Starting phenix.real_space_refine
on Wed Feb 12 19:18:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dzy_8942/02_2025/6dzy_8942_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dzy_8942/02_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_8942/02_2025/6dzy_8942.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dzy_8942/02_2025/6dzy_8942.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dzy_8942/02_2025/6dzy_8942_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dzy_8942/02_2025/6dzy_8942_neut.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.87, per 1000 atoms: 0.62
  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: 2.00
  Conformation dependent library (CDL) restraints added in 855.1 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: 0.98
  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: 2.34

  Time building geometry restraints manager: 2.21 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:             1.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.560
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.640
-------------------------------------------------------------------------------
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   0.119   8069  Z= 0.400
  Angle     :  0.878  26.534  10984  Z= 0.529
  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 : 9.20
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (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
 TRP   0.009   0.001   TRP H  52 
 HIS   0.006   0.001   HIS A 235 
 PHE   0.014   0.002   PHE A 213 
 TYR   0.017   0.001   TYR A 176 
 ARG   0.003   0.001   ARG V 245 

*********************** 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  : 0.770 
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: 0.2031
  time to fit residues: 128.5393
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  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0010
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0980
   chunk 88 optimal weight:   10.0000
   overall best weight:    1.2192

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.175742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.151812 restraints weight = 14666.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.157617 restraints weight = 8451.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.161853 restraints weight = 5404.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6434
moved from start:          0.3659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8069  Z= 0.245
  Angle     :  0.721   9.706  10984  Z= 0.370
  Chirality :  0.049   0.289   1215
  Planarity :  0.006   0.109   1354
  Dihedral  :  9.432  68.459   1202
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.91 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.29 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.25), residues: 978
  helix: -0.59 (0.24), residues: 377
  sheet: -1.03 (0.37), residues: 160
  loop : -1.38 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP V  62 
 HIS   0.005   0.001   HIS A 143 
 PHE   0.026   0.002   PHE V 220 
 TYR   0.029   0.002   TYR A 176 
 ARG   0.004   0.001   ARG V 117 

*********************** 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  : 0.801 
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: A   81 THR cc_start: 0.8898 (p) cc_final: 0.8596 (t)
REVERT: A   82 TRP cc_start: 0.5481 (m-10) cc_final: 0.5240 (m-10)
REVERT: A   84 LYS cc_start: 0.8397 (mptt) cc_final: 0.7876 (tptp)
REVERT: A  121 TYR cc_start: 0.9144 (t80) cc_final: 0.8703 (t80)
REVERT: A  171 TYR cc_start: 0.8776 (m-80) cc_final: 0.8554 (m-80)
REVERT: A  189 SER cc_start: 0.9593 (m) cc_final: 0.9355 (p)
REVERT: A  195 LEU cc_start: 0.8652 (mt) cc_final: 0.8062 (mt)
REVERT: A  197 TRP cc_start: 0.8548 (m-10) cc_final: 0.8083 (m-10)
REVERT: A  298 ARG cc_start: 0.8082 (tpm170) cc_final: 0.7701 (tpp-160)
REVERT: A  316 ASN cc_start: 0.7592 (t0) cc_final: 0.7270 (t0)
REVERT: A  370 MET cc_start: 0.7232 (mtm) cc_final: 0.6997 (mmm)
REVERT: A  385 TYR cc_start: 0.7355 (t80) cc_final: 0.6998 (t80)
REVERT: A  390 ARG cc_start: 0.8370 (mtt180) cc_final: 0.8085 (mtt180)
REVERT: A  393 ASP cc_start: 0.8668 (t70) cc_final: 0.8467 (t70)
REVERT: A  417 MET cc_start: 0.8182 (mtm) cc_final: 0.7609 (mtm)
REVERT: A  453 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8508 (mm-30)
REVERT: A  460 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7523 (ttpt)
REVERT: A  512 VAL cc_start: 0.8923 (p) cc_final: 0.8716 (p)
REVERT: A  538 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7237 (ttt-90)
REVERT: A  567 GLN cc_start: 0.9081 (pm20) cc_final: 0.8856 (pm20)
REVERT: A  581 ILE cc_start: 0.8488 (mt) cc_final: 0.8287 (mt)
REVERT: A  592 TYR cc_start: 0.8315 (t80) cc_final: 0.7362 (t80)
REVERT: A  593 ILE cc_start: 0.8609 (mt) cc_final: 0.8347 (mt)
REVERT: H   22 GLN cc_start: 0.6557 (mp10) cc_final: 0.6346 (mp10)
REVERT: H   76 ASP cc_start: 0.8574 (t0) cc_final: 0.8157 (t0)
REVERT: H  120 TYR cc_start: 0.7265 (m-80) cc_final: 0.6573 (m-80)
REVERT: L  114 GLN cc_start: 0.8006 (pm20) cc_final: 0.7446 (pm20)
REVERT: V   21 GLN cc_start: 0.6304 (mt0) cc_final: 0.5659 (mt0)
REVERT: V   37 CYS cc_start: 0.4323 (p) cc_final: 0.3693 (p)
REVERT: V   51 TRP cc_start: 0.8232 (m100) cc_final: 0.7796 (m100)
REVERT: V   56 HIS cc_start: 0.6465 (t70) cc_final: 0.6060 (p-80)
REVERT: V   62 TRP cc_start: 0.8732 (t60) cc_final: 0.8411 (t60)
REVERT: V   92 THR cc_start: 0.8697 (p) cc_final: 0.8208 (t)
REVERT: V   93 THR cc_start: 0.8274 (m) cc_final: 0.7915 (p)
REVERT: V  105 ASP cc_start: 0.8832 (m-30) cc_final: 0.8494 (m-30)
REVERT: V  176 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7489 (mm-40)
REVERT: V  184 TRP cc_start: 0.9139 (m100) cc_final: 0.8539 (m100)
REVERT: V  246 THR cc_start: 0.8131 (p) cc_final: 0.7713 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 400
  average time/residue: 0.1716
  time to fit residues: 94.9432
Evaluate side-chains
  328 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 13 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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**
H  58 GLN
V  69 ASN
V 186 GLN
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.174337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.150195 restraints weight = 16131.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.155953 restraints weight = 9644.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.160094 restraints weight = 6289.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8069  Z= 0.206
  Angle     :  0.659  11.470  10984  Z= 0.336
  Chirality :  0.045   0.347   1215
  Planarity :  0.005   0.088   1354
  Dihedral  :  6.737  46.134   1202
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.60 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.56 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.26), residues: 978
  helix: -0.00 (0.25), residues: 380
  sheet: -0.94 (0.36), residues: 175
  loop : -1.26 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H  55 
 HIS   0.005   0.001   HIS A 240 
 PHE   0.041   0.002   PHE A 440 
 TYR   0.020   0.002   TYR A 570 
 ARG   0.003   0.000   ARG H  38 

*********************** 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
  391 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 390
  time to evaluate  : 0.842 
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   80 GLU cc_start: 0.8589 (tp30) cc_final: 0.8365 (tm-30)
REVERT: A   81 THR cc_start: 0.8987 (p) cc_final: 0.8612 (t)
REVERT: A   82 TRP cc_start: 0.5711 (m-10) cc_final: 0.5288 (m-10)
REVERT: A   84 LYS cc_start: 0.8445 (mptt) cc_final: 0.7857 (tptm)
REVERT: A  121 TYR cc_start: 0.9155 (t80) cc_final: 0.8696 (t80)
REVERT: A  124 MET cc_start: 0.8925 (mmp) cc_final: 0.8724 (mmp)
REVERT: A  142 TYR cc_start: 0.8606 (t80) cc_final: 0.8345 (t80)
REVERT: A  184 LEU cc_start: 0.9069 (tp) cc_final: 0.8729 (tp)
REVERT: A  189 SER cc_start: 0.9611 (m) cc_final: 0.9356 (p)
REVERT: A  195 LEU cc_start: 0.8735 (mt) cc_final: 0.7916 (mt)
REVERT: A  197 TRP cc_start: 0.8749 (m-10) cc_final: 0.8066 (m-10)
REVERT: A  284 THR cc_start: 0.8852 (p) cc_final: 0.8641 (p)
REVERT: A  298 ARG cc_start: 0.7937 (tpm170) cc_final: 0.7223 (tpp-160)
REVERT: A  316 ASN cc_start: 0.7925 (t0) cc_final: 0.7558 (t0)
REVERT: A  333 ILE cc_start: 0.9211 (pt) cc_final: 0.8933 (pt)
REVERT: A  370 MET cc_start: 0.6892 (mtm) cc_final: 0.6650 (mmm)
REVERT: A  385 TYR cc_start: 0.7476 (t80) cc_final: 0.7126 (t80)
REVERT: A  410 TYR cc_start: 0.7729 (t80) cc_final: 0.7410 (t80)
REVERT: A  453 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8621 (mm-30)
REVERT: A  460 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7431 (ttpt)
REVERT: A  512 VAL cc_start: 0.8944 (p) cc_final: 0.8713 (p)
REVERT: A  538 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7102 (ttt-90)
REVERT: A  567 GLN cc_start: 0.9140 (pm20) cc_final: 0.8892 (pm20)
REVERT: A  570 TYR cc_start: 0.7300 (m-10) cc_final: 0.6855 (m-80)
REVERT: A  576 ILE cc_start: 0.8086 (tp) cc_final: 0.7837 (tp)
REVERT: H   22 GLN cc_start: 0.6732 (mp10) cc_final: 0.6471 (mp10)
REVERT: H   76 ASP cc_start: 0.8474 (t0) cc_final: 0.8008 (t0)
REVERT: H   93 LYS cc_start: 0.5583 (pttt) cc_final: 0.5286 (ptpp)
REVERT: H  120 TYR cc_start: 0.7447 (m-80) cc_final: 0.6392 (m-80)
REVERT: H  128 ASP cc_start: 0.8282 (t70) cc_final: 0.7860 (t70)
REVERT: L   60 PHE cc_start: 0.8143 (m-10) cc_final: 0.7893 (m-10)
REVERT: L  100 HIS cc_start: 0.6883 (m90) cc_final: 0.6415 (m90)
REVERT: L  121 THR cc_start: 0.6875 (p) cc_final: 0.5974 (t)
REVERT: V   18 GLN cc_start: 0.8544 (mm110) cc_final: 0.7965 (mp10)
REVERT: V   21 GLN cc_start: 0.6443 (mt0) cc_final: 0.5842 (mt0)
REVERT: V   37 CYS cc_start: 0.4748 (p) cc_final: 0.3749 (p)
REVERT: V   51 TRP cc_start: 0.8301 (m100) cc_final: 0.7985 (m100)
REVERT: V   62 TRP cc_start: 0.8879 (t60) cc_final: 0.8414 (t60)
REVERT: V   76 ASN cc_start: 0.8082 (t0) cc_final: 0.7307 (p0)
REVERT: V   92 THR cc_start: 0.8687 (p) cc_final: 0.8250 (t)
REVERT: V   93 THR cc_start: 0.8195 (m) cc_final: 0.7778 (p)
REVERT: V  105 ASP cc_start: 0.8805 (m-30) cc_final: 0.8455 (m-30)
REVERT: V  120 TYR cc_start: 0.6115 (p90) cc_final: 0.5847 (p90)
REVERT: V  173 LYS cc_start: 0.7635 (mmtm) cc_final: 0.7111 (tppt)
REVERT: V  176 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7523 (mm-40)
REVERT: V  184 TRP cc_start: 0.9245 (m100) cc_final: 0.8540 (m100)
REVERT: V  202 TYR cc_start: 0.7413 (m-80) cc_final: 0.7181 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 391
  average time/residue: 0.1813
  time to fit residues: 97.4994
Evaluate side-chains
  339 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 339
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 14 optimal weight:    9.9990
   chunk 32 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 18 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 391 ASN
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 187 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.170361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.146886 restraints weight = 15295.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.152364 restraints weight = 8852.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.156469 restraints weight = 5749.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6546
moved from start:          0.4963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8069  Z= 0.179
  Angle     :  0.629  11.171  10984  Z= 0.321
  Chirality :  0.044   0.342   1215
  Planarity :  0.005   0.070   1354
  Dihedral  :  6.150  44.074   1202
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.60 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.26), residues: 978
  helix:  0.24 (0.26), residues: 383
  sheet: -0.72 (0.37), residues: 176
  loop : -1.26 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP V 124 
 HIS   0.005   0.001   HIS A 240 
 PHE   0.042   0.002   PHE A 440 
 TYR   0.018   0.001   TYR A 495 
 ARG   0.005   0.000   ARG H  59 

*********************** 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
  375 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 375
  time to evaluate  : 0.863 
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   80 GLU cc_start: 0.8572 (tp30) cc_final: 0.8243 (tm-30)
REVERT: A   81 THR cc_start: 0.9061 (p) cc_final: 0.8681 (t)
REVERT: A   84 LYS cc_start: 0.8499 (mptt) cc_final: 0.7929 (tptm)
REVERT: A  121 TYR cc_start: 0.9134 (t80) cc_final: 0.8725 (t80)
REVERT: A  124 MET cc_start: 0.8933 (mmp) cc_final: 0.8677 (mmp)
REVERT: A  142 TYR cc_start: 0.8645 (t80) cc_final: 0.8262 (t80)
REVERT: A  184 LEU cc_start: 0.9124 (tp) cc_final: 0.8754 (tp)
REVERT: A  189 SER cc_start: 0.9562 (m) cc_final: 0.9285 (p)
REVERT: A  195 LEU cc_start: 0.8754 (mt) cc_final: 0.8083 (mt)
REVERT: A  197 TRP cc_start: 0.8863 (m-10) cc_final: 0.8120 (m-10)
REVERT: A  229 GLU cc_start: 0.8522 (tt0) cc_final: 0.8291 (tt0)
REVERT: A  266 ILE cc_start: 0.9263 (mt) cc_final: 0.8997 (tp)
REVERT: A  316 ASN cc_start: 0.7867 (t0) cc_final: 0.7511 (t0)
REVERT: A  333 ILE cc_start: 0.9197 (pt) cc_final: 0.8889 (pt)
REVERT: A  337 LEU cc_start: 0.9449 (mt) cc_final: 0.9248 (mt)
REVERT: A  370 MET cc_start: 0.6652 (mtm) cc_final: 0.6405 (mmm)
REVERT: A  385 TYR cc_start: 0.7523 (t80) cc_final: 0.7283 (t80)
REVERT: A  390 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8045 (mtt180)
REVERT: A  410 TYR cc_start: 0.7939 (t80) cc_final: 0.7512 (t80)
REVERT: A  431 LEU cc_start: 0.8998 (tp) cc_final: 0.8735 (tp)
REVERT: A  447 ILE cc_start: 0.9619 (mt) cc_final: 0.9411 (mt)
REVERT: A  453 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: A  460 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7421 (ttpt)
REVERT: A  538 ARG cc_start: 0.7765 (mtm180) cc_final: 0.7036 (ttt-90)
REVERT: A  567 GLN cc_start: 0.9101 (pm20) cc_final: 0.8848 (pm20)
REVERT: A  570 TYR cc_start: 0.7366 (m-10) cc_final: 0.7077 (m-80)
REVERT: H   22 GLN cc_start: 0.6715 (mp10) cc_final: 0.6437 (mp10)
REVERT: H   76 ASP cc_start: 0.8512 (t0) cc_final: 0.8012 (t0)
REVERT: H   93 LYS cc_start: 0.5658 (pttt) cc_final: 0.5424 (ptpp)
REVERT: H  120 TYR cc_start: 0.7737 (m-80) cc_final: 0.6509 (m-80)
REVERT: H  128 ASP cc_start: 0.8420 (t70) cc_final: 0.7780 (t70)
REVERT: L   62 GLN cc_start: 0.5977 (tp40) cc_final: 0.5277 (tp40)
REVERT: L   66 GLN cc_start: 0.8012 (mm110) cc_final: 0.7687 (mm-40)
REVERT: L  100 HIS cc_start: 0.7056 (m90) cc_final: 0.6537 (m90)
REVERT: L  114 GLN cc_start: 0.7777 (pm20) cc_final: 0.7498 (pm20)
REVERT: L  121 THR cc_start: 0.7050 (p) cc_final: 0.6638 (t)
REVERT: V   18 GLN cc_start: 0.8563 (mm110) cc_final: 0.8017 (mp10)
REVERT: V   20 GLN cc_start: 0.7318 (mm110) cc_final: 0.7072 (mm-40)
REVERT: V   37 CYS cc_start: 0.4534 (p) cc_final: 0.3737 (p)
REVERT: V   62 TRP cc_start: 0.8869 (t60) cc_final: 0.8466 (t60)
REVERT: V   63 ILE cc_start: 0.9412 (mt) cc_final: 0.9183 (mt)
REVERT: V   66 ILE cc_start: 0.7746 (tt) cc_final: 0.7334 (tt)
REVERT: V   76 ASN cc_start: 0.8127 (t0) cc_final: 0.7374 (p0)
REVERT: V   92 THR cc_start: 0.8678 (p) cc_final: 0.8230 (t)
REVERT: V  105 ASP cc_start: 0.8729 (m-30) cc_final: 0.8390 (m-30)
REVERT: V  173 LYS cc_start: 0.7621 (mmtm) cc_final: 0.7108 (tppt)
REVERT: V  176 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7537 (mm-40)
REVERT: V  184 TRP cc_start: 0.9218 (m100) cc_final: 0.8605 (m100)
REVERT: V  195 LEU cc_start: 0.9376 (tp) cc_final: 0.9134 (tp)
REVERT: V  202 TYR cc_start: 0.7544 (m-80) cc_final: 0.7322 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 375
  average time/residue: 0.1786
  time to fit residues: 93.2864
Evaluate side-chains
  330 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 330
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 69 optimal weight:    0.8980
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
H  24 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.161084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.137568 restraints weight = 16470.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.142700 restraints weight = 9973.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.146427 restraints weight = 6648.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.5752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8069  Z= 0.281
  Angle     :  0.725  12.468  10984  Z= 0.378
  Chirality :  0.046   0.379   1215
  Planarity :  0.005   0.068   1354
  Dihedral  :  5.888  41.596   1202
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.73 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.26), residues: 978
  helix:  0.13 (0.25), residues: 384
  sheet: -0.53 (0.37), residues: 186
  loop : -1.23 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP V  51 
 HIS   0.005   0.002   HIS A 240 
 PHE   0.034   0.002   PHE A 440 
 TYR   0.028   0.003   TYR A 171 
 ARG   0.008   0.001   ARG A 234 

*********************** 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
  369 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 369
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 THR cc_start: 0.9062 (p) cc_final: 0.8838 (t)
REVERT: A   84 LYS cc_start: 0.8682 (mptt) cc_final: 0.7975 (tptm)
REVERT: A  121 TYR cc_start: 0.9217 (t80) cc_final: 0.8588 (t80)
REVERT: A  124 MET cc_start: 0.8905 (mmp) cc_final: 0.8630 (mmp)
REVERT: A  145 ASN cc_start: 0.7811 (m-40) cc_final: 0.7601 (m-40)
REVERT: A  171 TYR cc_start: 0.9004 (m-80) cc_final: 0.8736 (m-80)
REVERT: A  184 LEU cc_start: 0.9289 (tp) cc_final: 0.8913 (tp)
REVERT: A  189 SER cc_start: 0.9584 (m) cc_final: 0.9354 (p)
REVERT: A  193 ASP cc_start: 0.8250 (p0) cc_final: 0.7776 (m-30)
REVERT: A  195 LEU cc_start: 0.8913 (mt) cc_final: 0.8503 (mt)
REVERT: A  197 TRP cc_start: 0.9232 (m-10) cc_final: 0.8687 (m-10)
REVERT: A  222 LEU cc_start: 0.9139 (mm) cc_final: 0.8756 (mm)
REVERT: A  225 THR cc_start: 0.7500 (p) cc_final: 0.7217 (p)
REVERT: A  245 LEU cc_start: 0.8640 (mm) cc_final: 0.8067 (mm)
REVERT: A  316 ASN cc_start: 0.8255 (t0) cc_final: 0.7748 (t0)
REVERT: A  333 ILE cc_start: 0.9233 (pt) cc_final: 0.8905 (pt)
REVERT: A  337 LEU cc_start: 0.9466 (mt) cc_final: 0.9214 (mt)
REVERT: A  370 MET cc_start: 0.6961 (mtm) cc_final: 0.6721 (mmm)
REVERT: A  390 ARG cc_start: 0.8536 (mtt180) cc_final: 0.7800 (mtt180)
REVERT: A  393 ASP cc_start: 0.8664 (t70) cc_final: 0.7747 (t70)
REVERT: A  422 PHE cc_start: 0.8000 (t80) cc_final: 0.7722 (t80)
REVERT: A  426 ILE cc_start: 0.9166 (mt) cc_final: 0.8835 (mt)
REVERT: A  447 ILE cc_start: 0.9605 (mt) cc_final: 0.9377 (mt)
REVERT: A  453 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8738 (mm-30)
REVERT: A  460 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7693 (mtpt)
REVERT: A  538 ARG cc_start: 0.7607 (mtm180) cc_final: 0.7085 (ttt-90)
REVERT: A  567 GLN cc_start: 0.9163 (pm20) cc_final: 0.8857 (pm20)
REVERT: A  570 TYR cc_start: 0.7794 (m-10) cc_final: 0.6849 (m-80)
REVERT: A  592 TYR cc_start: 0.8166 (t80) cc_final: 0.7137 (t80)
REVERT: H   22 GLN cc_start: 0.6752 (mp10) cc_final: 0.6448 (mp10)
REVERT: H   49 SER cc_start: 0.8431 (p) cc_final: 0.8193 (p)
REVERT: H  120 TYR cc_start: 0.7727 (m-80) cc_final: 0.6531 (m-80)
REVERT: L   57 LEU cc_start: 0.8555 (mt) cc_final: 0.8318 (mt)
REVERT: L   60 PHE cc_start: 0.8444 (m-10) cc_final: 0.8228 (m-10)
REVERT: L   95 PHE cc_start: 0.7769 (m-10) cc_final: 0.7289 (m-10)
REVERT: L  100 HIS cc_start: 0.7227 (m90) cc_final: 0.6717 (m90)
REVERT: L  121 THR cc_start: 0.7752 (p) cc_final: 0.7239 (t)
REVERT: V   18 GLN cc_start: 0.8509 (mm110) cc_final: 0.7926 (mp10)
REVERT: V   20 GLN cc_start: 0.7359 (mm110) cc_final: 0.7045 (mm-40)
REVERT: V   38 LYS cc_start: 0.7885 (tttt) cc_final: 0.7371 (ttmt)
REVERT: V   51 TRP cc_start: 0.8549 (m100) cc_final: 0.8168 (m100)
REVERT: V   62 TRP cc_start: 0.8916 (t60) cc_final: 0.8352 (t60)
REVERT: V   63 ILE cc_start: 0.9350 (mt) cc_final: 0.9088 (mt)
REVERT: V   67 ASN cc_start: 0.7875 (t0) cc_final: 0.7572 (t0)
REVERT: V   76 ASN cc_start: 0.8208 (t0) cc_final: 0.7626 (p0)
REVERT: V   79 PHE cc_start: 0.7150 (m-10) cc_final: 0.6193 (m-10)
REVERT: V   92 THR cc_start: 0.8634 (p) cc_final: 0.8217 (t)
REVERT: V  105 ASP cc_start: 0.8757 (m-30) cc_final: 0.8332 (m-30)
REVERT: V  151 ILE cc_start: 0.8084 (mt) cc_final: 0.7775 (mt)
REVERT: V  176 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7614 (mm-40)
REVERT: V  184 TRP cc_start: 0.9261 (m100) cc_final: 0.8656 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 369
  average time/residue: 0.1618
  time to fit residues: 83.5069
Evaluate side-chains
  310 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0010
   chunk 86 optimal weight:    0.1980
   chunk 81 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    1.4392

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

Flipped N/Q/H residues before XYZ refinement:
** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 391 ASN
** L  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  78 GLN
V  65 ASN
** 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 = 0.4069 r_free = 0.4069 target = 0.163728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.140566 restraints weight = 15248.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.145901 restraints weight = 8843.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.149789 restraints weight = 5740.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.6007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8069  Z= 0.202
  Angle     :  0.673  12.437  10984  Z= 0.341
  Chirality :  0.044   0.338   1215
  Planarity :  0.005   0.081   1354
  Dihedral  :  5.657  41.683   1202
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.01 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.27), residues: 978
  helix:  0.52 (0.26), residues: 384
  sheet: -0.29 (0.38), residues: 181
  loop : -1.21 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 220 
 HIS   0.006   0.001   HIS A 240 
 PHE   0.033   0.002   PHE A 440 
 TYR   0.016   0.002   TYR A 592 
 ARG   0.011   0.001   ARG H  59 

*********************** 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
  372 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 372
  time to evaluate  : 0.828 
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: 0.8697 (mptt) cc_final: 0.8055 (tptm)
REVERT: A  108 ILE cc_start: 0.8999 (mt) cc_final: 0.8532 (mt)
REVERT: A  111 GLN cc_start: 0.9167 (tt0) cc_final: 0.8755 (tm-30)
REVERT: A  121 TYR cc_start: 0.9100 (t80) cc_final: 0.8556 (t80)
REVERT: A  124 MET cc_start: 0.8970 (mmp) cc_final: 0.8672 (mmp)
REVERT: A  184 LEU cc_start: 0.9243 (tp) cc_final: 0.8891 (tp)
REVERT: A  189 SER cc_start: 0.9587 (m) cc_final: 0.9339 (p)
REVERT: A  193 ASP cc_start: 0.8336 (p0) cc_final: 0.7869 (m-30)
REVERT: A  195 LEU cc_start: 0.8853 (mt) cc_final: 0.8579 (mt)
REVERT: A  197 TRP cc_start: 0.9188 (m-10) cc_final: 0.8640 (m-10)
REVERT: A  245 LEU cc_start: 0.8838 (mm) cc_final: 0.8021 (mm)
REVERT: A  246 GLN cc_start: 0.7177 (tt0) cc_final: 0.6732 (pm20)
REVERT: A  266 ILE cc_start: 0.9237 (mt) cc_final: 0.8975 (tp)
REVERT: A  316 ASN cc_start: 0.8337 (t0) cc_final: 0.7817 (t0)
REVERT: A  333 ILE cc_start: 0.9191 (pt) cc_final: 0.8846 (pt)
REVERT: A  337 LEU cc_start: 0.9474 (mt) cc_final: 0.9254 (mt)
REVERT: A  370 MET cc_start: 0.6677 (mtm) cc_final: 0.6448 (mmm)
REVERT: A  410 TYR cc_start: 0.8161 (t80) cc_final: 0.7844 (t80)
REVERT: A  447 ILE cc_start: 0.9600 (mt) cc_final: 0.9385 (mt)
REVERT: A  453 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8705 (mm-30)
REVERT: A  460 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7682 (mtpt)
REVERT: A  538 ARG cc_start: 0.7512 (mtm180) cc_final: 0.6941 (ttt-90)
REVERT: A  570 TYR cc_start: 0.7725 (m-10) cc_final: 0.6889 (m-80)
REVERT: A  592 TYR cc_start: 0.8181 (t80) cc_final: 0.7166 (t80)
REVERT: H   22 GLN cc_start: 0.6470 (mp10) cc_final: 0.6175 (mp10)
REVERT: H   49 SER cc_start: 0.8395 (p) cc_final: 0.8130 (p)
REVERT: H   76 ASP cc_start: 0.8632 (t0) cc_final: 0.8316 (t0)
REVERT: H  120 TYR cc_start: 0.7960 (m-80) cc_final: 0.7459 (m-80)
REVERT: L   60 PHE cc_start: 0.8293 (m-10) cc_final: 0.8061 (m-10)
REVERT: L   77 ASN cc_start: 0.8821 (t0) cc_final: 0.8574 (t0)
REVERT: L  100 HIS cc_start: 0.7234 (m90) cc_final: 0.6701 (m90)
REVERT: V   18 GLN cc_start: 0.8538 (mm110) cc_final: 0.7979 (mp10)
REVERT: V   20 GLN cc_start: 0.7424 (mm110) cc_final: 0.7026 (mm-40)
REVERT: V   38 LYS cc_start: 0.7808 (tttt) cc_final: 0.7276 (mttt)
REVERT: V   51 TRP cc_start: 0.8440 (m100) cc_final: 0.8186 (m100)
REVERT: V   62 TRP cc_start: 0.8994 (t60) cc_final: 0.8461 (t60)
REVERT: V   67 ASN cc_start: 0.8068 (t0) cc_final: 0.7712 (t0)
REVERT: V   79 PHE cc_start: 0.6994 (m-10) cc_final: 0.6734 (m-10)
REVERT: V   92 THR cc_start: 0.8653 (p) cc_final: 0.8253 (t)
REVERT: V  105 ASP cc_start: 0.8580 (m-30) cc_final: 0.8190 (m-30)
REVERT: V  151 ILE cc_start: 0.8408 (mt) cc_final: 0.8141 (mt)
REVERT: V  173 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7567 (tppt)
REVERT: V  176 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7620 (mm-40)
REVERT: V  184 TRP cc_start: 0.9131 (m100) cc_final: 0.8458 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 372
  average time/residue: 0.1666
  time to fit residues: 87.2009
Evaluate side-chains
  316 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    2.5384

-------------------------------------------------------------------------------
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
** L  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3977 r_free = 0.3977 target = 0.157020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.133698 restraints weight = 16334.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.138838 restraints weight = 9720.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142601 restraints weight = 6453.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.6509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8069  Z= 0.258
  Angle     :  0.716  12.204  10984  Z= 0.366
  Chirality :  0.046   0.366   1215
  Planarity :  0.005   0.079   1354
  Dihedral  :  5.722  40.971   1202
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.85 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.27), residues: 978
  helix:  0.35 (0.26), residues: 380
  sheet: -0.32 (0.37), residues: 184
  loop : -1.17 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 220 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.025   0.002   PHE A 170 
 TYR   0.022   0.002   TYR V 204 
 ARG   0.005   0.001   ARG A 390 

*********************** 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
  357 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 357
  time to evaluate  : 0.891 
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   82 TRP cc_start: 0.6752 (m-10) cc_final: 0.6535 (m-10)
REVERT: A   84 LYS cc_start: 0.8812 (mptt) cc_final: 0.8267 (tptm)
REVERT: A  121 TYR cc_start: 0.9084 (t80) cc_final: 0.8403 (t80)
REVERT: A  124 MET cc_start: 0.8932 (mmp) cc_final: 0.8577 (mmp)
REVERT: A  147 CYS cc_start: 0.9002 (t) cc_final: 0.8770 (t)
REVERT: A  184 LEU cc_start: 0.9282 (tp) cc_final: 0.8932 (tp)
REVERT: A  189 SER cc_start: 0.9589 (m) cc_final: 0.9342 (p)
REVERT: A  193 ASP cc_start: 0.8369 (p0) cc_final: 0.8114 (m-30)
REVERT: A  197 TRP cc_start: 0.9245 (m-10) cc_final: 0.8921 (m-10)
REVERT: A  222 LEU cc_start: 0.9125 (mm) cc_final: 0.8773 (mm)
REVERT: A  238 GLN cc_start: 0.8813 (mp10) cc_final: 0.8427 (mp10)
REVERT: A  245 LEU cc_start: 0.8885 (mm) cc_final: 0.8180 (mm)
REVERT: A  246 GLN cc_start: 0.7412 (tt0) cc_final: 0.6908 (pm20)
REVERT: A  266 ILE cc_start: 0.9246 (mt) cc_final: 0.8979 (tp)
REVERT: A  310 LEU cc_start: 0.8048 (tt) cc_final: 0.7715 (mt)
REVERT: A  316 ASN cc_start: 0.8671 (t0) cc_final: 0.8069 (t0)
REVERT: A  333 ILE cc_start: 0.9180 (pt) cc_final: 0.8811 (pt)
REVERT: A  337 LEU cc_start: 0.9470 (mt) cc_final: 0.9203 (mt)
REVERT: A  344 LEU cc_start: 0.8324 (tt) cc_final: 0.8084 (tt)
REVERT: A  370 MET cc_start: 0.6691 (mtm) cc_final: 0.6473 (mmm)
REVERT: A  410 TYR cc_start: 0.8200 (t80) cc_final: 0.7842 (t80)
REVERT: A  447 ILE cc_start: 0.9608 (mt) cc_final: 0.9382 (mt)
REVERT: A  453 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8662 (mm-30)
REVERT: A  460 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7803 (mtpt)
REVERT: A  538 ARG cc_start: 0.7624 (mtm180) cc_final: 0.6980 (ttt-90)
REVERT: A  570 TYR cc_start: 0.8076 (m-10) cc_final: 0.7445 (m-80)
REVERT: A  592 TYR cc_start: 0.8213 (t80) cc_final: 0.7373 (t80)
REVERT: H   49 SER cc_start: 0.8723 (p) cc_final: 0.8522 (p)
REVERT: H   50 TYR cc_start: 0.8213 (m-80) cc_final: 0.7858 (m-80)
REVERT: H   76 ASP cc_start: 0.8555 (t0) cc_final: 0.8247 (t0)
REVERT: H  120 TYR cc_start: 0.7906 (m-80) cc_final: 0.7308 (m-80)
REVERT: L   37 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7343 (tp-100)
REVERT: L   60 PHE cc_start: 0.8195 (m-10) cc_final: 0.7642 (m-10)
REVERT: L   77 ASN cc_start: 0.8851 (t0) cc_final: 0.8588 (t0)
REVERT: L   78 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7418 (tp-100)
REVERT: L  100 HIS cc_start: 0.7381 (m90) cc_final: 0.6860 (m90)
REVERT: L  114 GLN cc_start: 0.7422 (pm20) cc_final: 0.6860 (pm20)
REVERT: V   18 GLN cc_start: 0.8539 (mm110) cc_final: 0.7952 (mp10)
REVERT: V   20 GLN cc_start: 0.7486 (mm110) cc_final: 0.7029 (mm-40)
REVERT: V   38 LYS cc_start: 0.7854 (tttt) cc_final: 0.7303 (mttt)
REVERT: V   43 THR cc_start: 0.7898 (m) cc_final: 0.7481 (p)
REVERT: V   51 TRP cc_start: 0.8682 (m100) cc_final: 0.8104 (m100)
REVERT: V   62 TRP cc_start: 0.9081 (t60) cc_final: 0.8365 (t60)
REVERT: V   67 ASN cc_start: 0.8100 (t0) cc_final: 0.7779 (t0)
REVERT: V   79 PHE cc_start: 0.7287 (m-10) cc_final: 0.6874 (m-10)
REVERT: V   92 THR cc_start: 0.8629 (p) cc_final: 0.8228 (t)
REVERT: V  105 ASP cc_start: 0.8448 (m-30) cc_final: 0.8028 (m-30)
REVERT: V  151 ILE cc_start: 0.8436 (mt) cc_final: 0.8123 (mt)
REVERT: V  176 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7652 (mm-40)
REVERT: V  184 TRP cc_start: 0.9097 (m100) cc_final: 0.8486 (m100)
REVERT: V  239 GLN cc_start: 0.7439 (tm-30) cc_final: 0.7026 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 357
  average time/residue: 0.1697
  time to fit residues: 84.2760
Evaluate side-chains
  295 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 295
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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
** L  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V  65 ASN
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 = 0.4001 r_free = 0.4001 target = 0.158323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135079 restraints weight = 15946.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.140456 restraints weight = 9273.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.144371 restraints weight = 6024.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.6786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8069  Z= 0.225
  Angle     :  0.705  11.972  10984  Z= 0.355
  Chirality :  0.045   0.338   1215
  Planarity :  0.005   0.065   1354
  Dihedral  :  5.731  40.483   1202
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.62 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.27), residues: 978
  helix:  0.42 (0.26), residues: 384
  sheet: -0.41 (0.37), residues: 180
  loop : -1.09 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 220 
 HIS   0.006   0.002   HIS A 223 
 PHE   0.024   0.002   PHE A 440 
 TYR   0.024   0.002   TYR A  95 
 ARG   0.003   0.001   ARG A 234 

*********************** 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
  357 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 357
  time to evaluate  : 0.800 
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: 0.8836 (mptt) cc_final: 0.8310 (tptm)
REVERT: A  111 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8677 (tm-30)
REVERT: A  121 TYR cc_start: 0.9100 (t80) cc_final: 0.8380 (t80)
REVERT: A  124 MET cc_start: 0.8966 (mmp) cc_final: 0.8587 (mmp)
REVERT: A  184 LEU cc_start: 0.9265 (tp) cc_final: 0.8923 (tp)
REVERT: A  189 SER cc_start: 0.9580 (m) cc_final: 0.9322 (p)
REVERT: A  195 LEU cc_start: 0.8972 (mt) cc_final: 0.8450 (mt)
REVERT: A  197 TRP cc_start: 0.9163 (m-10) cc_final: 0.8727 (m-10)
REVERT: A  229 GLU cc_start: 0.8707 (tt0) cc_final: 0.8172 (pt0)
REVERT: A  238 GLN cc_start: 0.8770 (mp10) cc_final: 0.8346 (mp10)
REVERT: A  245 LEU cc_start: 0.8865 (mm) cc_final: 0.8297 (mm)
REVERT: A  246 GLN cc_start: 0.7435 (tt0) cc_final: 0.6926 (pm20)
REVERT: A  316 ASN cc_start: 0.8699 (t0) cc_final: 0.8303 (t0)
REVERT: A  333 ILE cc_start: 0.9164 (pt) cc_final: 0.8798 (pt)
REVERT: A  337 LEU cc_start: 0.9460 (mt) cc_final: 0.9180 (mt)
REVERT: A  344 LEU cc_start: 0.8278 (tt) cc_final: 0.7897 (tt)
REVERT: A  410 TYR cc_start: 0.8146 (t80) cc_final: 0.7754 (t80)
REVERT: A  447 ILE cc_start: 0.9609 (mt) cc_final: 0.9399 (mt)
REVERT: A  453 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8646 (mm-30)
REVERT: A  460 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7840 (mtpt)
REVERT: A  538 ARG cc_start: 0.7495 (mtm180) cc_final: 0.6852 (ttt-90)
REVERT: A  579 TYR cc_start: 0.8121 (t80) cc_final: 0.7903 (t80)
REVERT: A  592 TYR cc_start: 0.8172 (t80) cc_final: 0.7563 (t80)
REVERT: A  600 THR cc_start: 0.8968 (m) cc_final: 0.8715 (p)
REVERT: H   22 GLN cc_start: 0.6647 (mp10) cc_final: 0.6420 (mp10)
REVERT: H   76 ASP cc_start: 0.8732 (t0) cc_final: 0.8343 (t0)
REVERT: H  120 TYR cc_start: 0.7860 (m-80) cc_final: 0.7274 (m-80)
REVERT: L   37 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7368 (tp-100)
REVERT: L   60 PHE cc_start: 0.8115 (m-10) cc_final: 0.7682 (m-10)
REVERT: L   71 LEU cc_start: 0.9003 (mt) cc_final: 0.8581 (mt)
REVERT: L   77 ASN cc_start: 0.8923 (t0) cc_final: 0.8625 (t0)
REVERT: L   83 PRO cc_start: 0.8857 (Cg_exo) cc_final: 0.8620 (Cg_endo)
REVERT: L  100 HIS cc_start: 0.7413 (m90) cc_final: 0.6882 (m90)
REVERT: L  114 GLN cc_start: 0.7758 (pm20) cc_final: 0.7243 (pm20)
REVERT: L  121 THR cc_start: 0.7336 (p) cc_final: 0.6871 (t)
REVERT: V   18 GLN cc_start: 0.8577 (mm110) cc_final: 0.8223 (mm110)
REVERT: V   20 GLN cc_start: 0.7605 (mm110) cc_final: 0.7118 (mm-40)
REVERT: V   38 LYS cc_start: 0.7849 (tttt) cc_final: 0.7350 (ttmt)
REVERT: V   43 THR cc_start: 0.8068 (m) cc_final: 0.7303 (p)
REVERT: V   51 TRP cc_start: 0.8428 (m100) cc_final: 0.7858 (m100)
REVERT: V   67 ASN cc_start: 0.8274 (t0) cc_final: 0.7913 (t0)
REVERT: V   92 THR cc_start: 0.8672 (p) cc_final: 0.8267 (t)
REVERT: V  105 ASP cc_start: 0.8414 (m-30) cc_final: 0.8020 (m-30)
REVERT: V  151 ILE cc_start: 0.8567 (mt) cc_final: 0.8230 (mt)
REVERT: V  176 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7744 (mm-40)
REVERT: V  184 TRP cc_start: 0.9020 (m100) cc_final: 0.8411 (m100)
REVERT: V  204 TYR cc_start: 0.7667 (t80) cc_final: 0.7413 (t80)
REVERT: V  239 GLN cc_start: 0.7841 (tm-30) cc_final: 0.6974 (tm-30)
REVERT: V  246 THR cc_start: 0.8762 (p) cc_final: 0.8467 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 357
  average time/residue: 0.1693
  time to fit residues: 84.3233
Evaluate side-chains
  293 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 84 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    2.5388

-------------------------------------------------------------------------------
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 223 HIS
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
A 456 HIS
** 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 = 0.3947 r_free = 0.3947 target = 0.153953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.131128 restraints weight = 15904.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.136301 restraints weight = 9162.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.140131 restraints weight = 5938.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.7096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8069  Z= 0.251
  Angle     :  0.733  11.903  10984  Z= 0.372
  Chirality :  0.046   0.308   1215
  Planarity :  0.005   0.070   1354
  Dihedral  :  5.782  42.856   1202
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.85 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.27), residues: 978
  helix:  0.19 (0.25), residues: 387
  sheet: -0.30 (0.37), residues: 196
  loop : -1.20 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 220 
 HIS   0.007   0.002   HIS A 143 
 PHE   0.021   0.002   PHE A 440 
 TYR   0.019   0.002   TYR A  95 
 ARG   0.004   0.001   ARG A 298 

*********************** 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
  337 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 0.683 
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   82 TRP cc_start: 0.6916 (m-10) cc_final: 0.6693 (m-10)
REVERT: A   84 LYS cc_start: 0.8865 (mptt) cc_final: 0.8368 (tptm)
REVERT: A  111 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8654 (tm-30)
REVERT: A  121 TYR cc_start: 0.9078 (t80) cc_final: 0.8549 (t80)
REVERT: A  124 MET cc_start: 0.8985 (mmp) cc_final: 0.8625 (mmp)
REVERT: A  184 LEU cc_start: 0.9281 (tp) cc_final: 0.8954 (tp)
REVERT: A  189 SER cc_start: 0.9590 (m) cc_final: 0.9336 (p)
REVERT: A  195 LEU cc_start: 0.9032 (mt) cc_final: 0.8615 (mt)
REVERT: A  197 TRP cc_start: 0.9194 (m-10) cc_final: 0.8848 (m-10)
REVERT: A  222 LEU cc_start: 0.9155 (mm) cc_final: 0.8829 (mm)
REVERT: A  238 GLN cc_start: 0.8806 (mp10) cc_final: 0.8530 (mp-120)
REVERT: A  245 LEU cc_start: 0.8949 (mm) cc_final: 0.8285 (mm)
REVERT: A  246 GLN cc_start: 0.7486 (tt0) cc_final: 0.6970 (pm20)
REVERT: A  316 ASN cc_start: 0.8789 (t0) cc_final: 0.8256 (t0)
REVERT: A  328 ASP cc_start: 0.8269 (m-30) cc_final: 0.7828 (m-30)
REVERT: A  333 ILE cc_start: 0.9141 (pt) cc_final: 0.8786 (pt)
REVERT: A  337 LEU cc_start: 0.9477 (mt) cc_final: 0.9178 (mt)
REVERT: A  344 LEU cc_start: 0.8285 (tt) cc_final: 0.7843 (tt)
REVERT: A  447 ILE cc_start: 0.9611 (mt) cc_final: 0.9395 (mt)
REVERT: A  453 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8767 (mm-30)
REVERT: A  460 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7811 (mtpt)
REVERT: A  538 ARG cc_start: 0.7487 (mtm180) cc_final: 0.6889 (ttt-90)
REVERT: A  592 TYR cc_start: 0.8245 (t80) cc_final: 0.7769 (t80)
REVERT: H   22 GLN cc_start: 0.6587 (mp10) cc_final: 0.6370 (mp10)
REVERT: H   49 SER cc_start: 0.8737 (p) cc_final: 0.8411 (p)
REVERT: H   50 TYR cc_start: 0.7901 (m-80) cc_final: 0.7030 (m-80)
REVERT: H   76 ASP cc_start: 0.8555 (t0) cc_final: 0.8064 (t0)
REVERT: L   37 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7285 (tp40)
REVERT: L   60 PHE cc_start: 0.8189 (m-10) cc_final: 0.7860 (m-10)
REVERT: L   71 LEU cc_start: 0.9033 (mt) cc_final: 0.8651 (mt)
REVERT: L   77 ASN cc_start: 0.8981 (t0) cc_final: 0.8737 (t0)
REVERT: L   83 PRO cc_start: 0.8907 (Cg_exo) cc_final: 0.8679 (Cg_endo)
REVERT: L   86 PHE cc_start: 0.8807 (m-80) cc_final: 0.8527 (m-80)
REVERT: L  100 HIS cc_start: 0.7460 (m90) cc_final: 0.6932 (m90)
REVERT: L  114 GLN cc_start: 0.7728 (pm20) cc_final: 0.7174 (pm20)
REVERT: L  121 THR cc_start: 0.7160 (p) cc_final: 0.6598 (t)
REVERT: V   18 GLN cc_start: 0.8576 (mm110) cc_final: 0.8265 (mp10)
REVERT: V   38 LYS cc_start: 0.7844 (tttt) cc_final: 0.7355 (ttmt)
REVERT: V   43 THR cc_start: 0.7820 (m) cc_final: 0.7285 (m)
REVERT: V   51 TRP cc_start: 0.8482 (m100) cc_final: 0.7760 (m100)
REVERT: V   62 TRP cc_start: 0.9102 (t60) cc_final: 0.8637 (t60)
REVERT: V   67 ASN cc_start: 0.8265 (t0) cc_final: 0.7945 (t0)
REVERT: V  105 ASP cc_start: 0.8425 (m-30) cc_final: 0.7957 (m-30)
REVERT: V  176 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7806 (mm-40)
REVERT: V  184 TRP cc_start: 0.9055 (m100) cc_final: 0.8546 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.1636
  time to fit residues: 77.2481
Evaluate side-chains
  308 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0030
   chunk 50 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    3.1998

-------------------------------------------------------------------------------
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 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 HIS
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
** L  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V  65 ASN
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 = 0.3925 r_free = 0.3925 target = 0.151953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.129367 restraints weight = 15887.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.134447 restraints weight = 9236.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.138200 restraints weight = 6043.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.7398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8069  Z= 0.288
  Angle     :  0.745  11.988  10984  Z= 0.382
  Chirality :  0.046   0.336   1215
  Planarity :  0.005   0.061   1354
  Dihedral  :  5.998  47.595   1202
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 16.22
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.27), residues: 978
  helix:  0.15 (0.25), residues: 384
  sheet: -0.32 (0.37), residues: 195
  loop : -1.21 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 220 
 HIS   0.007   0.002   HIS A 143 
 PHE   0.022   0.002   PHE A 440 
 TYR   0.017   0.002   TYR A  95 
 ARG   0.005   0.001   ARG A 390 

********************** 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
  333 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 333
  time to evaluate  : 0.778 
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: 0.8925 (mptt) cc_final: 0.8372 (tptm)
REVERT: A  121 TYR cc_start: 0.9142 (t80) cc_final: 0.8659 (t80)
REVERT: A  184 LEU cc_start: 0.9300 (tp) cc_final: 0.8960 (tp)
REVERT: A  189 SER cc_start: 0.9580 (m) cc_final: 0.9340 (p)
REVERT: A  197 TRP cc_start: 0.9173 (m-10) cc_final: 0.8803 (m-10)
REVERT: A  222 LEU cc_start: 0.9110 (mm) cc_final: 0.8769 (mm)
REVERT: A  238 GLN cc_start: 0.8820 (mp10) cc_final: 0.8605 (mp-120)
REVERT: A  245 LEU cc_start: 0.9026 (mm) cc_final: 0.8506 (mm)
REVERT: A  246 GLN cc_start: 0.7421 (tt0) cc_final: 0.6937 (pm20)
REVERT: A  316 ASN cc_start: 0.8832 (t0) cc_final: 0.8367 (t0)
REVERT: A  328 ASP cc_start: 0.8365 (m-30) cc_final: 0.7996 (m-30)
REVERT: A  333 ILE cc_start: 0.9139 (pt) cc_final: 0.8788 (pt)
REVERT: A  337 LEU cc_start: 0.9466 (mt) cc_final: 0.9137 (mt)
REVERT: A  344 LEU cc_start: 0.8399 (tt) cc_final: 0.8011 (tt)
REVERT: A  431 LEU cc_start: 0.9118 (tp) cc_final: 0.8904 (tp)
REVERT: A  447 ILE cc_start: 0.9612 (mt) cc_final: 0.9389 (mt)
REVERT: A  453 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8830 (mm-30)
REVERT: A  460 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7747 (mtpt)
REVERT: A  538 ARG cc_start: 0.7584 (mtm180) cc_final: 0.6934 (ttt-90)
REVERT: A  592 TYR cc_start: 0.8218 (t80) cc_final: 0.7850 (t80)
REVERT: H   49 SER cc_start: 0.8750 (p) cc_final: 0.8473 (p)
REVERT: H   50 TYR cc_start: 0.8027 (m-80) cc_final: 0.7246 (m-80)
REVERT: H   76 ASP cc_start: 0.8627 (t0) cc_final: 0.8158 (t0)
REVERT: H  120 TYR cc_start: 0.7703 (m-80) cc_final: 0.7368 (m-80)
REVERT: L   60 PHE cc_start: 0.8171 (m-10) cc_final: 0.7863 (m-10)
REVERT: L   71 LEU cc_start: 0.8982 (mt) cc_final: 0.8554 (mt)
REVERT: L   77 ASN cc_start: 0.8989 (t0) cc_final: 0.8730 (t0)
REVERT: L   86 PHE cc_start: 0.8819 (m-80) cc_final: 0.8516 (m-80)
REVERT: L  100 HIS cc_start: 0.7398 (m90) cc_final: 0.6877 (m90)
REVERT: L  114 GLN cc_start: 0.7675 (pm20) cc_final: 0.7096 (pm20)
REVERT: V   18 GLN cc_start: 0.8580 (mm110) cc_final: 0.8265 (mp10)
REVERT: V   38 LYS cc_start: 0.7911 (tttt) cc_final: 0.7400 (ttmt)
REVERT: V   44 PHE cc_start: 0.8089 (t80) cc_final: 0.7830 (t80)
REVERT: V   51 TRP cc_start: 0.8535 (m100) cc_final: 0.7813 (m100)
REVERT: V   62 TRP cc_start: 0.9121 (t60) cc_final: 0.8688 (t60)
REVERT: V   67 ASN cc_start: 0.8363 (t0) cc_final: 0.8026 (t0)
REVERT: V   92 THR cc_start: 0.8741 (p) cc_final: 0.8369 (t)
REVERT: V  105 ASP cc_start: 0.8333 (m-30) cc_final: 0.7807 (m-30)
REVERT: V  184 TRP cc_start: 0.9063 (m100) cc_final: 0.8474 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 333
  average time/residue: 0.1779
  time to fit residues: 82.5154
Evaluate side-chains
  287 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 87 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 82 optimal weight:    0.5980
   chunk 65 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 89 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0030
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 HIS
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 176 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 = 0.4007 r_free = 0.4007 target = 0.159691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.136478 restraints weight = 15350.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.141857 restraints weight = 8827.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.145791 restraints weight = 5692.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.7415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8069  Z= 0.191
  Angle     :  0.713  11.587  10984  Z= 0.358
  Chirality :  0.045   0.316   1215
  Planarity :  0.005   0.062   1354
  Dihedral  :  5.805  50.703   1202
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.73 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.27), residues: 978
  helix:  0.49 (0.26), residues: 385
  sheet: -0.29 (0.36), residues: 204
  loop : -1.13 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 220 
 HIS   0.007   0.002   HIS A 223 
 PHE   0.022   0.002   PHE A 170 
 TYR   0.019   0.002   TYR V 236 
 ARG   0.008   0.001   ARG V 203 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2768.50 seconds
wall clock time: 50 minutes 21.32 seconds (3021.32 seconds total)