01
  angle pdb=" CA  TYR H 103 "
        pdb=" CB  TYR H 103 "
        pdb=" CG  TYR H 103 "
      ideal   model   delta    sigma   weight residual
     113.90  126.51  -12.61 1.80e+00 3.09e-01 4.90e+01
  ... (remaining 14843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 5908
       17.44 -    34.87: 448
       34.87 -    52.31: 85
       52.31 -    69.74: 10
       69.74 -    87.17: 12
  Dihedral angle restraints: 6463
    sinusoidal: 2542
      harmonic: 3921
  Sorted by residual:
  dihedral pdb=" CA  SER A 410 "
           pdb=" C   SER A 410 "
           pdb=" N   THR A 411 "
           pdb=" CA  THR A 411 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.61   40.39     0      5.00e+00 4.00e-02 6.53e+01
  dihedral pdb=" CA  TRP A 557 "
           pdb=" C   TRP A 557 "
           pdb=" N   ASP A 558 "
           pdb=" CA  ASP A 558 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.52  -30.48     0      5.00e+00 4.00e-02 3.72e+01
  dihedral pdb=" CA  SER A 494 "
           pdb=" C   SER A 494 "
           pdb=" N   SER A 495 "
           pdb=" CA  SER A 495 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.06  -29.94     0      5.00e+00 4.00e-02 3.59e+01
  ... (remaining 6460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 1464
       0.125 -    0.251: 227
       0.251 -    0.376: 18
       0.376 -    0.501: 2
       0.501 -    0.627: 1
  Chirality restraints: 1712
  Sorted by residual:
  chirality pdb=" CA  PRO A 548 "
            pdb=" N   PRO A 548 "
            pdb=" C   PRO A 548 "
            pdb=" CB  PRO A 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.09    0.63 2.00e-01 2.50e+01 9.82e+00
  chirality pdb=" CA  HIS L  97 "
            pdb=" N   HIS L  97 "
            pdb=" C   HIS L  97 "
            pdb=" CB  HIS L  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.45e+00
  chirality pdb=" CA  TYR H 103 "
            pdb=" N   TYR H 103 "
            pdb=" C   TYR H 103 "
            pdb=" CB  TYR H 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.80e+00
  ... (remaining 1709 not shown)

  Planarity restraints: 1860
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "   -0.098 2.00e-02 2.50e+03   8.11e-02 8.22e+01
        pdb=" C7  NAG A 702 "    0.035 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "   -0.076 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "    0.127 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H 100 "   -0.538 9.50e-02 1.11e+02   2.41e-01 3.59e+01
        pdb=" NE  ARG H 100 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG H 100 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG H 100 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG H 100 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 525 "    0.400 9.50e-02 1.11e+02   1.79e-01 2.02e+01
        pdb=" NE  ARG A 525 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 525 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 525 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 525 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1857 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2869
        2.84 -     3.35: 10352
        3.35 -     3.87: 17377
        3.87 -     4.38: 20679
        4.38 -     4.90: 34808
  Nonbonded interactions: 86085
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 250 "
            pdb=" OE2 GLU A 471 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OH  TYR B 103 "
            pdb=" OD1 ASP B 116 "
     model   vdw
     2.454 3.040
  nonbonded pdb=" O   TRP A 219 "
            pdb=" OG1 THR A 463 "
     model   vdw
     2.491 3.040
  nonbonded pdb=" OH  TYR A 404 "
            pdb=" O   LEU A 418 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" OD2 ASP H  73 "
            pdb=" OG  SER H  76 "
     model   vdw
     2.533 3.040
  ... (remaining 86080 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.140
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.360
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
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      :  0.012   0.136  10903  Z= 0.783
  Angle     :  1.895  19.849  14870  Z= 1.242
  Chirality :  0.091   0.627   1712
  Planarity :  0.012   0.241   1856
  Dihedral  : 13.464  87.175   3932
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.52 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  5.08 %
    Favored  : 93.72 %
  Cbeta Deviations :  0.79 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.21), residues: 1351
  helix: -1.74 (0.18), residues: 518
  sheet: -0.23 (0.30), residues: 273
  loop : -0.85 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG A 530 
 TYR   0.032   0.005   TYR H  59 
 PHE   0.035   0.004   PHE A 551 
 TRP   0.043   0.006   TRP H  47 
 HIS   0.011   0.002   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01226 /  0.78 (10894)
  covalent geometry    : angle       1.88357 /  1.24 (14848)
  SS BOND              : bond        0.07369 /  3.85 (    5)
  SS BOND              : angle       6.76233 /  3.19 (   10)
  hydrogen bonds       : bond        0.18179 / 12.50 (  536)
  hydrogen bonds       : angle       8.23136 /  6.03 ( 1455)
  link_NAG-ASN         : bond        0.01364 /  0.68 (    4)
  link_NAG-ASN         : angle       4.73517 /  2.63 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 304
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 TRP cc_start: 0.7305 (m100) cc_final: 0.7095 (m-10)
REVERT: A  307 ASP cc_start: 0.9149 (t0) cc_final: 0.8840 (t0)
REVERT: A  315 GLU cc_start: 0.8945 (tt0) cc_final: 0.8714 (pm20)
REVERT: A  391 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8365 (mt)
REVERT: A  456 MET cc_start: 0.8761 (ttp) cc_final: 0.8227 (ttm)
REVERT: A  468 TYR cc_start: 0.8575 (p90) cc_final: 0.8369 (p90)
REVERT: A  489 MET cc_start: 0.8954 (tpt) cc_final: 0.8547 (tpt)
REVERT: A  579 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7546 (pt0)
REVERT: A  610 GLU cc_start: 0.7739 (mp0) cc_final: 0.7491 (tt0)
REVERT: A  614 LEU cc_start: 0.8534 (tp) cc_final: 0.8237 (tp)
REVERT: A  628 TYR cc_start: 0.8719 (t80) cc_final: 0.8355 (t80)
REVERT: B   54 ASN cc_start: 0.7731 (m-40) cc_final: 0.7437 (m110)
REVERT: B  122 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8549 (mm-30)
REVERT: B  195 ARG cc_start: 0.7164 (mtp85) cc_final: 0.6524 (ptt180)
REVERT: B  218 GLN cc_start: 0.7098 (tp40) cc_final: 0.6783 (tm-30)
REVERT: B  245 LEU cc_start: 0.6188 (mt) cc_final: 0.5927 (tp)
REVERT: B  257 TRP cc_start: 0.8866 (p-90) cc_final: 0.8560 (p90)
REVERT: B  267 MET cc_start: 0.8452 (mmm) cc_final: 0.8180 (mmm)
REVERT: B  276 LEU cc_start: 0.8148 (tp) cc_final: 0.7834 (tp)
REVERT: B  290 VAL cc_start: 0.7958 (m) cc_final: 0.7581 (t)
REVERT: B  346 SER cc_start: 0.8848 (t) cc_final: 0.8503 (p)
REVERT: B  356 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8392 (mm-30)
REVERT: B  365 MET cc_start: 0.8653 (mmt) cc_final: 0.7735 (mmm)
REVERT: B  391 LYS cc_start: 0.7609 (tptt) cc_final: 0.7319 (mmtm)
REVERT: B  426 GLU cc_start: 0.7261 (tt0) cc_final: 0.6969 (tp30)
REVERT: B  447 ILE cc_start: 0.7711 (mt) cc_final: 0.7471 (mt)
REVERT: B  484 TRP cc_start: 0.5625 (p90) cc_final: 0.4869 (t60)
REVERT: B  497 GLN cc_start: 0.8944 (mt0) cc_final: 0.8708 (mm110)
REVERT: B  505 GLN cc_start: 0.8102 (pm20) cc_final: 0.7763 (tm-30)
REVERT: B  506 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7486 (mm-30)
REVERT: L    1 ASP cc_start: 0.8625 (m-30) cc_final: 0.8411 (p0)
REVERT: L   37 ASN cc_start: 0.7743 (m-40) cc_final: 0.7479 (m-40)
REVERT: L   98 TYR cc_start: 0.9055 (t80) cc_final: 0.8805 (t80)
REVERT: L  124 PHE cc_start: 0.8282 (m-80) cc_final: 0.7475 (m-80)
REVERT: L  130 GLN cc_start: 0.7933 (tt0) cc_final: 0.7732 (tp40)
REVERT: L  145 PHE cc_start: 0.7339 (p90) cc_final: 0.6664 (p90)
REVERT: L  173 ASP cc_start: 0.7723 (t0) cc_final: 0.7473 (t0)
REVERT: L  181 MET cc_start: 0.8239 (ttp) cc_final: 0.8034 (ttt)
REVERT: H   57 TYR cc_start: 0.8915 (t80) cc_final: 0.8501 (t80)
REVERT: H   63 ASN cc_start: 0.8844 (m-40) cc_final: 0.8576 (t0)
REVERT: H  128 ASP cc_start: 0.8422 (m-30) cc_final: 0.7912 (t0)
REVERT: H  140 ASN cc_start: 0.7239 (m110) cc_final: 0.7012 (p0)
REVERT: H  215 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6442 (tppp)
  outliers start: 14
  outliers final: 2
  residues processed: 314
  average time/residue: 0.0807
  time to fit residues: 35.8513
Evaluate side-chains
  196 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 192
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  579 GLN
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain H residue   83 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    2.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 HIS
A 231 GLN
A 339 GLN
A 352 ASN
A 579 GLN
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 273 ASN
L 130 GLN
L 195 HIS
H 140 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.136425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.088207 restraints weight = 17185.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.088696 restraints weight = 13723.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.089036 restraints weight = 12962.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.089266 restraints weight = 11140.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.089513 restraints weight = 10744.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10903  Z= 0.198
  Angle     :  0.761  15.634  14870  Z= 0.386
  Chirality :  0.049   0.543   1712
  Planarity :  0.005   0.042   1856
  Dihedral  :  7.445  73.646   1554
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.05 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.22), residues: 1351
  helix:  0.59 (0.22), residues: 521
  sheet:  0.36 (0.31), residues: 278
  loop : -0.27 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 613 
 TYR   0.032   0.002   TYR H 103 
 PHE   0.020   0.002   PHE A 541 
 TRP   0.024   0.002   TRP H  47 
 HIS   0.006   0.002   HIS A 556 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.20 (10894)
  covalent geometry    : angle       0.74158 /  0.38 (14848)
  SS BOND              : bond        0.00521 /  0.26 (    5)
  SS BOND              : angle       2.23357 /  1.12 (   10)
  hydrogen bonds       : bond        0.05084 /  3.43 (  536)
  hydrogen bonds       : angle       5.52887 /  4.00 ( 1455)
  link_NAG-ASN         : bond        0.00440 /  0.23 (    4)
  link_NAG-ASN         : angle       5.78700 /  3.47 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 218
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 HIS cc_start: 0.6519 (m-70) cc_final: 0.6080 (m-70)
REVERT: A  398 LEU cc_start: 0.9069 (tp) cc_final: 0.8777 (tt)
REVERT: A  452 LEU cc_start: 0.9338 (tp) cc_final: 0.9026 (tt)
REVERT: A  507 MET cc_start: 0.7769 (mtm) cc_final: 0.7468 (ttm)
REVERT: A  579 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8723 (mt0)
REVERT: A  628 TYR cc_start: 0.8849 (t80) cc_final: 0.8532 (t80)
REVERT: B   50 ILE cc_start: 0.9062 (mp) cc_final: 0.8805 (tp)
REVERT: B   77 LYS cc_start: 0.7788 (ttpp) cc_final: 0.7046 (mmtt)
REVERT: B  136 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7326 (mm-30)
REVERT: B  195 ARG cc_start: 0.7113 (mtp85) cc_final: 0.6689 (ptt90)
REVERT: B  197 GLN cc_start: 0.8359 (tt0) cc_final: 0.7826 (tt0)
REVERT: B  218 GLN cc_start: 0.6873 (tp40) cc_final: 0.6518 (tm-30)
REVERT: B  276 LEU cc_start: 0.8189 (tp) cc_final: 0.7910 (tp)
REVERT: B  306 LEU cc_start: 0.8097 (mt) cc_final: 0.7782 (pp)
REVERT: B  346 SER cc_start: 0.8998 (t) cc_final: 0.8775 (p)
REVERT: B  365 MET cc_start: 0.8126 (mmt) cc_final: 0.7794 (mmm)
REVERT: B  391 LYS cc_start: 0.8434 (tptt) cc_final: 0.7590 (mmtm)
REVERT: B  484 TRP cc_start: 0.5958 (p90) cc_final: 0.4954 (t60)
REVERT: B  500 MET cc_start: 0.5175 (tpp) cc_final: 0.4724 (tpt)
REVERT: L   88 ASP cc_start: 0.8979 (m-30) cc_final: 0.8659 (m-30)
REVERT: L  116 ASP cc_start: 0.8117 (m-30) cc_final: 0.7037 (m-30)
REVERT: L  123 ILE cc_start: 0.7561 (tt) cc_final: 0.7321 (tp)
REVERT: L  124 PHE cc_start: 0.7566 (m-80) cc_final: 0.7283 (m-80)
REVERT: L  145 PHE cc_start: 0.8015 (p90) cc_final: 0.7418 (p90)
REVERT: L  146 TYR cc_start: 0.8172 (t80) cc_final: 0.7564 (t80)
REVERT: L  181 MET cc_start: 0.8535 (ttp) cc_final: 0.7991 (ttp)
REVERT: H  147 CYS cc_start: 0.6031 (t) cc_final: 0.5681 (t)
REVERT: H  180 ASP cc_start: 0.7758 (m-30) cc_final: 0.7528 (m-30)
REVERT: H  215 LYS cc_start: 0.8360 (mmmt) cc_final: 0.7919 (tppp)
  outliers start: 29
  outliers final: 13
  residues processed: 240
  average time/residue: 0.0735
  time to fit residues: 26.3015
Evaluate side-chains
  171 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  579 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  182 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 96 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 112 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 74 optimal weight:    0.8980
   chunk 86 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 195 HIS
** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.135497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.086678 restraints weight = 17285.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.088425 restraints weight = 13027.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.089822 restraints weight = 10847.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.090468 restraints weight = 9586.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.091093 restraints weight = 8933.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10903  Z= 0.199
  Angle     :  0.683  12.898  14870  Z= 0.346
  Chirality :  0.048   0.513   1712
  Planarity :  0.005   0.038   1856
  Dihedral  :  6.715  72.298   1552
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 13.51 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.23), residues: 1351
  helix:  1.02 (0.22), residues: 527
  sheet:  0.40 (0.31), residues: 273
  loop : -0.13 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 141 
 TYR   0.031   0.002   TYR H 103 
 PHE   0.020   0.002   PHE A 541 
 TRP   0.024   0.002   TRP H  47 
 HIS   0.004   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00468 /  0.20 (10894)
  covalent geometry    : angle       0.67022 /  0.34 (14848)
  SS BOND              : bond        0.00529 /  0.25 (    5)
  SS BOND              : angle       1.53126 /  0.81 (   10)
  hydrogen bonds       : bond        0.04385 /  2.97 (  536)
  hydrogen bonds       : angle       5.10486 /  3.70 ( 1455)
  link_NAG-ASN         : bond        0.00526 /  0.27 (    4)
  link_NAG-ASN         : angle       4.50466 /  2.83 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 181
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 HIS cc_start: 0.6076 (m-70) cc_final: 0.5668 (m-70)
REVERT: A  392 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8296 (mt)
REVERT: B   50 ILE cc_start: 0.9113 (mp) cc_final: 0.8883 (tp)
REVERT: B   77 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7477 (mmtt)
REVERT: B  105 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7052 (tp30)
REVERT: B  136 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7292 (mm-30)
REVERT: B  195 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6699 (ptt90)
REVERT: B  197 GLN cc_start: 0.8340 (tt0) cc_final: 0.7801 (tt0)
REVERT: B  218 GLN cc_start: 0.7027 (tp40) cc_final: 0.6562 (tm-30)
REVERT: B  276 LEU cc_start: 0.8225 (tp) cc_final: 0.8008 (tp)
REVERT: B  296 TYR cc_start: 0.8245 (m-10) cc_final: 0.7957 (m-10)
REVERT: B  303 GLU cc_start: 0.7674 (mp0) cc_final: 0.7166 (tp30)
REVERT: B  306 LEU cc_start: 0.8017 (mt) cc_final: 0.7806 (pp)
REVERT: B  346 SER cc_start: 0.9131 (t) cc_final: 0.8756 (p)
REVERT: B  365 MET cc_start: 0.8107 (mmt) cc_final: 0.7874 (mmm)
REVERT: B  391 LYS cc_start: 0.8527 (tptt) cc_final: 0.7544 (mmtm)
REVERT: B  438 PHE cc_start: 0.8223 (t80) cc_final: 0.7939 (t80)
REVERT: B  484 TRP cc_start: 0.6031 (p90) cc_final: 0.4838 (t60)
REVERT: B  500 MET cc_start: 0.5142 (OUTLIER) cc_final: 0.4907 (tpt)
REVERT: L   88 ASP cc_start: 0.9187 (m-30) cc_final: 0.8618 (m-30)
REVERT: L  116 ASP cc_start: 0.8138 (m-30) cc_final: 0.7029 (m-30)
REVERT: L  123 ILE cc_start: 0.7646 (tt) cc_final: 0.7421 (tp)
REVERT: L  124 PHE cc_start: 0.7540 (m-80) cc_final: 0.7234 (m-80)
REVERT: L  145 PHE cc_start: 0.8198 (p90) cc_final: 0.7816 (p90)
REVERT: L  146 TYR cc_start: 0.8504 (t80) cc_final: 0.7603 (t80)
REVERT: L  154 TRP cc_start: 0.7754 (m100) cc_final: 0.7469 (m100)
REVERT: L  181 MET cc_start: 0.8693 (ttp) cc_final: 0.8302 (ttt)
REVERT: H  142 MET cc_start: 0.8112 (mmp) cc_final: 0.7865 (mmm)
REVERT: H  180 ASP cc_start: 0.7663 (m-30) cc_final: 0.7462 (m-30)
  outliers start: 36
  outliers final: 24
  residues processed: 203
  average time/residue: 0.0766
  time to fit residues: 23.1231
Evaluate side-chains
  178 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 CYS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  500 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  182 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain H residue  145 LEU
Chi-restraints excluded: chain H residue  202 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 33 optimal weight:    0.2980
   chunk 129 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 231 GLN
L  43 GLN
H 206 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.091584 restraints weight = 17169.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.092971 restraints weight = 11800.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.092546 restraints weight = 9480.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.092668 restraints weight = 9746.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.092738 restraints weight = 9222.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10903  Z= 0.130
  Angle     :  0.627   8.291  14870  Z= 0.312
  Chirality :  0.044   0.314   1712
  Planarity :  0.004   0.047   1856
  Dihedral  :  6.236  73.004   1547
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 14.72 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.23), residues: 1351
  helix:  1.32 (0.22), residues: 528
  sheet:  0.51 (0.32), residues: 271
  loop : -0.06 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.027   0.002   TYR H 129 
 PHE   0.017   0.001   PHE A 541 
 TRP   0.017   0.001   TRP H 106 
 HIS   0.005   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 (10894)
  covalent geometry    : angle       0.62185 /  0.31 (14848)
  SS BOND              : bond        0.00355 /  0.15 (    5)
  SS BOND              : angle       1.54684 /  0.83 (   10)
  hydrogen bonds       : bond        0.03789 /  2.56 (  536)
  hydrogen bonds       : angle       4.80416 /  3.49 ( 1455)
  link_NAG-ASN         : bond        0.00397 /  0.20 (    4)
  link_NAG-ASN         : angle       2.59893 /  1.58 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 178
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 LEU cc_start: 0.8628 (mt) cc_final: 0.8269 (mt)
REVERT: A  398 LEU cc_start: 0.8992 (tp) cc_final: 0.8777 (tt)
REVERT: A  452 LEU cc_start: 0.9322 (tp) cc_final: 0.8987 (tt)
REVERT: A  583 LEU cc_start: 0.5902 (tp) cc_final: 0.5535 (tp)
REVERT: B   50 ILE cc_start: 0.9127 (mp) cc_final: 0.8908 (tp)
REVERT: B   77 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7406 (mmtt)
REVERT: B  105 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7164 (tp30)
REVERT: B  136 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7318 (mm-30)
REVERT: B  195 ARG cc_start: 0.7019 (mtp85) cc_final: 0.6634 (ptt90)
REVERT: B  218 GLN cc_start: 0.7112 (tp40) cc_final: 0.6372 (tm-30)
REVERT: B  276 LEU cc_start: 0.8231 (tp) cc_final: 0.7967 (tp)
REVERT: B  303 GLU cc_start: 0.7769 (mp0) cc_final: 0.7489 (pp20)
REVERT: B  306 LEU cc_start: 0.8029 (mt) cc_final: 0.7750 (pp)
REVERT: B  346 SER cc_start: 0.9081 (t) cc_final: 0.8847 (p)
REVERT: B  365 MET cc_start: 0.7957 (mmt) cc_final: 0.7629 (mmm)
REVERT: B  391 LYS cc_start: 0.8544 (tptt) cc_final: 0.7541 (mmtm)
REVERT: B  438 PHE cc_start: 0.8364 (t80) cc_final: 0.8138 (t80)
REVERT: B  484 TRP cc_start: 0.6169 (p90) cc_final: 0.4749 (t60)
REVERT: B  487 GLN cc_start: 0.7243 (pt0) cc_final: 0.5945 (tm-30)
REVERT: B  497 GLN cc_start: 0.8422 (mt0) cc_final: 0.8024 (mt0)
REVERT: L   42 TYR cc_start: 0.9339 (m-80) cc_final: 0.9126 (m-80)
REVERT: L   58 SER cc_start: 0.9199 (p) cc_final: 0.8975 (t)
REVERT: L   87 GLU cc_start: 0.8165 (pm20) cc_final: 0.7676 (pp20)
REVERT: L  123 ILE cc_start: 0.7609 (tt) cc_final: 0.7407 (tt)
REVERT: L  124 PHE cc_start: 0.7743 (m-80) cc_final: 0.7435 (m-80)
REVERT: L  145 PHE cc_start: 0.8142 (p90) cc_final: 0.7856 (p90)
REVERT: H  102 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8461 (p)
  outliers start: 33
  outliers final: 21
  residues processed: 198
  average time/residue: 0.0738
  time to fit residues: 22.2472
Evaluate side-chains
  180 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  210 CYS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  123 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 93 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 132 optimal weight:    0.0030
   chunk 89 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 73 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.138681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.091258 restraints weight = 17044.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.092686 restraints weight = 13263.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.092880 restraints weight = 11086.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.093122 restraints weight = 10281.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.093379 restraints weight = 9956.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10903  Z= 0.118
  Angle     :  0.616  10.793  14870  Z= 0.303
  Chirality :  0.045   0.430   1712
  Planarity :  0.004   0.043   1856
  Dihedral  :  6.089  72.959   1547
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 14.03 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.23), residues: 1351
  helix:  1.58 (0.22), residues: 527
  sheet:  0.62 (0.32), residues: 270
  loop : -0.07 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 613 
 TYR   0.030   0.002   TYR L 146 
 PHE   0.016   0.001   PHE A 541 
 TRP   0.021   0.001   TRP B 478 
 HIS   0.006   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 (10894)
  covalent geometry    : angle       0.60482 /  0.30 (14848)
  SS BOND              : bond        0.00365 /  0.16 (    5)
  SS BOND              : angle       2.25503 /  1.22 (   10)
  hydrogen bonds       : bond        0.03534 /  2.38 (  536)
  hydrogen bonds       : angle       4.59516 /  3.36 ( 1455)
  link_NAG-ASN         : bond        0.00236 /  0.11 (    4)
  link_NAG-ASN         : angle       3.73224 /  2.31 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 181
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8366 (pt)
REVERT: A  392 LEU cc_start: 0.8610 (mt) cc_final: 0.8237 (mt)
REVERT: A  452 LEU cc_start: 0.9311 (tp) cc_final: 0.8975 (tt)
REVERT: A  583 LEU cc_start: 0.6211 (tp) cc_final: 0.5819 (tp)
REVERT: B   77 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7423 (mmtt)
REVERT: B  105 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6854 (tp30)
REVERT: B  195 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6522 (ptt90)
REVERT: B  197 GLN cc_start: 0.8292 (tt0) cc_final: 0.7739 (tt0)
REVERT: B  218 GLN cc_start: 0.7074 (tp40) cc_final: 0.6400 (tm-30)
REVERT: B  303 GLU cc_start: 0.7761 (mp0) cc_final: 0.7513 (pp20)
REVERT: B  306 LEU cc_start: 0.7991 (mt) cc_final: 0.7749 (pp)
REVERT: B  346 SER cc_start: 0.9080 (t) cc_final: 0.8766 (p)
REVERT: B  391 LYS cc_start: 0.8573 (tptt) cc_final: 0.7467 (mmtm)
REVERT: B  438 PHE cc_start: 0.8239 (t80) cc_final: 0.8026 (t80)
REVERT: B  484 TRP cc_start: 0.6175 (p90) cc_final: 0.4901 (t60)
REVERT: B  505 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7335 (tm-30)
REVERT: L   42 TYR cc_start: 0.9315 (m-80) cc_final: 0.9104 (m-80)
REVERT: L   87 GLU cc_start: 0.8275 (pm20) cc_final: 0.7421 (pp20)
REVERT: L  145 PHE cc_start: 0.8069 (p90) cc_final: 0.7781 (p90)
REVERT: L  181 MET cc_start: 0.8523 (ttp) cc_final: 0.7291 (ttt)
REVERT: H   63 ASN cc_start: 0.8069 (m-40) cc_final: 0.7766 (t0)
REVERT: H  102 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8341 (p)
REVERT: H  152 TYR cc_start: 0.7253 (p90) cc_final: 0.6728 (p90)
REVERT: H  155 GLU cc_start: 0.7828 (tp30) cc_final: 0.7620 (tp30)
REVERT: H  215 LYS cc_start: 0.8145 (tppp) cc_final: 0.7837 (tppp)
  outliers start: 37
  outliers final: 23
  residues processed: 204
  average time/residue: 0.0713
  time to fit residues: 21.8269
Evaluate side-chains
  182 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  210 CYS
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  182 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain H residue  202 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 128 optimal weight:   20.0000
   chunk 108 optimal weight:   10.0000
   chunk 119 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 69 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 117 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 132 optimal weight:    6.9990
   overall best weight:    2.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  43 GLN
H 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.135329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.086932 restraints weight = 17376.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.088737 restraints weight = 13024.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.089774 restraints weight = 10812.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.090776 restraints weight = 9629.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.091196 restraints weight = 8883.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10903  Z= 0.217
  Angle     :  0.676  12.177  14870  Z= 0.333
  Chirality :  0.047   0.434   1712
  Planarity :  0.004   0.042   1856
  Dihedral  :  6.153  71.728   1547
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.80 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.23), residues: 1351
  helix:  1.36 (0.22), residues: 535
  sheet:  0.61 (0.32), residues: 284
  loop : -0.19 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 206 
 TYR   0.029   0.002   TYR H 103 
 PHE   0.021   0.002   PHE A 541 
 TRP   0.023   0.002   TRP H  47 
 HIS   0.005   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00515 /  0.22 (10894)
  covalent geometry    : angle       0.66637 /  0.33 (14848)
  SS BOND              : bond        0.00486 /  0.23 (    5)
  SS BOND              : angle       2.01478 /  1.12 (   10)
  hydrogen bonds       : bond        0.03858 /  2.57 (  536)
  hydrogen bonds       : angle       4.72976 /  3.45 ( 1455)
  link_NAG-ASN         : bond        0.00326 /  0.16 (    4)
  link_NAG-ASN         : angle       3.63031 /  2.30 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 160
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8203 (mt)
REVERT: B   77 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7521 (mmtt)
REVERT: B  105 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.6886 (tp30)
REVERT: B  195 ARG cc_start: 0.7094 (mtp85) cc_final: 0.6526 (ptt90)
REVERT: B  218 GLN cc_start: 0.7118 (tp40) cc_final: 0.6346 (tm-30)
REVERT: B  306 LEU cc_start: 0.7943 (mt) cc_final: 0.7727 (pp)
REVERT: B  346 SER cc_start: 0.9116 (t) cc_final: 0.8848 (p)
REVERT: B  391 LYS cc_start: 0.8574 (tptt) cc_final: 0.7485 (mmtm)
REVERT: B  438 PHE cc_start: 0.8232 (t80) cc_final: 0.7944 (t80)
REVERT: B  484 TRP cc_start: 0.6231 (p90) cc_final: 0.4815 (t60)
REVERT: L   87 GLU cc_start: 0.8062 (pm20) cc_final: 0.7472 (pp20)
REVERT: L  145 PHE cc_start: 0.8218 (p90) cc_final: 0.7880 (p90)
REVERT: L  168 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7696 (m)
REVERT: L  181 MET cc_start: 0.8663 (ttp) cc_final: 0.7259 (ttt)
REVERT: H   63 ASN cc_start: 0.8070 (m-40) cc_final: 0.7756 (t0)
REVERT: H  102 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8464 (p)
REVERT: H  152 TYR cc_start: 0.7348 (p90) cc_final: 0.6800 (p90)
  outliers start: 40
  outliers final: 29
  residues processed: 188
  average time/residue: 0.0697
  time to fit residues: 19.8541
Evaluate side-chains
  179 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  210 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain H residue  203 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 105 optimal weight:    6.9990
   chunk 129 optimal weight:    4.9990
   chunk 116 optimal weight:    0.9990
   chunk 130 optimal weight:    8.9990
   chunk 126 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 38 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    2.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.135675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.087082 restraints weight = 17213.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.088977 restraints weight = 12926.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.090078 restraints weight = 10746.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.090791 restraints weight = 9617.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.091362 restraints weight = 8950.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  10903  Z= 0.193
  Angle     :  0.658  12.749  14870  Z= 0.323
  Chirality :  0.046   0.407   1712
  Planarity :  0.004   0.042   1856
  Dihedral  :  6.122  71.586   1547
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 15.32 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.23), residues: 1351
  helix:  1.40 (0.22), residues: 534
  sheet:  0.51 (0.32), residues: 284
  loop : -0.24 (0.28), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  40 
 TYR   0.027   0.002   TYR A 468 
 PHE   0.026   0.002   PHE B 399 
 TRP   0.023   0.002   TRP H 195 
 HIS   0.005   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00460 /  0.19 (10894)
  covalent geometry    : angle       0.65002 /  0.32 (14848)
  SS BOND              : bond        0.00598 /  0.33 (    5)
  SS BOND              : angle       1.56326 /  1.02 (   10)
  hydrogen bonds       : bond        0.03774 /  2.53 (  536)
  hydrogen bonds       : angle       4.73586 /  3.47 ( 1455)
  link_NAG-ASN         : bond        0.00323 /  0.16 (    4)
  link_NAG-ASN         : angle       3.39434 /  2.15 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 157
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8325 (mt)
REVERT: A  396 LYS cc_start: 0.8123 (mmtp) cc_final: 0.7770 (mmmt)
REVERT: B   50 ILE cc_start: 0.8913 (tp) cc_final: 0.8693 (tp)
REVERT: B   77 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7468 (mmtt)
REVERT: B  105 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.6883 (tp30)
REVERT: B  195 ARG cc_start: 0.7118 (mtp85) cc_final: 0.6523 (ptt90)
REVERT: B  218 GLN cc_start: 0.7115 (tp40) cc_final: 0.6328 (tm-30)
REVERT: B  346 SER cc_start: 0.9125 (t) cc_final: 0.8854 (p)
REVERT: B  391 LYS cc_start: 0.8611 (tptt) cc_final: 0.7546 (mmtm)
REVERT: B  438 PHE cc_start: 0.8233 (t80) cc_final: 0.7963 (t80)
REVERT: B  484 TRP cc_start: 0.6388 (p90) cc_final: 0.4849 (t60)
REVERT: B  497 GLN cc_start: 0.8127 (mt0) cc_final: 0.7854 (mt0)
REVERT: B  500 MET cc_start: 0.4573 (tpt) cc_final: 0.4201 (mmt)
REVERT: L   87 GLU cc_start: 0.7945 (pm20) cc_final: 0.7320 (pp20)
REVERT: L  145 PHE cc_start: 0.8100 (p90) cc_final: 0.7783 (p90)
REVERT: L  168 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7661 (m)
REVERT: L  181 MET cc_start: 0.8658 (ttp) cc_final: 0.7473 (ttt)
REVERT: H   63 ASN cc_start: 0.8064 (m-40) cc_final: 0.7714 (t0)
REVERT: H  102 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8441 (p)
REVERT: H  152 TYR cc_start: 0.7291 (p90) cc_final: 0.6738 (p90)
  outliers start: 42
  outliers final: 29
  residues processed: 184
  average time/residue: 0.0719
  time to fit residues: 19.9393
Evaluate side-chains
  181 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 148
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  210 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain H residue  202 CYS
Chi-restraints excluded: chain H residue  203 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 92 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 23 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 125 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.136627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.088942 restraints weight = 17116.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.090589 restraints weight = 13127.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.091040 restraints weight = 10063.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.091210 restraints weight = 9742.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.091248 restraints weight = 9673.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10903  Z= 0.152
  Angle     :  0.639  12.881  14870  Z= 0.310
  Chirality :  0.045   0.391   1712
  Planarity :  0.004   0.042   1856
  Dihedral  :  6.075  71.565   1547
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.35 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.23), residues: 1351
  helix:  1.52 (0.22), residues: 536
  sheet:  0.46 (0.32), residues: 283
  loop : -0.21 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  40 
 TYR   0.027   0.002   TYR A 468 
 PHE   0.023   0.002   PHE B 399 
 TRP   0.027   0.002   TRP B 478 
 HIS   0.005   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 (10894)
  covalent geometry    : angle       0.63126 /  0.31 (14848)
  SS BOND              : bond        0.00397 /  0.19 (    5)
  SS BOND              : angle       1.99529 /  1.45 (   10)
  hydrogen bonds       : bond        0.03626 /  2.44 (  536)
  hydrogen bonds       : angle       4.68245 /  3.41 ( 1455)
  link_NAG-ASN         : bond        0.00348 /  0.17 (    4)
  link_NAG-ASN         : angle       3.20658 /  2.02 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  396 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7739 (mmmt)
REVERT: A  452 LEU cc_start: 0.9315 (tp) cc_final: 0.8988 (tt)
REVERT: B   47 GLN cc_start: 0.7862 (mp10) cc_final: 0.7553 (mp10)
REVERT: B   77 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7480 (mmtt)
REVERT: B  105 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6917 (tp30)
REVERT: B  195 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6512 (ptt90)
REVERT: B  218 GLN cc_start: 0.7100 (tp40) cc_final: 0.6304 (tm-30)
REVERT: B  346 SER cc_start: 0.9007 (t) cc_final: 0.8727 (p)
REVERT: B  391 LYS cc_start: 0.8612 (tptt) cc_final: 0.7543 (mmtm)
REVERT: B  438 PHE cc_start: 0.8287 (t80) cc_final: 0.8071 (t80)
REVERT: B  484 TRP cc_start: 0.6407 (p90) cc_final: 0.4855 (t60)
REVERT: B  497 GLN cc_start: 0.8122 (mt0) cc_final: 0.7303 (mt0)
REVERT: B  500 MET cc_start: 0.4608 (tpt) cc_final: 0.4345 (mmt)
REVERT: L   42 TYR cc_start: 0.9281 (m-80) cc_final: 0.8971 (m-80)
REVERT: L   87 GLU cc_start: 0.7986 (pm20) cc_final: 0.7309 (pp20)
REVERT: L  124 PHE cc_start: 0.6922 (m-80) cc_final: 0.6423 (m-80)
REVERT: L  145 PHE cc_start: 0.8107 (p90) cc_final: 0.7770 (p90)
REVERT: L  168 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7611 (m)
REVERT: L  181 MET cc_start: 0.8618 (ttp) cc_final: 0.7357 (ttt)
REVERT: H   63 ASN cc_start: 0.8063 (m-40) cc_final: 0.7767 (t0)
REVERT: H  102 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8363 (p)
REVERT: H  152 TYR cc_start: 0.7262 (p90) cc_final: 0.6700 (p90)
  outliers start: 34
  outliers final: 26
  residues processed: 177
  average time/residue: 0.0738
  time to fit residues: 19.8513
Evaluate side-chains
  177 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  210 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain H residue  202 CYS
Chi-restraints excluded: chain H residue  203 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 102 optimal weight:    7.9990
   chunk 81 optimal weight:    9.9990
   chunk 133 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0570
   chunk 92 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  43 GLN
H 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.137956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.089310 restraints weight = 17101.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.091291 restraints weight = 12701.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.092522 restraints weight = 10471.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.093159 restraints weight = 9308.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.093712 restraints weight = 8627.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10903  Z= 0.119
  Angle     :  0.628  12.088  14870  Z= 0.303
  Chirality :  0.044   0.375   1712
  Planarity :  0.004   0.042   1856
  Dihedral  :  5.982  72.203   1547
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.04 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.23), residues: 1351
  helix:  1.61 (0.22), residues: 538
  sheet:  0.53 (0.32), residues: 282
  loop : -0.19 (0.28), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  40 
 TYR   0.028   0.001   TYR A 468 
 PHE   0.023   0.001   PHE B 399 
 TRP   0.034   0.002   TRP B 478 
 HIS   0.006   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 (10894)
  covalent geometry    : angle       0.62193 /  0.30 (14848)
  SS BOND              : bond        0.00356 /  0.15 (    5)
  SS BOND              : angle       1.20045 /  0.73 (   10)
  hydrogen bonds       : bond        0.03450 /  2.33 (  536)
  hydrogen bonds       : angle       4.59143 /  3.35 ( 1455)
  link_NAG-ASN         : bond        0.00375 /  0.18 (    4)
  link_NAG-ASN         : angle       2.98562 /  1.87 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  392 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8204 (mt)
REVERT: A  452 LEU cc_start: 0.9266 (tp) cc_final: 0.8954 (tt)
REVERT: B   77 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7470 (mmtt)
REVERT: B  105 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6858 (tp30)
REVERT: B  195 ARG cc_start: 0.7001 (mtp85) cc_final: 0.6431 (ptt90)
REVERT: B  197 GLN cc_start: 0.8575 (tt0) cc_final: 0.8232 (tt0)
REVERT: B  218 GLN cc_start: 0.7065 (tp40) cc_final: 0.6340 (tm-30)
REVERT: B  259 TYR cc_start: 0.8647 (m-10) cc_final: 0.8421 (m-10)
REVERT: B  346 SER cc_start: 0.8950 (t) cc_final: 0.8644 (p)
REVERT: B  391 LYS cc_start: 0.8609 (tptt) cc_final: 0.7555 (mmtm)
REVERT: B  484 TRP cc_start: 0.6714 (p90) cc_final: 0.4624 (t60)
REVERT: B  497 GLN cc_start: 0.8056 (mt0) cc_final: 0.7793 (mt0)
REVERT: L   42 TYR cc_start: 0.9232 (m-80) cc_final: 0.8934 (m-80)
REVERT: L   87 GLU cc_start: 0.7947 (pm20) cc_final: 0.7267 (pp20)
REVERT: L  124 PHE cc_start: 0.6881 (m-80) cc_final: 0.6342 (m-80)
REVERT: L  145 PHE cc_start: 0.8099 (p90) cc_final: 0.7776 (p90)
REVERT: L  168 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7682 (m)
REVERT: H   63 ASN cc_start: 0.8002 (m-40) cc_final: 0.7696 (t0)
REVERT: H  102 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8231 (p)
REVERT: H  152 TYR cc_start: 0.7047 (p90) cc_final: 0.6572 (p90)
  outliers start: 28
  outliers final: 20
  residues processed: 184
  average time/residue: 0.0747
  time to fit residues: 20.5137
Evaluate side-chains
  174 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  216 PHE
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain H residue  202 CYS
Chi-restraints excluded: chain H residue  203 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0030
   chunk 50 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 133 optimal weight:   20.0000
   chunk 72 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 100 optimal weight:    7.9990
   overall best weight:    1.7594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 130 GLN
H 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.136682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.088284 restraints weight = 17105.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.090532 restraints weight = 13391.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.091324 restraints weight = 10092.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.091404 restraints weight = 9149.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.091520 restraints weight = 9418.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.4571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10903  Z= 0.157
  Angle     :  0.654  11.601  14870  Z= 0.318
  Chirality :  0.045   0.361   1712
  Planarity :  0.004   0.042   1856
  Dihedral  :  5.976  71.635   1547
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.95 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.23), residues: 1351
  helix:  1.63 (0.22), residues: 537
  sheet:  0.47 (0.32), residues: 281
  loop : -0.18 (0.28), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  40 
 TYR   0.038   0.002   TYR L 146 
 PHE   0.025   0.002   PHE B 445 
 TRP   0.036   0.002   TRP B 478 
 HIS   0.005   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.16 (10894)
  covalent geometry    : angle       0.64841 /  0.32 (14848)
  SS BOND              : bond        0.00386 /  0.17 (    5)
  SS BOND              : angle       1.16760 /  0.65 (   10)
  hydrogen bonds       : bond        0.03498 /  2.36 (  536)
  hydrogen bonds       : angle       4.62882 /  3.37 ( 1455)
  link_NAG-ASN         : bond        0.00328 /  0.16 (    4)
  link_NAG-ASN         : angle       2.93750 /  1.85 (   12)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: A  392 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8261 (mt)
REVERT: A  452 LEU cc_start: 0.9321 (tp) cc_final: 0.8991 (tt)
REVERT: B   77 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7507 (mmtp)
REVERT: B  105 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6902 (tp30)
REVERT: B  195 ARG cc_start: 0.6970 (mtp85) cc_final: 0.6377 (ptt90)
REVERT: B  197 GLN cc_start: 0.8585 (tt0) cc_final: 0.8266 (tt0)
REVERT: B  218 GLN cc_start: 0.7118 (tp40) cc_final: 0.6321 (tm-30)
REVERT: B  346 SER cc_start: 0.9109 (t) cc_final: 0.8813 (p)
REVERT: B  391 LYS cc_start: 0.8614 (tptt) cc_final: 0.7548 (mmtm)
REVERT: B  484 TRP cc_start: 0.6751 (p90) cc_final: 0.4642 (t60)
REVERT: B  497 GLN cc_start: 0.8105 (mt0) cc_final: 0.7307 (mt0)
REVERT: L   42 TYR cc_start: 0.9288 (m-80) cc_final: 0.8994 (m-80)
REVERT: L   87 GLU cc_start: 0.8008 (pm20) cc_final: 0.7295 (pp20)
REVERT: L  124 PHE cc_start: 0.6814 (m-80) cc_final: 0.6098 (m-80)
REVERT: L  145 PHE cc_start: 0.8162 (p90) cc_final: 0.7796 (p90)
REVERT: L  168 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7618 (m)
REVERT: L  169 TRP cc_start: 0.8470 (m-90) cc_final: 0.7923 (m-90)
REVERT: H   63 ASN cc_start: 0.8018 (m-40) cc_final: 0.7770 (t0)
REVERT: H  102 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8282 (p)
REVERT: H  140 ASN cc_start: 0.7234 (p0) cc_final: 0.7017 (p0)
REVERT: H  152 TYR cc_start: 0.7212 (p90) cc_final: 0.6713 (p90)
  outliers start: 28
  outliers final: 22
  residues processed: 178
  average time/residue: 0.0874
  time to fit residues: 23.4058
Evaluate side-chains
  177 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  210 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  216 PHE
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  156 ILE
Chi-restraints excluded: chain L residue  168 SER
Chi-restraints excluded: chain L residue  184 THR
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  102 THR
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain H residue  202 CYS
Chi-restraints excluded: chain H residue  203 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 108 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 203 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.137658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.089053 restraints weight = 17216.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.090951 restraints weight = 12786.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.092337 restraints weight = 10545.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.092874 restraints weight = 9316.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.093489 restraints weight = 8699.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10903  Z= 0.132
  Angle     :  0.635   9.819  14870  Z= 0.307
  Chirality :  0.044   0.352   1712
  Planarity :  0.004   0.042   1856
  Dihedral  :  5.954  71.491   1547
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.21 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.23), residues: 1351
  helix:  1.70 (0.22), residues: 539
  sheet:  0.51 (0.31), residues: 280
  loop : -0.17 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 141 
 TYR   0.036   0.001   TYR L 146 
 PHE   0.024   0.001   PHE B 445 
 TRP   0.032   0.002   TRP B 478 
 HIS   0.005   0.001   HIS H 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 (10894)
  covalent geometry    : angle       0.63008 /  0.31 (14848)
  SS BOND              : bond        0.00357 /  0.16 (    5)
  SS BOND              : angle       1.18069 /  0.71 (   10)
  hydrogen bonds       : bond        0.03412 /  2.30 (  536)
  hydrogen bonds       : angle       4.57257 /  3.32 ( 1455)
  link_NAG-ASN         : bond        0.00343 /  0.17 (    4)
  link_NAG-ASN         : angle       2.81444 /  1.77 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1568.74 seconds
wall clock time: 27 minutes 55.61 seconds (1675.61 seconds total)