Starting phenix.real_space_refine
on Fri Dec 19 17:59:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dzy_8942/12_2025/6dzy_8942_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dzy_8942/12_2025/6dzy_8942.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dzy_8942/12_2025/6dzy_8942.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dzy_8942/12_2025/6dzy_8942.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dzy_8942/12_2025/6dzy_8942_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dzy_8942/12_2025/6dzy_8942_neut.cif"
  }
  resolution = 4.1
  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=   0.003 sd=   1.383
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 99 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    5117      2.51       5
     N    1249      2.21       5
     O    1436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7842
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4282
          Classifications: {'peptide': 537}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "H"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 913
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 830
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "V"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1744
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HJM': 1, 'LMT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.08, per 1000 atoms: 0.27
  Number of scatterers: 7842
  At special positions: 0
  Unit cell: (90.828, 103.356, 120.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1436      8.00
     N    1249      7.00
     C    5117      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS V  37 " - pdb=" SG  CYS V 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS V 172 " - pdb=" SG  CYS V 237 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 208 "
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 495.0 milliseconds
  

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1804

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 13 sheets defined
      48.6% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.646A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 110
      removed outlier: 3.965A  pdb=" N   VAL A 102 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
      removed outlier: 4.403A  pdb=" N   TYR A 110 " --> pdb=" O   PRO A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 128
      Proline residue:  A 120  - end of helix
    Processing helix  chain 'A' and resid 128 through 144
      removed outlier: 3.959A  pdb=" N   LEU A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLU A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TYR A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
    Processing helix  chain 'A' and resid 156 through 158
      No H-bonds generated for 'chain 'A' and resid 156 through 158'
    Processing helix  chain 'A' and resid 159 through 191
      removed outlier: 4.269A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 181 " --> pdb=" O   ASN A 177 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TYR A 186 " --> pdb=" O   TRP A 182 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 209
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 272
      removed outlier: 3.784A  pdb=" N   MET A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.632A  pdb=" N   GLY A 278 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   LYS A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL A 280 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 302
      removed outlier: 4.060A  pdb=" N   ARG A 298 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 314
    Processing helix  chain 'A' and resid 316 through 321
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.043A  pdb=" N   TRP A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 349
      removed outlier: 3.594A  pdb=" N   SER A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 391
      removed outlier: 3.643A  pdb=" N   VAL A 363 " --> pdb=" O   GLN A 359 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   TYR A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 417
      removed outlier: 3.506A  pdb=" N   TYR A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 454
      removed outlier: 3.702A  pdb=" N   PHE A 428 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE A 432 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 443 " --> pdb=" O   SER A 439 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 459
    Processing helix  chain 'A' and resid 461 through 482
      removed outlier: 3.624A  pdb=" N   VAL A 466 " --> pdb=" O   ARG A 462 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   THR A 480 " --> pdb=" O   GLY A 476 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU A 481 " --> pdb=" O   SER A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 497
      removed outlier: 3.704A  pdb=" N   LEU A 491 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   TYR A 495 " --> pdb=" O   LEU A 491 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   THR A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
      removed outlier: 3.571A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 530
      removed outlier: 3.885A  pdb=" N   MET A 528 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 543
    Processing helix  chain 'A' and resid 543 through 557
      removed outlier: 3.666A  pdb=" N   LEU A 547 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ILE A 552 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE A 556 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 557 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 585
      removed outlier: 3.797A  pdb=" N   ILE A 575 " --> pdb=" O   PRO A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 600
    Processing helix  chain 'A' and resid 603 through 613
      removed outlier: 3.582A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 47 through 51
    Processing helix  chain 'H' and resid 82 through 85
      removed outlier: 3.886A  pdb=" N   GLY H  85 " --> pdb=" O   LYS H  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 82 through 85'
    Processing helix  chain 'H' and resid 106 through 110
    Processing helix  chain 'H' and resid 120 through 124
    Processing helix  chain 'L' and resid 103 through 107
    Processing helix  chain 'V' and resid 43 through 47
      removed outlier: 4.101A  pdb=" N   TYR V  47 " --> pdb=" O   PHE V  44 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 77 through 80
      removed outlier: 3.678A  pdb=" N   LYS V  80 " --> pdb=" O   GLN V  77 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'V' and resid 77 through 80'
    Processing helix  chain 'V' and resid 89 through 91
      No H-bonds generated for 'chain 'V' and resid 89 through 91'
    Processing helix  chain 'V' and resid 102 through 106
    Processing helix  chain 'V' and resid 228 through 232
    Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 25
      removed outlier: 3.652A  pdb=" N   GLN H  22 " --> pdb=" O   SER H  44 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   SER H  44 " --> pdb=" O   GLN H  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 29 through 30
      removed outlier: 3.803A  pdb=" N   THR H 137 " --> pdb=" O   GLU H  29 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL H 112 " --> pdb=" O   GLN H  58 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA H 116 " --> pdb=" O   ASN H  54 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY H  68 " --> pdb=" O   TRP H  55 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   LYS H  57 " --> pdb=" O   TRP H  66 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   TRP H  66 " --> pdb=" O   LYS H  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 37 through 39
      removed outlier: 3.668A  pdb=" N   THR H  97 " --> pdb=" O   ASP H  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 24 through 25
      removed outlier: 3.604A  pdb=" N   ALA L  39 " --> pdb=" O   ILE L  99 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE L  41 " --> pdb=" O   LEU L  97 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE L  95 " --> pdb=" O   CYS L  43 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER L  89 " --> pdb=" O   SER L  96 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 32
      removed outlier: 3.963A  pdb=" N   GLU L 129 " --> pdb=" O   LEU L  31 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR L 126 " --> pdb=" O   TYR L 110 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL L 128 " --> pdb=" O   ALA L 108 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE L 111 " --> pdb=" O   PHE L  60 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   LEU L  57 " --> pdb=" O   TYR L  73 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   TYR L  73 " --> pdb=" O   LEU L  57 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 30 through 32
      removed outlier: 3.963A  pdb=" N   GLU L 129 " --> pdb=" O   LEU L  31 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR L 126 " --> pdb=" O   TYR L 110 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL L 128 " --> pdb=" O   ALA L 108 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR L 121 " --> pdb=" O   GLN L 114 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 50 through 51
      removed outlier: 3.738A  pdb=" N   ASN L  51 " --> pdb=" O   ILE L  54 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'V' and resid 18 through 21
      removed outlier: 3.562A  pdb=" N   THR V  86 " --> pdb=" O   TYR V  95 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'V' and resid 25 through 26
      removed outlier: 6.519A  pdb=" N   GLU V  25 " --> pdb=" O   THR V 131 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL V  52 " --> pdb=" O   TYR V 110 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   TRP V  51 " --> pdb=" O   ILE V  63 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'V' and resid 25 through 26
      removed outlier: 6.519A  pdb=" N   GLU V  25 " --> pdb=" O   THR V 131 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   TYR V 123 " --> pdb=" O   ARG V 113 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'V' and resid 153 through 155
      removed outlier: 11.889A  pdb=" N   CYS V 172 " --> pdb=" O   THR V 223 " (cutoff:3.500A)
      removed outlier: 11.038A  pdb=" N   THR V 223 " --> pdb=" O   CYS V 172 " (cutoff:3.500A)
      removed outlier: 11.846A  pdb=" N   ALA V 174 " --> pdb=" O   THR V 221 " (cutoff:3.500A)
      removed outlier: 11.915A  pdb=" N   THR V 221 " --> pdb=" O   ALA V 174 " (cutoff:3.500A)
      removed outlier: 11.529A  pdb=" N   GLN V 176 " --> pdb=" O   ASP V 219 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   ASP V 219 " --> pdb=" O   GLN V 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'V' and resid 184 through 185
      removed outlier: 6.744A  pdb=" N   TRP V 184 " --> pdb=" O   LEU V 196 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'V' and resid 234 through 235
      removed outlier: 3.573A  pdb=" N   THR V 251 " --> pdb=" O   TYR V 235 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    954 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: 1.23

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1194
        1.27 -     1.41: 2235
        1.41 -     1.54: 4523
        1.54 -     1.68: 58
        1.68 -     1.82: 59
  Bond restraints: 8069
  Sorted by residual:
  bond pdb=" C   VAL A 367 "
       pdb=" N   ASN A 368 "
    ideal  model  delta    sigma   weight residual
    1.335  1.454 -0.119 1.31e-02 5.83e+03 8.25e+01
  bond pdb=" C   ASN A 208 "
       pdb=" O   ASN A 208 "
    ideal  model  delta    sigma   weight residual
    1.235  1.137  0.098 1.26e-02 6.30e+03 6.07e+01
  bond pdb=" C   PRO A 571 "
       pdb=" N   TYR A 572 "
    ideal  model  delta    sigma   weight residual
    1.333  1.221  0.112 1.45e-02 4.76e+03 5.92e+01
  bond pdb=" C   ASN A 368 "
       pdb=" N   CYS A 369 "
    ideal  model  delta    sigma   weight residual
    1.334  1.437 -0.103 1.43e-02 4.89e+03 5.21e+01
  bond pdb=" C1  HJM A 701 "
       pdb=" N1  HJM A 701 "
    ideal  model  delta    sigma   weight residual
    1.463  1.568 -0.105 2.00e-02 2.50e+03 2.78e+01
  ... (remaining 8064 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.31: 10946
        5.31 -    10.61: 34
       10.61 -    15.92: 3
       15.92 -    21.23: 0
       21.23 -    26.53: 1
  Bond angle restraints: 10984
  Sorted by residual:
  angle pdb=" N   TYR V 119 "
        pdb=" CA  TYR V 119 "
        pdb=" CB  TYR V 119 "
      ideal   model   delta    sigma   weight residual
     111.62  138.15  -26.53 1.43e+00 4.89e-01 3.44e+02
  angle pdb=" C   TYR A 176 "
        pdb=" N   ASN A 177 "
        pdb=" CA  ASN A 177 "
      ideal   model   delta    sigma   weight residual
     120.29  133.18  -12.89 1.42e+00 4.96e-01 8.23e+01
  angle pdb=" N   TYR V 119 "
        pdb=" CA  TYR V 119 "
        pdb=" C   TYR V 119 "
      ideal   model   delta    sigma   weight residual
     111.30   99.18   12.12 1.36e+00 5.41e-01 7.94e+01
  angle pdb=" N   TYR A 176 "
        pdb=" CA  TYR A 176 "
        pdb=" C   TYR A 176 "
      ideal   model   delta    sigma   weight residual
     111.36  120.93   -9.57 1.09e+00 8.42e-01 7.70e+01
  angle pdb=" C   SER A 532 "
        pdb=" N   PRO A 533 "
        pdb=" CA  PRO A 533 "
      ideal   model   delta    sigma   weight residual
     121.00  130.13   -9.13 1.16e+00 7.43e-01 6.19e+01
  ... (remaining 10979 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.45: 4586
       22.45 -    44.90: 89
       44.90 -    67.35: 19
       67.35 -    89.79: 9
       89.79 -   112.24: 13
  Dihedral angle restraints: 4716
    sinusoidal: 1870
      harmonic: 2846
  Sorted by residual:
  dihedral pdb=" N   TYR V 119 "
           pdb=" C   TYR V 119 "
           pdb=" CA  TYR V 119 "
           pdb=" CB  TYR V 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.95  -29.15     0      2.50e+00 1.60e-01 1.36e+02
  dihedral pdb=" CA  GLU L  47 "
           pdb=" C   GLU L  47 "
           pdb=" N   SER L  48 "
           pdb=" CA  SER L  48 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   38.41  -38.41     0      5.00e+00 4.00e-02 5.90e+01
  dihedral pdb=" C   TYR V 119 "
           pdb=" N   TYR V 119 "
           pdb=" CA  TYR V 119 "
           pdb=" CB  TYR V 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.33   16.73     0      2.50e+00 1.60e-01 4.48e+01
  ... (remaining 4713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.211: 1206
       0.211 -    0.422: 6
       0.422 -    0.633: 2
       0.633 -    0.844: 0
       0.844 -    1.055: 1
  Chirality restraints: 1215
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-02 2.50e+03 1.20e+02
  chirality pdb=" CA  TYR V 119 "
            pdb=" N   TYR V 119 "
            pdb=" C   TYR V 119 "
            pdb=" CB  TYR V 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.45    1.06 2.00e-01 2.50e+01 2.79e+01
  chirality pdb=" N1  HJM A 701 "
            pdb=" C1  HJM A 701 "
            pdb=" C7  HJM A 701 "
            pdb=" C9  HJM A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      1.76    2.30   -0.55 2.00e-01 2.50e+01 7.43e+00
  ... (remaining 1212 not shown)

  Planarity restraints: 1355
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   2 "   -0.345 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG B   2 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG B   2 "   -0.077 2.00e-02 2.50e+03
        pdb=" N2  NAG B   2 "    0.528 2.00e-02 2.50e+03
        pdb=" O7  NAG B   2 "   -0.187 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "   -0.322 2.00e-02 2.50e+03   2.73e-01 9.35e+02
        pdb=" C7  NAG B   1 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "   -0.182 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "    0.477 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" O   HJM A 701 "    0.166 2.00e-02 2.50e+03   8.51e-02 2.17e+02
        pdb=" C11 HJM A 701 "    0.113 2.00e-02 2.50e+03
        pdb=" C12 HJM A 701 "   -0.117 2.00e-02 2.50e+03
        pdb=" C13 HJM A 701 "    0.002 2.00e-02 2.50e+03
        pdb=" C15 HJM A 701 "   -0.043 2.00e-02 2.50e+03
        pdb=" C16 HJM A 701 "   -0.127 2.00e-02 2.50e+03
        pdb=" C17 HJM A 701 "   -0.021 2.00e-02 2.50e+03
        pdb=" C18 HJM A 701 "   -0.029 2.00e-02 2.50e+03
        pdb=" C19 HJM A 701 "   -0.039 2.00e-02 2.50e+03
        pdb=" C2  HJM A 701 "    0.054 2.00e-02 2.50e+03
        pdb=" C8  HJM A 701 "    0.085 2.00e-02 2.50e+03
        pdb=" N2  HJM A 701 "   -0.045 2.00e-02 2.50e+03
  ... (remaining 1352 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.09: 3
        2.09 -     2.79: 1967
        2.79 -     3.49: 10494
        3.49 -     4.20: 18630
        4.20 -     4.90: 32250
  Nonbonded interactions: 63344
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 220 "
            pdb=" CG2 VAL V 116 "
     model   vdw
     1.386 3.460
  nonbonded pdb=" CD1 ILE A 327 "
            pdb=" CE2 PHE A 551 "
     model   vdw
     1.638 3.760
  nonbonded pdb=" CB  PRO V 118 "
            pdb=" CD1 TYR V 120 "
     model   vdw
     1.909 3.740
  nonbonded pdb=" OE1 GLU A 494 "
            pdb=" O2B LMT A 702 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" O   GLU A 229 "
            pdb=" OG1 THR A 233 "
     model   vdw
     2.126 3.040
  ... (remaining 63339 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:             3.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.430
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6273
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.255   8076  Z= 0.358
  Angle     :  0.924  26.534  11000  Z= 0.538
  Chirality :  0.064   1.055   1215
  Planarity :  0.013   0.298   1354
  Dihedral  : 12.392 112.243   2897
  Min Nonbonded Distance : 1.386

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.70 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  0.60 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.44 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.99 (0.24), residues: 978
  helix: -2.35 (0.21), residues: 357
  sheet: -2.11 (0.35), residues: 157
  loop : -1.46 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG V 245 
 TYR   0.017   0.001   TYR A 176 
 PHE   0.014   0.002   PHE A 213 
 TRP   0.009   0.001   TRP H  52 
 HIS   0.006   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 ( 8069)
  covalent geometry    : angle       0.87772 (10984)
  SS BOND              : bond        0.00281 (    5)
  SS BOND              : angle       0.59811 (   10)
  hydrogen bonds       : bond        0.29693 (  349)
  hydrogen bonds       : angle       9.62099 (  954)
  link_BETA1-4         : bond        0.00592 (    1)
  link_BETA1-4         : angle       2.11207 (    3)
  link_NAG-ASN         : bond        0.25458 (    1)
  link_NAG-ASN         : angle      17.49589 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  482 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 471
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 THR cc_start: 0.8792 (p) cc_final: 0.8538 (t)
REVERT: A   82 TRP cc_start: 0.5796 (m-10) cc_final: 0.5371 (m-10)
REVERT: A  121 TYR cc_start: 0.9167 (t80) cc_final: 0.8563 (t80)
REVERT: A  158 PHE cc_start: 0.7206 (m-80) cc_final: 0.6870 (m-80)
REVERT: A  184 LEU cc_start: 0.9093 (tp) cc_final: 0.8627 (tp)
REVERT: A  189 SER cc_start: 0.9611 (m) cc_final: 0.9332 (p)
REVERT: A  195 LEU cc_start: 0.8511 (mt) cc_final: 0.8095 (mt)
REVERT: A  197 TRP cc_start: 0.8024 (m-10) cc_final: 0.7629 (m-10)
REVERT: A  268 PHE cc_start: 0.8591 (m-80) cc_final: 0.8385 (m-80)
REVERT: A  326 TRP cc_start: 0.8560 (m100) cc_final: 0.8295 (m-10)
REVERT: A  333 ILE cc_start: 0.9162 (pt) cc_final: 0.8877 (pt)
REVERT: A  369 CYS cc_start: 0.9027 (m) cc_final: 0.8764 (m)
REVERT: A  386 MET cc_start: 0.7877 (mmm) cc_final: 0.7651 (mmm)
REVERT: A  390 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7481 (mtt180)
REVERT: A  410 TYR cc_start: 0.8215 (t80) cc_final: 0.7887 (t80)
REVERT: A  417 MET cc_start: 0.8004 (mtm) cc_final: 0.7641 (mtm)
REVERT: A  422 PHE cc_start: 0.7805 (t80) cc_final: 0.7379 (t80)
REVERT: A  460 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7340 (ttpt)
REVERT: A  464 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7874 (ttm110)
REVERT: A  478 LEU cc_start: 0.8702 (tp) cc_final: 0.8410 (tp)
REVERT: A  538 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7504 (ttt-90)
REVERT: A  549 LEU cc_start: 0.9293 (mp) cc_final: 0.8952 (pp)
REVERT: A  555 SER cc_start: 0.8248 (p) cc_final: 0.8005 (p)
REVERT: A  570 TYR cc_start: 0.6643 (m-10) cc_final: 0.6019 (m-80)
REVERT: A  592 TYR cc_start: 0.7948 (t80) cc_final: 0.7717 (t80)
REVERT: A  593 ILE cc_start: 0.8339 (mt) cc_final: 0.8070 (mt)
REVERT: A  597 LEU cc_start: 0.8210 (mt) cc_final: 0.7917 (tt)
REVERT: H   21 VAL cc_start: 0.8059 (t) cc_final: 0.7641 (t)
REVERT: L   71 LEU cc_start: 0.8324 (mt) cc_final: 0.8110 (mt)
REVERT: L   72 ILE cc_start: 0.8701 (mm) cc_final: 0.8054 (tp)
REVERT: L   83 PRO cc_start: 0.8309 (Cg_exo) cc_final: 0.8060 (Cg_endo)
REVERT: L  121 THR cc_start: 0.7359 (p) cc_final: 0.6575 (m)
REVERT: V   43 THR cc_start: 0.8404 (m) cc_final: 0.8075 (t)
REVERT: V   47 TYR cc_start: 0.4447 (p90) cc_final: 0.2915 (p90)
REVERT: V   56 HIS cc_start: 0.6481 (t70) cc_final: 0.6070 (p-80)
REVERT: V   93 THR cc_start: 0.8861 (m) cc_final: 0.8499 (p)
REVERT: V  195 LEU cc_start: 0.8989 (tp) cc_final: 0.8503 (tp)
REVERT: V  236 TYR cc_start: 0.7410 (m-80) cc_final: 0.7187 (m-80)
REVERT: V  241 TYR cc_start: 0.8559 (t80) cc_final: 0.7786 (t80)
  outliers start: 11
  outliers final: 8
  residues processed: 478
  average time/residue: 0.0914
  time to fit residues: 58.9446
Evaluate side-chains
  353 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 345
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
A 211 ASN
A 235 HIS
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
H  58 GLN
L  61 GLN
V 239 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.172454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.148556 restraints weight = 14932.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.154113 restraints weight = 8648.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.158348 restraints weight = 5603.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.161348 restraints weight = 3810.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.163546 restraints weight = 2708.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6458
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   8076  Z= 0.189
  Angle     :  0.744  10.853  11000  Z= 0.378
  Chirality :  0.049   0.309   1215
  Planarity :  0.006   0.110   1354
  Dihedral  :  9.520  69.478   1202
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.01 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.17 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.61 (0.25), residues: 978
  helix: -0.59 (0.23), residues: 382
  sheet: -1.07 (0.36), residues: 164
  loop : -1.39 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 234 
 TYR   0.026   0.002   TYR V  48 
 PHE   0.026   0.002   PHE V 220 
 TRP   0.032   0.002   TRP V  62 
 HIS   0.007   0.002   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8069)
  covalent geometry    : angle       0.72704 (10984)
  SS BOND              : bond        0.00832 (    5)
  SS BOND              : angle       1.99024 (   10)
  hydrogen bonds       : bond        0.06215 (  349)
  hydrogen bonds       : angle       5.78374 (  954)
  link_BETA1-4         : bond        0.00809 (    1)
  link_BETA1-4         : angle       1.75217 (    3)
  link_NAG-ASN         : bond        0.01249 (    1)
  link_NAG-ASN         : angle       8.75383 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 400
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8464 (mptt) cc_final: 0.7815 (tptp)
REVERT: A  121 TYR cc_start: 0.9169 (t80) cc_final: 0.8658 (t80)
REVERT: A  171 TYR cc_start: 0.8800 (m-80) cc_final: 0.8592 (m-80)
REVERT: A  189 SER cc_start: 0.9597 (m) cc_final: 0.9360 (p)
REVERT: A  195 LEU cc_start: 0.8662 (mt) cc_final: 0.7846 (mt)
REVERT: A  197 TRP cc_start: 0.8661 (m-10) cc_final: 0.7990 (m-10)
REVERT: A  298 ARG cc_start: 0.8064 (tpm170) cc_final: 0.7684 (tpp-160)
REVERT: A  316 ASN cc_start: 0.7633 (t0) cc_final: 0.7377 (t0)
REVERT: A  370 MET cc_start: 0.7214 (mtm) cc_final: 0.6986 (mmm)
REVERT: A  385 TYR cc_start: 0.7429 (t80) cc_final: 0.7054 (t80)
REVERT: A  390 ARG cc_start: 0.8369 (mtt180) cc_final: 0.8071 (mtt180)
REVERT: A  393 ASP cc_start: 0.8625 (t70) cc_final: 0.8361 (t70)
REVERT: A  417 MET cc_start: 0.8170 (mtm) cc_final: 0.7605 (mtm)
REVERT: A  453 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8554 (mm-30)
REVERT: A  460 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7344 (ttpt)
REVERT: A  538 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7288 (ttt-90)
REVERT: A  567 GLN cc_start: 0.9069 (pm20) cc_final: 0.8818 (pm20)
REVERT: A  570 TYR cc_start: 0.6858 (m-10) cc_final: 0.5934 (m-80)
REVERT: A  581 ILE cc_start: 0.8487 (mt) cc_final: 0.8280 (mt)
REVERT: A  592 TYR cc_start: 0.8313 (t80) cc_final: 0.7338 (t80)
REVERT: A  593 ILE cc_start: 0.8602 (mt) cc_final: 0.8327 (mt)
REVERT: H   22 GLN cc_start: 0.6614 (mp10) cc_final: 0.6386 (mp10)
REVERT: H   76 ASP cc_start: 0.8595 (t0) cc_final: 0.8137 (t0)
REVERT: H  128 ASP cc_start: 0.8228 (t0) cc_final: 0.7937 (t0)
REVERT: L   78 GLN cc_start: 0.7996 (pp30) cc_final: 0.7741 (tm-30)
REVERT: L   83 PRO cc_start: 0.8862 (Cg_exo) cc_final: 0.8188 (Cg_endo)
REVERT: L  114 GLN cc_start: 0.7965 (pm20) cc_final: 0.7415 (pm20)
REVERT: V   21 GLN cc_start: 0.6374 (mt0) cc_final: 0.5712 (mt0)
REVERT: V   37 CYS cc_start: 0.3939 (p) cc_final: 0.3381 (p)
REVERT: V   51 TRP cc_start: 0.8285 (m100) cc_final: 0.7841 (m100)
REVERT: V   62 TRP cc_start: 0.8710 (t60) cc_final: 0.8282 (t60)
REVERT: V   76 ASN cc_start: 0.8117 (t0) cc_final: 0.7372 (p0)
REVERT: V   79 PHE cc_start: 0.6744 (m-10) cc_final: 0.6006 (m-10)
REVERT: V   92 THR cc_start: 0.8719 (p) cc_final: 0.8222 (t)
REVERT: V   93 THR cc_start: 0.8311 (m) cc_final: 0.7946 (p)
REVERT: V  105 ASP cc_start: 0.8857 (m-30) cc_final: 0.8474 (m-30)
REVERT: V  176 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7516 (mm-40)
REVERT: V  184 TRP cc_start: 0.9141 (m100) cc_final: 0.8570 (m100)
REVERT: V  241 TYR cc_start: 0.8152 (t80) cc_final: 0.7438 (t80)
REVERT: V  246 THR cc_start: 0.8206 (p) cc_final: 0.7843 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 401
  average time/residue: 0.0763
  time to fit residues: 43.2724
Evaluate side-chains
  324 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 324
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 96 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0070
   chunk 17 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
A 235 HIS
A 368 ASN
A 391 ASN
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.173186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.149459 restraints weight = 15922.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.155074 restraints weight = 9477.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.159137 restraints weight = 6207.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162072 restraints weight = 4293.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.164186 restraints weight = 3087.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6523
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8076  Z= 0.145
  Angle     :  0.675  11.464  11000  Z= 0.339
  Chirality :  0.045   0.371   1215
  Planarity :  0.005   0.091   1354
  Dihedral  :  6.544  44.199   1202
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.29 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.81 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 (0.26), residues: 978
  helix:  0.04 (0.25), residues: 384
  sheet: -0.81 (0.36), residues: 181
  loop : -1.22 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  38 
 TYR   0.019   0.002   TYR A 176 
 PHE   0.045   0.002   PHE A 440 
 TRP   0.033   0.002   TRP H  55 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8069)
  covalent geometry    : angle       0.66375 (10984)
  SS BOND              : bond        0.00769 (    5)
  SS BOND              : angle       1.30861 (   10)
  hydrogen bonds       : bond        0.04999 (  349)
  hydrogen bonds       : angle       5.23279 (  954)
  link_BETA1-4         : bond        0.00515 (    1)
  link_BETA1-4         : angle       1.43594 (    3)
  link_NAG-ASN         : bond        0.00880 (    1)
  link_NAG-ASN         : angle       6.92111 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 380
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLU cc_start: 0.8324 (tp30) cc_final: 0.7801 (tm-30)
REVERT: A   84 LYS cc_start: 0.8504 (mptt) cc_final: 0.7888 (tptm)
REVERT: A  121 TYR cc_start: 0.9160 (t80) cc_final: 0.8668 (t80)
REVERT: A  124 MET cc_start: 0.8913 (mmp) cc_final: 0.8686 (mmp)
REVERT: A  142 TYR cc_start: 0.8608 (t80) cc_final: 0.8374 (t80)
REVERT: A  184 LEU cc_start: 0.9065 (tp) cc_final: 0.8736 (tp)
REVERT: A  189 SER cc_start: 0.9607 (m) cc_final: 0.9386 (p)
REVERT: A  195 LEU cc_start: 0.8730 (mt) cc_final: 0.8056 (mt)
REVERT: A  197 TRP cc_start: 0.8878 (m-10) cc_final: 0.8141 (m-10)
REVERT: A  284 THR cc_start: 0.8846 (p) cc_final: 0.8626 (p)
REVERT: A  298 ARG cc_start: 0.7827 (tpm170) cc_final: 0.7113 (tpp-160)
REVERT: A  316 ASN cc_start: 0.7868 (t0) cc_final: 0.7503 (t0)
REVERT: A  333 ILE cc_start: 0.9188 (pt) cc_final: 0.8899 (pt)
REVERT: A  370 MET cc_start: 0.6862 (mtm) cc_final: 0.6615 (mmm)
REVERT: A  385 TYR cc_start: 0.7585 (t80) cc_final: 0.7231 (t80)
REVERT: A  393 ASP cc_start: 0.8779 (t70) cc_final: 0.8512 (t70)
REVERT: A  410 TYR cc_start: 0.7792 (t80) cc_final: 0.7493 (t80)
REVERT: A  453 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8670 (mm-30)
REVERT: A  460 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7461 (ttpt)
REVERT: A  538 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7055 (ttt-90)
REVERT: A  567 GLN cc_start: 0.9078 (pm20) cc_final: 0.8821 (pm20)
REVERT: A  570 TYR cc_start: 0.6926 (m-10) cc_final: 0.5376 (m-80)
REVERT: A  576 ILE cc_start: 0.8045 (tp) cc_final: 0.7796 (tp)
REVERT: A  606 GLU cc_start: 0.7891 (tp30) cc_final: 0.7558 (tp30)
REVERT: A  609 ILE cc_start: 0.9504 (tp) cc_final: 0.9301 (pt)
REVERT: H   22 GLN cc_start: 0.6689 (mp10) cc_final: 0.6398 (mp10)
REVERT: H   49 SER cc_start: 0.8612 (p) cc_final: 0.8386 (p)
REVERT: H   50 TYR cc_start: 0.7821 (m-80) cc_final: 0.7492 (m-80)
REVERT: H   76 ASP cc_start: 0.8495 (t0) cc_final: 0.8058 (t0)
REVERT: H   93 LYS cc_start: 0.5673 (pttt) cc_final: 0.5387 (ptpp)
REVERT: H  120 TYR cc_start: 0.7706 (m-80) cc_final: 0.6458 (m-80)
REVERT: L  100 HIS cc_start: 0.6797 (m90) cc_final: 0.6383 (m90)
REVERT: L  121 THR cc_start: 0.6877 (p) cc_final: 0.5708 (t)
REVERT: V   18 GLN cc_start: 0.8548 (mm110) cc_final: 0.8011 (mp10)
REVERT: V   21 GLN cc_start: 0.6554 (mt0) cc_final: 0.5904 (mt0)
REVERT: V   37 CYS cc_start: 0.4343 (p) cc_final: 0.3856 (p)
REVERT: V   51 TRP cc_start: 0.8261 (m100) cc_final: 0.7995 (m100)
REVERT: V   62 TRP cc_start: 0.8932 (t60) cc_final: 0.8465 (t60)
REVERT: V   76 ASN cc_start: 0.8075 (t0) cc_final: 0.7345 (p0)
REVERT: V   79 PHE cc_start: 0.6936 (m-10) cc_final: 0.6172 (m-10)
REVERT: V   92 THR cc_start: 0.8755 (p) cc_final: 0.8317 (t)
REVERT: V  105 ASP cc_start: 0.8792 (m-30) cc_final: 0.8446 (m-30)
REVERT: V  124 TRP cc_start: 0.8643 (m100) cc_final: 0.8428 (m-10)
REVERT: V  151 ILE cc_start: 0.8013 (mt) cc_final: 0.7792 (mt)
REVERT: V  173 LYS cc_start: 0.7683 (mmtm) cc_final: 0.7182 (tppt)
REVERT: V  176 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7527 (mm-40)
REVERT: V  184 TRP cc_start: 0.9271 (m100) cc_final: 0.8563 (m100)
REVERT: V  220 PHE cc_start: 0.7726 (m-10) cc_final: 0.7419 (m-10)
REVERT: V  236 TYR cc_start: 0.8179 (m-80) cc_final: 0.7542 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 382
  average time/residue: 0.0745
  time to fit residues: 40.3034
Evaluate side-chains
  331 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 330
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 61 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 391 ASN
V 186 GLN
V 239 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.166588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.143287 restraints weight = 15594.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.148913 restraints weight = 8971.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.152903 restraints weight = 5753.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.155790 restraints weight = 3946.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.157920 restraints weight = 2812.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.5259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8076  Z= 0.136
  Angle     :  0.643  12.057  11000  Z= 0.326
  Chirality :  0.044   0.323   1215
  Planarity :  0.005   0.076   1354
  Dihedral  :  6.051  44.387   1202
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.70 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.17 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    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: -0.82 (0.26), residues: 978
  helix:  0.31 (0.26), residues: 385
  sheet: -0.56 (0.36), residues: 182
  loop : -1.28 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  69 
 TYR   0.017   0.001   TYR A 176 
 PHE   0.035   0.002   PHE A 440 
 TRP   0.015   0.001   TRP V  62 
 HIS   0.004   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8069)
  covalent geometry    : angle       0.63437 (10984)
  SS BOND              : bond        0.00440 (    5)
  SS BOND              : angle       0.80402 (   10)
  hydrogen bonds       : bond        0.04426 (  349)
  hydrogen bonds       : angle       5.00366 (  954)
  link_BETA1-4         : bond        0.00780 (    1)
  link_BETA1-4         : angle       1.69785 (    3)
  link_NAG-ASN         : bond        0.00347 (    1)
  link_NAG-ASN         : angle       6.19060 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 366
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8541 (mptt) cc_final: 0.7831 (tptm)
REVERT: A  121 TYR cc_start: 0.9151 (t80) cc_final: 0.8672 (t80)
REVERT: A  124 MET cc_start: 0.9002 (mmp) cc_final: 0.8736 (mmp)
REVERT: A  142 TYR cc_start: 0.8723 (t80) cc_final: 0.8337 (t80)
REVERT: A  184 LEU cc_start: 0.9087 (tp) cc_final: 0.8735 (tp)
REVERT: A  189 SER cc_start: 0.9597 (m) cc_final: 0.9371 (p)
REVERT: A  195 LEU cc_start: 0.8871 (mt) cc_final: 0.8448 (mt)
REVERT: A  197 TRP cc_start: 0.8999 (m-10) cc_final: 0.8389 (m-10)
REVERT: A  229 GLU cc_start: 0.8636 (tt0) cc_final: 0.8402 (tt0)
REVERT: A  260 MET cc_start: 0.7947 (mmm) cc_final: 0.7670 (mmm)
REVERT: A  316 ASN cc_start: 0.8068 (t0) cc_final: 0.7627 (t0)
REVERT: A  333 ILE cc_start: 0.9181 (pt) cc_final: 0.8869 (pt)
REVERT: A  337 LEU cc_start: 0.9466 (mt) cc_final: 0.9250 (mt)
REVERT: A  370 MET cc_start: 0.6874 (mtm) cc_final: 0.6627 (mmm)
REVERT: A  385 TYR cc_start: 0.7616 (t80) cc_final: 0.7368 (t80)
REVERT: A  390 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7980 (mtt180)
REVERT: A  393 ASP cc_start: 0.8702 (t70) cc_final: 0.8482 (t70)
REVERT: A  410 TYR cc_start: 0.8005 (t80) cc_final: 0.7696 (t80)
REVERT: A  422 PHE cc_start: 0.7796 (t80) cc_final: 0.7448 (t80)
REVERT: A  426 ILE cc_start: 0.9143 (mt) cc_final: 0.8637 (mt)
REVERT: A  431 LEU cc_start: 0.8947 (tp) cc_final: 0.8685 (tp)
REVERT: A  447 ILE cc_start: 0.9606 (mt) cc_final: 0.9397 (mt)
REVERT: A  460 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7511 (mtpt)
REVERT: A  538 ARG cc_start: 0.7668 (mtm180) cc_final: 0.6968 (ttt-90)
REVERT: A  567 GLN cc_start: 0.9097 (pm20) cc_final: 0.8816 (pm20)
REVERT: A  570 TYR cc_start: 0.7061 (m-10) cc_final: 0.5644 (m-80)
REVERT: A  592 TYR cc_start: 0.8260 (t80) cc_final: 0.6885 (t80)
REVERT: A  596 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7300 (mmm160)
REVERT: A  609 ILE cc_start: 0.9510 (tp) cc_final: 0.9300 (pt)
REVERT: H   22 GLN cc_start: 0.6663 (mp10) cc_final: 0.6377 (mp10)
REVERT: H   76 ASP cc_start: 0.8574 (t0) cc_final: 0.8219 (t0)
REVERT: H   93 LYS cc_start: 0.5696 (pttt) cc_final: 0.5468 (ptpp)
REVERT: H  120 TYR cc_start: 0.7798 (m-80) cc_final: 0.7321 (m-80)
REVERT: H  128 ASP cc_start: 0.8426 (t70) cc_final: 0.7898 (t70)
REVERT: L   60 PHE cc_start: 0.8216 (m-10) cc_final: 0.7985 (m-10)
REVERT: L  100 HIS cc_start: 0.6992 (m90) cc_final: 0.6487 (m90)
REVERT: V   18 GLN cc_start: 0.8573 (mm110) cc_final: 0.8020 (mp10)
REVERT: V   20 GLN cc_start: 0.7437 (mm110) cc_final: 0.7159 (mm-40)
REVERT: V   37 CYS cc_start: 0.4027 (p) cc_final: 0.3533 (p)
REVERT: V   51 TRP cc_start: 0.8393 (m100) cc_final: 0.8179 (m100)
REVERT: V   62 TRP cc_start: 0.8932 (t60) cc_final: 0.8480 (t60)
REVERT: V   79 PHE cc_start: 0.6987 (m-10) cc_final: 0.6764 (m-10)
REVERT: V   92 THR cc_start: 0.8719 (p) cc_final: 0.8298 (t)
REVERT: V  105 ASP cc_start: 0.8833 (m-30) cc_final: 0.8498 (m-30)
REVERT: V  124 TRP cc_start: 0.8628 (m100) cc_final: 0.8355 (m-10)
REVERT: V  173 LYS cc_start: 0.7638 (mmtm) cc_final: 0.7267 (tppt)
REVERT: V  176 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7563 (mm-40)
REVERT: V  184 TRP cc_start: 0.9201 (m100) cc_final: 0.8579 (m100)
REVERT: V  236 TYR cc_start: 0.8308 (m-80) cc_final: 0.7721 (m-80)
REVERT: V  251 THR cc_start: 0.8044 (m) cc_final: 0.7690 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 366
  average time/residue: 0.0738
  time to fit residues: 38.7379
Evaluate side-chains
  323 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 323
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 53 optimal weight:   20.0000
   chunk 71 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 391 ASN
H  24 GLN
V  65 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.161448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.137335 restraints weight = 16541.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142566 restraints weight = 9867.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.146417 restraints weight = 6560.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.149269 restraints weight = 4619.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.151429 restraints weight = 3432.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.5914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8076  Z= 0.191
  Angle     :  0.727  12.115  11000  Z= 0.368
  Chirality :  0.046   0.412   1215
  Planarity :  0.005   0.069   1354
  Dihedral  :  5.983  40.797   1202
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.52 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    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: -0.92 (0.26), residues: 978
  helix:  0.10 (0.25), residues: 387
  sheet: -0.53 (0.36), residues: 186
  loop : -1.25 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 234 
 TYR   0.026   0.002   TYR A 171 
 PHE   0.027   0.002   PHE V 220 
 TRP   0.019   0.002   TRP A 220 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 8069)
  covalent geometry    : angle       0.72079 (10984)
  SS BOND              : bond        0.00405 (    5)
  SS BOND              : angle       0.98505 (   10)
  hydrogen bonds       : bond        0.04660 (  349)
  hydrogen bonds       : angle       5.05499 (  954)
  link_BETA1-4         : bond        0.01411 (    1)
  link_BETA1-4         : angle       2.19247 (    3)
  link_NAG-ASN         : bond        0.00784 (    1)
  link_NAG-ASN         : angle       5.44987 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 358
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8661 (mptt) cc_final: 0.7899 (tptm)
REVERT: A  121 TYR cc_start: 0.9129 (t80) cc_final: 0.8494 (t80)
REVERT: A  124 MET cc_start: 0.8943 (mmp) cc_final: 0.8642 (mmp)
REVERT: A  171 TYR cc_start: 0.8889 (m-80) cc_final: 0.8664 (m-80)
REVERT: A  184 LEU cc_start: 0.9182 (tp) cc_final: 0.8829 (tp)
REVERT: A  189 SER cc_start: 0.9589 (m) cc_final: 0.9369 (p)
REVERT: A  193 ASP cc_start: 0.8203 (p0) cc_final: 0.7720 (m-30)
REVERT: A  195 LEU cc_start: 0.8919 (mt) cc_final: 0.8557 (mt)
REVERT: A  197 TRP cc_start: 0.9263 (m-10) cc_final: 0.8733 (m-10)
REVERT: A  205 ASN cc_start: 0.8614 (t0) cc_final: 0.8409 (t0)
REVERT: A  245 LEU cc_start: 0.8364 (mm) cc_final: 0.8018 (mm)
REVERT: A  316 ASN cc_start: 0.8256 (t0) cc_final: 0.7731 (t0)
REVERT: A  333 ILE cc_start: 0.9195 (pt) cc_final: 0.8850 (pt)
REVERT: A  337 LEU cc_start: 0.9467 (mt) cc_final: 0.9251 (mt)
REVERT: A  344 LEU cc_start: 0.8338 (tt) cc_final: 0.7939 (tt)
REVERT: A  370 MET cc_start: 0.6873 (mtm) cc_final: 0.6641 (mmm)
REVERT: A  390 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7447 (mtt180)
REVERT: A  422 PHE cc_start: 0.7949 (t80) cc_final: 0.7726 (t80)
REVERT: A  426 ILE cc_start: 0.9136 (mt) cc_final: 0.8799 (mt)
REVERT: A  447 ILE cc_start: 0.9598 (mt) cc_final: 0.9365 (mt)
REVERT: A  453 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8745 (mm-30)
REVERT: A  460 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7712 (mtpt)
REVERT: A  538 ARG cc_start: 0.7644 (mtm180) cc_final: 0.7077 (ttt-90)
REVERT: A  565 LEU cc_start: 0.7291 (tp) cc_final: 0.6858 (tt)
REVERT: A  567 GLN cc_start: 0.9122 (pm20) cc_final: 0.8804 (pm20)
REVERT: A  570 TYR cc_start: 0.7607 (m-10) cc_final: 0.6704 (m-80)
REVERT: A  592 TYR cc_start: 0.8140 (t80) cc_final: 0.6953 (t80)
REVERT: H   22 GLN cc_start: 0.6502 (mp10) cc_final: 0.6232 (mp10)
REVERT: H   49 SER cc_start: 0.8439 (p) cc_final: 0.8185 (p)
REVERT: H   76 ASP cc_start: 0.8803 (t0) cc_final: 0.8516 (t0)
REVERT: H  120 TYR cc_start: 0.7888 (m-80) cc_final: 0.7326 (m-80)
REVERT: L   60 PHE cc_start: 0.8468 (m-10) cc_final: 0.8203 (m-10)
REVERT: L   71 LEU cc_start: 0.9061 (mt) cc_final: 0.8654 (mt)
REVERT: L  100 HIS cc_start: 0.7186 (m90) cc_final: 0.6688 (m90)
REVERT: V   18 GLN cc_start: 0.8551 (mm110) cc_final: 0.7966 (mp10)
REVERT: V   20 GLN cc_start: 0.7348 (mm110) cc_final: 0.7005 (mm-40)
REVERT: V   38 LYS cc_start: 0.7903 (tttt) cc_final: 0.7389 (ttmt)
REVERT: V   43 THR cc_start: 0.8135 (m) cc_final: 0.7471 (p)
REVERT: V   51 TRP cc_start: 0.8664 (m100) cc_final: 0.8193 (m100)
REVERT: V   62 TRP cc_start: 0.8993 (t60) cc_final: 0.8394 (t60)
REVERT: V   67 ASN cc_start: 0.7986 (t0) cc_final: 0.7599 (t0)
REVERT: V   79 PHE cc_start: 0.7201 (m-10) cc_final: 0.6795 (m-10)
REVERT: V   92 THR cc_start: 0.8638 (p) cc_final: 0.8223 (t)
REVERT: V  105 ASP cc_start: 0.8755 (m-30) cc_final: 0.8352 (m-30)
REVERT: V  124 TRP cc_start: 0.8704 (m100) cc_final: 0.8352 (m-10)
REVERT: V  151 ILE cc_start: 0.8331 (mt) cc_final: 0.7981 (mt)
REVERT: V  173 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7433 (tppt)
REVERT: V  176 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7698 (mm-40)
REVERT: V  184 TRP cc_start: 0.9237 (m100) cc_final: 0.8664 (m100)
REVERT: V  251 THR cc_start: 0.8385 (m) cc_final: 0.8055 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 358
  average time/residue: 0.0735
  time to fit residues: 37.7449
Evaluate side-chains
  300 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 223 HIS
A 368 ASN
A 391 ASN
** L  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 238 GLN
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.138642 restraints weight = 15529.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.144077 restraints weight = 9019.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.148027 restraints weight = 5842.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.150851 restraints weight = 4045.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.152978 restraints weight = 2942.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.6221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8076  Z= 0.142
  Angle     :  0.672  11.937  11000  Z= 0.339
  Chirality :  0.045   0.362   1215
  Planarity :  0.004   0.061   1354
  Dihedral  :  5.781  41.116   1202
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.11 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    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: -0.65 (0.27), residues: 978
  helix:  0.44 (0.26), residues: 382
  sheet: -0.59 (0.38), residues: 176
  loop : -1.09 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 234 
 TYR   0.019   0.002   TYR A 175 
 PHE   0.029   0.002   PHE A 440 
 TRP   0.020   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8069)
  covalent geometry    : angle       0.66515 (10984)
  SS BOND              : bond        0.00358 (    5)
  SS BOND              : angle       0.94284 (   10)
  hydrogen bonds       : bond        0.04374 (  349)
  hydrogen bonds       : angle       4.93295 (  954)
  link_BETA1-4         : bond        0.01158 (    1)
  link_BETA1-4         : angle       2.41501 (    3)
  link_NAG-ASN         : bond        0.00432 (    1)
  link_NAG-ASN         : angle       5.28752 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 361
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8689 (mptt) cc_final: 0.8152 (tptm)
REVERT: A  111 GLN cc_start: 0.9119 (tt0) cc_final: 0.8876 (tm-30)
REVERT: A  121 TYR cc_start: 0.9106 (t80) cc_final: 0.8513 (t80)
REVERT: A  124 MET cc_start: 0.8954 (mmp) cc_final: 0.8657 (mmp)
REVERT: A  147 CYS cc_start: 0.8776 (t) cc_final: 0.8522 (t)
REVERT: A  171 TYR cc_start: 0.8913 (m-80) cc_final: 0.8711 (m-80)
REVERT: A  184 LEU cc_start: 0.9171 (tp) cc_final: 0.8824 (tp)
REVERT: A  189 SER cc_start: 0.9555 (m) cc_final: 0.9343 (p)
REVERT: A  193 ASP cc_start: 0.8315 (p0) cc_final: 0.8004 (m-30)
REVERT: A  195 LEU cc_start: 0.8966 (mt) cc_final: 0.8659 (mt)
REVERT: A  197 TRP cc_start: 0.9212 (m-10) cc_final: 0.8690 (m-10)
REVERT: A  205 ASN cc_start: 0.8661 (t0) cc_final: 0.8307 (t0)
REVERT: A  245 LEU cc_start: 0.8574 (mm) cc_final: 0.7920 (mm)
REVERT: A  246 GLN cc_start: 0.7109 (tt0) cc_final: 0.6688 (pm20)
REVERT: A  316 ASN cc_start: 0.8589 (t0) cc_final: 0.7972 (t0)
REVERT: A  333 ILE cc_start: 0.9193 (pt) cc_final: 0.8830 (pt)
REVERT: A  337 LEU cc_start: 0.9464 (mt) cc_final: 0.9238 (mt)
REVERT: A  344 LEU cc_start: 0.8229 (tt) cc_final: 0.7878 (tt)
REVERT: A  370 MET cc_start: 0.6589 (mtm) cc_final: 0.6357 (mmm)
REVERT: A  447 ILE cc_start: 0.9604 (mt) cc_final: 0.9383 (mt)
REVERT: A  453 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8654 (mm-30)
REVERT: A  460 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7741 (mtpt)
REVERT: A  538 ARG cc_start: 0.7454 (mtm180) cc_final: 0.6885 (ttt-90)
REVERT: A  565 LEU cc_start: 0.7545 (tp) cc_final: 0.7139 (tt)
REVERT: A  570 TYR cc_start: 0.7657 (m-10) cc_final: 0.6807 (m-80)
REVERT: A  592 TYR cc_start: 0.8113 (t80) cc_final: 0.7055 (t80)
REVERT: H   22 GLN cc_start: 0.6480 (mp10) cc_final: 0.6190 (mp10)
REVERT: H   49 SER cc_start: 0.8527 (p) cc_final: 0.8275 (p)
REVERT: H   76 ASP cc_start: 0.8866 (t0) cc_final: 0.8376 (t0)
REVERT: H  120 TYR cc_start: 0.7975 (m-80) cc_final: 0.7522 (m-80)
REVERT: L   60 PHE cc_start: 0.8160 (m-10) cc_final: 0.7944 (m-10)
REVERT: L   78 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7546 (tp-100)
REVERT: L  100 HIS cc_start: 0.7234 (m90) cc_final: 0.6735 (m90)
REVERT: L  114 GLN cc_start: 0.7810 (pm20) cc_final: 0.7117 (pm20)
REVERT: L  121 THR cc_start: 0.7356 (p) cc_final: 0.7106 (p)
REVERT: V   18 GLN cc_start: 0.8577 (mm110) cc_final: 0.8001 (mp10)
REVERT: V   20 GLN cc_start: 0.7440 (mm110) cc_final: 0.7014 (mm-40)
REVERT: V   37 CYS cc_start: 0.4365 (p) cc_final: 0.3876 (p)
REVERT: V   38 LYS cc_start: 0.7821 (tttt) cc_final: 0.7309 (mttt)
REVERT: V   43 THR cc_start: 0.8122 (m) cc_final: 0.7785 (p)
REVERT: V   51 TRP cc_start: 0.8251 (m100) cc_final: 0.7938 (m100)
REVERT: V   62 TRP cc_start: 0.9110 (t60) cc_final: 0.8782 (t60)
REVERT: V   67 ASN cc_start: 0.8210 (t0) cc_final: 0.7900 (t0)
REVERT: V   92 THR cc_start: 0.8658 (p) cc_final: 0.8237 (t)
REVERT: V  105 ASP cc_start: 0.8596 (m-30) cc_final: 0.8212 (m-30)
REVERT: V  124 TRP cc_start: 0.8694 (m100) cc_final: 0.8355 (m-10)
REVERT: V  151 ILE cc_start: 0.8630 (mt) cc_final: 0.8342 (mt)
REVERT: V  173 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7241 (tppt)
REVERT: V  176 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7701 (mm-40)
REVERT: V  184 TRP cc_start: 0.9039 (m100) cc_final: 0.8448 (m100)
REVERT: V  204 TYR cc_start: 0.7189 (t80) cc_final: 0.6463 (t80)
REVERT: V  251 THR cc_start: 0.8092 (m) cc_final: 0.7703 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 361
  average time/residue: 0.0685
  time to fit residues: 35.7879
Evaluate side-chains
  314 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 314
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 92 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0670
   chunk 28 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   overall best weight:    3.1724

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

Flipped N/Q/H residues before XYZ refinement:
A 223 HIS
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
A 456 HIS
L  26 GLN
V  65 ASN
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.155060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.132123 restraints weight = 15819.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.137380 restraints weight = 9114.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.141197 restraints weight = 5863.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.143968 restraints weight = 4068.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.146038 restraints weight = 2950.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.6792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8076  Z= 0.199
  Angle     :  0.733  11.561  11000  Z= 0.373
  Chirality :  0.046   0.396   1215
  Planarity :  0.005   0.064   1354
  Dihedral  :  5.882  41.284   1202
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.75 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 (0.27), residues: 978
  helix:  0.17 (0.26), residues: 384
  sheet: -0.56 (0.36), residues: 196
  loop : -1.22 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 234 
 TYR   0.029   0.002   TYR V  48 
 PHE   0.024   0.002   PHE A 170 
 TRP   0.022   0.002   TRP A 271 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 8069)
  covalent geometry    : angle       0.72648 (10984)
  SS BOND              : bond        0.00345 (    5)
  SS BOND              : angle       1.06942 (   10)
  hydrogen bonds       : bond        0.04591 (  349)
  hydrogen bonds       : angle       5.08209 (  954)
  link_BETA1-4         : bond        0.01696 (    1)
  link_BETA1-4         : angle       2.82086 (    3)
  link_NAG-ASN         : bond        0.00527 (    1)
  link_NAG-ASN         : angle       4.91112 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 340
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8842 (mptt) cc_final: 0.8207 (tptm)
REVERT: A  121 TYR cc_start: 0.9112 (t80) cc_final: 0.8406 (t80)
REVERT: A  124 MET cc_start: 0.8936 (mmp) cc_final: 0.8585 (mmp)
REVERT: A  184 LEU cc_start: 0.9220 (tp) cc_final: 0.8886 (tp)
REVERT: A  189 SER cc_start: 0.9611 (m) cc_final: 0.9409 (p)
REVERT: A  205 ASN cc_start: 0.8871 (t0) cc_final: 0.8321 (t0)
REVERT: A  222 LEU cc_start: 0.9125 (mm) cc_final: 0.8729 (mm)
REVERT: A  223 HIS cc_start: 0.8410 (m-70) cc_final: 0.8011 (m170)
REVERT: A  240 HIS cc_start: 0.9003 (p-80) cc_final: 0.8802 (p-80)
REVERT: A  245 LEU cc_start: 0.8687 (mm) cc_final: 0.7753 (mm)
REVERT: A  246 GLN cc_start: 0.7363 (tt0) cc_final: 0.6887 (pm20)
REVERT: A  316 ASN cc_start: 0.8730 (t0) cc_final: 0.8262 (t0)
REVERT: A  328 ASP cc_start: 0.8215 (m-30) cc_final: 0.7907 (m-30)
REVERT: A  333 ILE cc_start: 0.9167 (pt) cc_final: 0.8796 (pt)
REVERT: A  337 LEU cc_start: 0.9469 (mt) cc_final: 0.9197 (mt)
REVERT: A  447 ILE cc_start: 0.9605 (mt) cc_final: 0.9378 (mt)
REVERT: A  453 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8743 (mm-30)
REVERT: A  460 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7791 (mtpt)
REVERT: A  538 ARG cc_start: 0.7671 (mtm180) cc_final: 0.6982 (ttt-90)
REVERT: A  570 TYR cc_start: 0.7886 (m-10) cc_final: 0.7084 (m-80)
REVERT: A  592 TYR cc_start: 0.8207 (t80) cc_final: 0.7251 (t80)
REVERT: H   49 SER cc_start: 0.8709 (p) cc_final: 0.8493 (p)
REVERT: H   76 ASP cc_start: 0.8793 (t0) cc_final: 0.8315 (t0)
REVERT: L   37 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7479 (tp-100)
REVERT: L   60 PHE cc_start: 0.8259 (m-10) cc_final: 0.7700 (m-10)
REVERT: L   71 LEU cc_start: 0.9033 (mt) cc_final: 0.8621 (mt)
REVERT: L   77 ASN cc_start: 0.8920 (t0) cc_final: 0.8633 (t0)
REVERT: L  100 HIS cc_start: 0.7345 (m90) cc_final: 0.6858 (m90)
REVERT: L  114 GLN cc_start: 0.7837 (pm20) cc_final: 0.7014 (pm20)
REVERT: L  121 THR cc_start: 0.7174 (p) cc_final: 0.6790 (p)
REVERT: V   18 GLN cc_start: 0.8504 (mm110) cc_final: 0.7941 (mp10)
REVERT: V   20 GLN cc_start: 0.7658 (mm110) cc_final: 0.7180 (mm-40)
REVERT: V   38 LYS cc_start: 0.7951 (tttt) cc_final: 0.7421 (ttmt)
REVERT: V   43 THR cc_start: 0.8067 (m) cc_final: 0.7299 (p)
REVERT: V   51 TRP cc_start: 0.8506 (m100) cc_final: 0.8016 (m100)
REVERT: V   67 ASN cc_start: 0.8325 (t0) cc_final: 0.7983 (t0)
REVERT: V   92 THR cc_start: 0.8692 (p) cc_final: 0.8290 (t)
REVERT: V  105 ASP cc_start: 0.8505 (m-30) cc_final: 0.8139 (m-30)
REVERT: V  124 TRP cc_start: 0.8729 (m100) cc_final: 0.8346 (m-10)
REVERT: V  151 ILE cc_start: 0.8487 (mt) cc_final: 0.8092 (mt)
REVERT: V  176 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7846 (mm-40)
REVERT: V  184 TRP cc_start: 0.9103 (m100) cc_final: 0.8456 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 340
  average time/residue: 0.0712
  time to fit residues: 34.8181
Evaluate side-chains
  305 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 92 optimal weight:    8.9990
   chunk 78 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0030
   chunk 42 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 391 ASN
L  26 GLN
V  65 ASN
V 238 GLN
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.156365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.132418 restraints weight = 15961.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.137928 restraints weight = 9259.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.141950 restraints weight = 6009.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.144855 restraints weight = 4153.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.147048 restraints weight = 3011.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          0.6998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8076  Z= 0.155
  Angle     :  0.704  11.551  11000  Z= 0.355
  Chirality :  0.045   0.352   1215
  Planarity :  0.004   0.055   1354
  Dihedral  :  5.833  43.249   1202
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.73 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.77 (0.27), residues: 978
  helix:  0.26 (0.26), residues: 385
  sheet: -0.43 (0.37), residues: 195
  loop : -1.22 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 234 
 TYR   0.026   0.002   TYR A  95 
 PHE   0.020   0.002   PHE A 440 
 TRP   0.029   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8069)
  covalent geometry    : angle       0.69834 (10984)
  SS BOND              : bond        0.00382 (    5)
  SS BOND              : angle       1.04148 (   10)
  hydrogen bonds       : bond        0.04442 (  349)
  hydrogen bonds       : angle       5.10801 (  954)
  link_BETA1-4         : bond        0.01636 (    1)
  link_BETA1-4         : angle       2.66757 (    3)
  link_NAG-ASN         : bond        0.00517 (    1)
  link_NAG-ASN         : angle       4.64952 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 340
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8868 (mptt) cc_final: 0.8254 (tptm)
REVERT: A  121 TYR cc_start: 0.9049 (t80) cc_final: 0.8425 (t80)
REVERT: A  124 MET cc_start: 0.8993 (mmp) cc_final: 0.8587 (mmp)
REVERT: A  184 LEU cc_start: 0.9182 (tp) cc_final: 0.8862 (tp)
REVERT: A  189 SER cc_start: 0.9605 (m) cc_final: 0.9397 (p)
REVERT: A  195 LEU cc_start: 0.9054 (mt) cc_final: 0.8811 (mt)
REVERT: A  205 ASN cc_start: 0.8821 (t0) cc_final: 0.8272 (t0)
REVERT: A  223 HIS cc_start: 0.8301 (m-70) cc_final: 0.7866 (m170)
REVERT: A  245 LEU cc_start: 0.8621 (mm) cc_final: 0.7528 (mm)
REVERT: A  246 GLN cc_start: 0.7324 (tt0) cc_final: 0.6861 (pm20)
REVERT: A  316 ASN cc_start: 0.8738 (t0) cc_final: 0.8296 (t0)
REVERT: A  328 ASP cc_start: 0.8230 (m-30) cc_final: 0.7855 (m-30)
REVERT: A  333 ILE cc_start: 0.9104 (pt) cc_final: 0.8742 (pt)
REVERT: A  337 LEU cc_start: 0.9447 (mt) cc_final: 0.9188 (mt)
REVERT: A  344 LEU cc_start: 0.8390 (tt) cc_final: 0.7978 (tt)
REVERT: A  447 ILE cc_start: 0.9599 (mt) cc_final: 0.9369 (mt)
REVERT: A  460 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7809 (mtpt)
REVERT: A  538 ARG cc_start: 0.7449 (mtm180) cc_final: 0.6835 (ttt-90)
REVERT: A  570 TYR cc_start: 0.7898 (m-10) cc_final: 0.7607 (m-80)
REVERT: A  592 TYR cc_start: 0.8161 (t80) cc_final: 0.7366 (t80)
REVERT: H   22 GLN cc_start: 0.6658 (mp10) cc_final: 0.6446 (mp10)
REVERT: H   49 SER cc_start: 0.8723 (p) cc_final: 0.8478 (p)
REVERT: H   76 ASP cc_start: 0.8813 (t0) cc_final: 0.8291 (t0)
REVERT: H  120 TYR cc_start: 0.7676 (m-80) cc_final: 0.7239 (m-80)
REVERT: L   37 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7516 (tp-100)
REVERT: L   60 PHE cc_start: 0.8135 (m-10) cc_final: 0.7898 (m-10)
REVERT: L   77 ASN cc_start: 0.8980 (t0) cc_final: 0.8701 (t0)
REVERT: L  100 HIS cc_start: 0.7367 (m90) cc_final: 0.6853 (m90)
REVERT: V   18 GLN cc_start: 0.8550 (mm110) cc_final: 0.7971 (mp10)
REVERT: V   20 GLN cc_start: 0.7636 (mm110) cc_final: 0.7131 (mm-40)
REVERT: V   37 CYS cc_start: 0.4095 (p) cc_final: 0.3884 (p)
REVERT: V   38 LYS cc_start: 0.7894 (tttt) cc_final: 0.7380 (ttmt)
REVERT: V   51 TRP cc_start: 0.8354 (m100) cc_final: 0.7783 (m100)
REVERT: V   62 TRP cc_start: 0.9023 (t60) cc_final: 0.8604 (t60)
REVERT: V   67 ASN cc_start: 0.8360 (t0) cc_final: 0.8072 (t0)
REVERT: V   92 THR cc_start: 0.8673 (p) cc_final: 0.8264 (t)
REVERT: V  105 ASP cc_start: 0.8449 (m-30) cc_final: 0.7981 (m-30)
REVERT: V  124 TRP cc_start: 0.8687 (m100) cc_final: 0.8333 (m-10)
REVERT: V  151 ILE cc_start: 0.8448 (mt) cc_final: 0.8034 (mt)
REVERT: V  176 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7978 (mm-40)
REVERT: V  184 TRP cc_start: 0.9048 (m100) cc_final: 0.8443 (m100)
REVERT: V  251 THR cc_start: 0.8135 (m) cc_final: 0.7731 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 340
  average time/residue: 0.0707
  time to fit residues: 34.8297
Evaluate side-chains
  294 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 294
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 84 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
L  26 GLN
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.156820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.133548 restraints weight = 15867.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.138807 restraints weight = 9258.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.142655 restraints weight = 6066.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.145507 restraints weight = 4230.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.147631 restraints weight = 3083.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.7129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8076  Z= 0.156
  Angle     :  0.704  11.307  11000  Z= 0.357
  Chirality :  0.046   0.315   1215
  Planarity :  0.005   0.072   1354
  Dihedral  :  5.875  43.472   1202
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.95 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.72 (0.27), residues: 978
  helix:  0.33 (0.26), residues: 382
  sheet: -0.40 (0.37), residues: 195
  loop : -1.21 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 390 
 TYR   0.018   0.002   TYR A 171 
 PHE   0.018   0.002   PHE A 170 
 TRP   0.030   0.002   TRP A 220 
 HIS   0.003   0.001   HIS V 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8069)
  covalent geometry    : angle       0.69873 (10984)
  SS BOND              : bond        0.00272 (    5)
  SS BOND              : angle       0.90447 (   10)
  hydrogen bonds       : bond        0.04466 (  349)
  hydrogen bonds       : angle       5.10193 (  954)
  link_BETA1-4         : bond        0.01273 (    1)
  link_BETA1-4         : angle       2.58834 (    3)
  link_NAG-ASN         : bond        0.00505 (    1)
  link_NAG-ASN         : angle       4.27439 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 338
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8891 (mptt) cc_final: 0.8303 (tptm)
REVERT: A  111 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8820 (tm-30)
REVERT: A  119 LEU cc_start: 0.8674 (tt) cc_final: 0.8401 (tp)
REVERT: A  121 TYR cc_start: 0.9079 (t80) cc_final: 0.8389 (t80)
REVERT: A  124 MET cc_start: 0.9009 (mmp) cc_final: 0.8594 (mmp)
REVERT: A  147 CYS cc_start: 0.9019 (t) cc_final: 0.8765 (t)
REVERT: A  184 LEU cc_start: 0.9188 (tp) cc_final: 0.8868 (tp)
REVERT: A  189 SER cc_start: 0.9609 (m) cc_final: 0.9393 (p)
REVERT: A  205 ASN cc_start: 0.8895 (t0) cc_final: 0.8322 (t0)
REVERT: A  223 HIS cc_start: 0.8395 (m-70) cc_final: 0.7906 (m170)
REVERT: A  245 LEU cc_start: 0.8657 (mm) cc_final: 0.7938 (mm)
REVERT: A  246 GLN cc_start: 0.7374 (tt0) cc_final: 0.6908 (pm20)
REVERT: A  316 ASN cc_start: 0.8773 (t0) cc_final: 0.8353 (t0)
REVERT: A  333 ILE cc_start: 0.9113 (pt) cc_final: 0.8746 (pt)
REVERT: A  337 LEU cc_start: 0.9428 (mt) cc_final: 0.9149 (mt)
REVERT: A  344 LEU cc_start: 0.8337 (tt) cc_final: 0.8038 (tt)
REVERT: A  345 LEU cc_start: 0.8604 (tt) cc_final: 0.8363 (tt)
REVERT: A  447 ILE cc_start: 0.9608 (mt) cc_final: 0.9369 (mt)
REVERT: A  453 GLU cc_start: 0.8607 (tp30) cc_final: 0.8274 (mm-30)
REVERT: A  460 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7870 (mtpt)
REVERT: A  538 ARG cc_start: 0.7402 (mtm180) cc_final: 0.6785 (ttt-90)
REVERT: A  565 LEU cc_start: 0.7866 (tt) cc_final: 0.7610 (tt)
REVERT: A  570 TYR cc_start: 0.7951 (m-10) cc_final: 0.7687 (m-80)
REVERT: A  592 TYR cc_start: 0.8129 (t80) cc_final: 0.7541 (t80)
REVERT: H   22 GLN cc_start: 0.6559 (mp10) cc_final: 0.6345 (mp10)
REVERT: H   49 SER cc_start: 0.8846 (p) cc_final: 0.8518 (p)
REVERT: H   50 TYR cc_start: 0.7718 (m-80) cc_final: 0.6902 (m-80)
REVERT: H   76 ASP cc_start: 0.8780 (t0) cc_final: 0.8340 (t0)
REVERT: H  109 ASP cc_start: 0.9136 (m-30) cc_final: 0.8630 (m-30)
REVERT: H  120 TYR cc_start: 0.7774 (m-80) cc_final: 0.7283 (m-80)
REVERT: L   37 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7608 (tp40)
REVERT: L   77 ASN cc_start: 0.9035 (t0) cc_final: 0.8724 (t0)
REVERT: L  100 HIS cc_start: 0.7356 (m90) cc_final: 0.6853 (m90)
REVERT: V   18 GLN cc_start: 0.8590 (mm110) cc_final: 0.8244 (mp10)
REVERT: V   37 CYS cc_start: 0.4367 (p) cc_final: 0.4010 (p)
REVERT: V   38 LYS cc_start: 0.7878 (tttt) cc_final: 0.7390 (ttmt)
REVERT: V   43 THR cc_start: 0.7812 (m) cc_final: 0.7242 (m)
REVERT: V   51 TRP cc_start: 0.8424 (m100) cc_final: 0.7989 (m100)
REVERT: V   67 ASN cc_start: 0.8447 (t0) cc_final: 0.8106 (t0)
REVERT: V   92 THR cc_start: 0.8705 (p) cc_final: 0.8310 (t)
REVERT: V  105 ASP cc_start: 0.8402 (m-30) cc_final: 0.7954 (m-30)
REVERT: V  124 TRP cc_start: 0.8704 (m100) cc_final: 0.8353 (m-10)
REVERT: V  176 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7924 (mm-40)
REVERT: V  184 TRP cc_start: 0.9033 (m100) cc_final: 0.8460 (m100)
REVERT: V  251 THR cc_start: 0.8160 (m) cc_final: 0.7764 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 338
  average time/residue: 0.0712
  time to fit residues: 34.5618
Evaluate side-chains
  288 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 288
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 391 ASN
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.153281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.130595 restraints weight = 15826.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.135800 restraints weight = 9134.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.139612 restraints weight = 5931.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142442 restraints weight = 4112.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.144463 restraints weight = 2971.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.7463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8076  Z= 0.186
  Angle     :  0.739  11.426  11000  Z= 0.376
  Chirality :  0.046   0.329   1215
  Planarity :  0.005   0.060   1354
  Dihedral  :  6.062  48.459   1202
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 15.06
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.54 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.81 (0.27), residues: 978
  helix:  0.16 (0.26), residues: 382
  sheet: -0.37 (0.37), residues: 195
  loop : -1.20 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 298 
 TYR   0.022   0.002   TYR A  95 
 PHE   0.022   0.002   PHE H 125 
 TRP   0.026   0.002   TRP A 220 
 HIS   0.004   0.001   HIS V 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 8069)
  covalent geometry    : angle       0.73461 (10984)
  SS BOND              : bond        0.00375 (    5)
  SS BOND              : angle       1.00294 (   10)
  hydrogen bonds       : bond        0.04586 (  349)
  hydrogen bonds       : angle       5.26581 (  954)
  link_BETA1-4         : bond        0.01241 (    1)
  link_BETA1-4         : angle       2.79440 (    3)
  link_NAG-ASN         : bond        0.00447 (    1)
  link_NAG-ASN         : angle       4.02762 (    3)

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 341
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8936 (mptt) cc_final: 0.8325 (tptm)
REVERT: A  108 ILE cc_start: 0.9007 (mt) cc_final: 0.8603 (mt)
REVERT: A  111 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8736 (tm-30)
REVERT: A  121 TYR cc_start: 0.9099 (t80) cc_final: 0.8535 (t80)
REVERT: A  124 MET cc_start: 0.8949 (mmp) cc_final: 0.8583 (mmp)
REVERT: A  184 LEU cc_start: 0.9243 (tp) cc_final: 0.8924 (tp)
REVERT: A  189 SER cc_start: 0.9604 (m) cc_final: 0.9384 (p)
REVERT: A  205 ASN cc_start: 0.8938 (t0) cc_final: 0.8438 (t0)
REVERT: A  222 LEU cc_start: 0.9164 (mm) cc_final: 0.8786 (mm)
REVERT: A  223 HIS cc_start: 0.8395 (m-70) cc_final: 0.7904 (m170)
REVERT: A  245 LEU cc_start: 0.8739 (mm) cc_final: 0.7585 (mm)
REVERT: A  246 GLN cc_start: 0.7441 (tt0) cc_final: 0.7000 (pm20)
REVERT: A  316 ASN cc_start: 0.8850 (t0) cc_final: 0.8429 (t0)
REVERT: A  328 ASP cc_start: 0.8339 (m-30) cc_final: 0.7895 (m-30)
REVERT: A  333 ILE cc_start: 0.9124 (pt) cc_final: 0.8768 (pt)
REVERT: A  337 LEU cc_start: 0.9455 (mt) cc_final: 0.9137 (mt)
REVERT: A  344 LEU cc_start: 0.8343 (tt) cc_final: 0.7953 (tt)
REVERT: A  410 TYR cc_start: 0.8124 (t80) cc_final: 0.7648 (t80)
REVERT: A  447 ILE cc_start: 0.9601 (mt) cc_final: 0.9361 (mt)
REVERT: A  453 GLU cc_start: 0.8723 (tp30) cc_final: 0.8410 (mm-30)
REVERT: A  460 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7728 (mtpt)
REVERT: A  538 ARG cc_start: 0.7421 (mtm180) cc_final: 0.6791 (ttt-90)
REVERT: A  570 TYR cc_start: 0.8055 (m-10) cc_final: 0.7796 (m-80)
REVERT: A  592 TYR cc_start: 0.8182 (t80) cc_final: 0.7817 (t80)
REVERT: H   22 GLN cc_start: 0.6660 (mp10) cc_final: 0.6417 (mp10)
REVERT: H   49 SER cc_start: 0.8941 (p) cc_final: 0.8611 (p)
REVERT: H   50 TYR cc_start: 0.7905 (m-80) cc_final: 0.7162 (m-80)
REVERT: H   76 ASP cc_start: 0.8759 (t0) cc_final: 0.8277 (t0)
REVERT: H   84 LYS cc_start: 0.8538 (mmmm) cc_final: 0.8237 (tppt)
REVERT: H   86 LYS cc_start: 0.8310 (ptpp) cc_final: 0.7302 (mmtt)
REVERT: H  109 ASP cc_start: 0.9136 (m-30) cc_final: 0.8673 (m-30)
REVERT: H  120 TYR cc_start: 0.7817 (m-80) cc_final: 0.7444 (m-80)
REVERT: L   77 ASN cc_start: 0.9054 (t0) cc_final: 0.8764 (t0)
REVERT: L  100 HIS cc_start: 0.7374 (m90) cc_final: 0.6875 (m90)
REVERT: L  114 GLN cc_start: 0.8099 (pm20) cc_final: 0.7878 (pm20)
REVERT: V   18 GLN cc_start: 0.8571 (mm110) cc_final: 0.8231 (mp10)
REVERT: V   38 LYS cc_start: 0.7928 (tttt) cc_final: 0.7405 (ttmt)
REVERT: V   43 THR cc_start: 0.7714 (m) cc_final: 0.7170 (m)
REVERT: V   51 TRP cc_start: 0.8521 (m100) cc_final: 0.8002 (m100)
REVERT: V   67 ASN cc_start: 0.8433 (t0) cc_final: 0.8121 (t0)
REVERT: V  105 ASP cc_start: 0.8383 (m-30) cc_final: 0.7929 (m-30)
REVERT: V  124 TRP cc_start: 0.8699 (m100) cc_final: 0.8259 (m-10)
REVERT: V  151 ILE cc_start: 0.8306 (mm) cc_final: 0.7919 (mm)
REVERT: V  176 GLN cc_start: 0.8221 (mm-40) cc_final: 0.8006 (mm-40)
REVERT: V  184 TRP cc_start: 0.9046 (m100) cc_final: 0.8422 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 341
  average time/residue: 0.0724
  time to fit residues: 35.3014
Evaluate side-chains
  290 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 391 ASN
V  65 ASN
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.159389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.136236 restraints weight = 15839.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.141671 restraints weight = 9177.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.145640 restraints weight = 5944.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.148460 restraints weight = 4096.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.150515 restraints weight = 2956.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.7543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8076  Z= 0.132
  Angle     :  0.706  11.204  11000  Z= 0.352
  Chirality :  0.045   0.327   1215
  Planarity :  0.004   0.060   1354
  Dihedral  :  5.963  52.217   1202
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.13 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.65 (0.27), residues: 978
  helix:  0.39 (0.26), residues: 384
  sheet: -0.46 (0.36), residues: 203
  loop : -1.14 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 390 
 TYR   0.020   0.002   TYR A  95 
 PHE   0.028   0.002   PHE A 311 
 TRP   0.031   0.002   TRP A 220 
 HIS   0.006   0.001   HIS V 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8069)
  covalent geometry    : angle       0.70149 (10984)
  SS BOND              : bond        0.00380 (    5)
  SS BOND              : angle       0.96039 (   10)
  hydrogen bonds       : bond        0.04331 (  349)
  hydrogen bonds       : angle       5.09235 (  954)
  link_BETA1-4         : bond        0.01259 (    1)
  link_BETA1-4         : angle       2.57491 (    3)
  link_NAG-ASN         : bond        0.00524 (    1)
  link_NAG-ASN         : angle       3.77089 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1482.36 seconds
wall clock time: 26 minutes 24.06 seconds (1584.06 seconds total)