Starting phenix.real_space_refine
on Sat Jun 14 18:27:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vak_43093/06_2025/8vak_43093.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vak_43093/06_2025/8vak_43093.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vak_43093/06_2025/8vak_43093.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vak_43093/06_2025/8vak_43093.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vak_43093/06_2025/8vak_43093.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vak_43093/06_2025/8vak_43093.cif"
  }
  resolution = 3.3
  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=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      19      5.49       5
     S      66      5.16       5
     C   10135      2.51       5
     N    2880      2.21       5
     O    3210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 155 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16310
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 5306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 695, 5306
          Classifications: {'peptide': 695}
          Link IDs: {'PTRANS': 28, 'TRANS': 666}
    Chain: "B"
      Number of atoms: 5306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 695, 5306
          Classifications: {'peptide': 695}
          Link IDs: {'PTRANS': 28, 'TRANS': 666}
    Chain: "C"
      Number of atoms: 5306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 695, 5306
          Classifications: {'peptide': 695}
          Link IDs: {'PTRANS': 28, 'TRANS': 666}
    Chain: "G"
      Number of atoms: 122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 122
          Inner-chain residues flagged as termini: ['pdbres="  A G  13 "']
          Classifications: {'DNA': 2, 'RNA': 7}
          Modifications used: {'5*END': 2, 'rna2p_pur': 3, 'rna3p_pur': 4}
          Link IDs: {'rna2p': 3, 'rna3p': 5}
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'  A%rna2p_pur:plan': 3, '  A%rna2p_pur:plan2': 3, '  A%rna3p_pur:plan2': 3, '  A%rna3p_pur:plan': 3}
          Unresolved non-hydrogen planarities: 66
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 42
          Classifications: {'RNA': 2}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 1}
    Chain: "D"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 48
          Classifications: {'RNA': 2}
          Modifications used: {'rna2p': 1, 'rna3p': 1}
          Link IDs: {'rna3p': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
    Chain: "E"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 42
          Classifications: {'RNA': 2}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 1}
    Chain: "E"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 48
          Classifications: {'RNA': 2}
          Modifications used: {'rna3p': 2}
          Link IDs: {'rna3p': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
    Chain: "F"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 42
          Classifications: {'RNA': 2}
          Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 1}
    Chain: "F"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 48
          Classifications: {'RNA': 2}
          Modifications used: {'rna3p': 2}
          Link IDs: {'rna3p': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" C1'   A G  13 " occ=0.30
      ... (9 atoms not shown)
      pdb=" C4    A G  13 " occ=0.30
    residue:
      pdb=" C1'   A G  14 " occ=0.30
      ... (9 atoms not shown)
      pdb=" C4    A G  14 " occ=0.30
  Time building chain proxies: 10.54, per 1000 atoms: 0.65
  Number of scatterers: 16310
  At special positions: 0
  Unit cell: (142.88, 111.86, 129.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      66     16.00
     P      19     15.00
     O    3210      8.00
     N    2880      7.00
     C   10135      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=7, symmetry=0
  Number of additional bonds: simple=7, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.19
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3798

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 26 sheets defined
      37.9% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 85 through 103
      Proline residue:  A  98  - end of helix
      Proline residue:  A 101  - end of helix
    Processing helix  chain 'A' and resid 125 through 142
      removed outlier: 4.534A  pdb=" N   VAL A 129 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLY A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 171
      removed outlier: 3.725A  pdb=" N   LYS A 171 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 227
      removed outlier: 4.344A  pdb=" N   VAL A 214 " --> pdb=" O   GLU A 210 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL A 215 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 248
    Processing helix  chain 'A' and resid 251 through 258
    Processing helix  chain 'A' and resid 262 through 285
    Processing helix  chain 'A' and resid 289 through 312
      removed outlier: 3.739A  pdb=" N   LEU A 293 " --> pdb=" O   ASP A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 362
      removed outlier: 3.625A  pdb=" N   ALA A 362 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 412
    Processing helix  chain 'A' and resid 437 through 454
      removed outlier: 3.571A  pdb=" N   GLY A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 489
      removed outlier: 4.151A  pdb=" N   HIS A 487 " --> pdb=" O   GLY A 483 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   LEU A 488 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 541
      removed outlier: 3.676A  pdb=" N   MET A 519 " --> pdb=" O   THR A 515 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLN A 539 " --> pdb=" O   GLY A 535 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ALA A 540 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ILE A 541 " --> pdb=" O   MET A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 563
      No H-bonds generated for 'chain 'A' and resid 561 through 563'
    Processing helix  chain 'A' and resid 564 through 570
      removed outlier: 4.025A  pdb=" N   VAL A 568 " --> pdb=" O   LYS A 564 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   GLY A 570 " --> pdb=" O   LYS A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 584
    Processing helix  chain 'A' and resid 601 through 615
      removed outlier: 3.666A  pdb=" N   ILE A 615 " --> pdb=" O   ARG A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 665
      removed outlier: 3.516A  pdb=" N   ASP A 664 " --> pdb=" O   LYS A 661 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR A 665 " --> pdb=" O   VAL A 662 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 661 through 665'
    Processing helix  chain 'A' and resid 689 through 694
      removed outlier: 3.727A  pdb=" N   GLU A 694 " --> pdb=" O   LYS A 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 100
      Proline residue:  B  98  - end of helix
    Processing helix  chain 'B' and resid 125 through 142
      removed outlier: 4.501A  pdb=" N   VAL B 129 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY B 142 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 171
    Processing helix  chain 'B' and resid 197 through 227
      removed outlier: 5.041A  pdb=" N   VAL B 214 " --> pdb=" O   GLU B 210 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   VAL B 215 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 260
      removed outlier: 4.134A  pdb=" N   LEU B 249 " --> pdb=" O   ARG B 245 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ALA B 252 " --> pdb=" O   ALA B 248 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   ARG B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE B 260 " --> pdb=" O   ASP B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 285
      removed outlier: 3.563A  pdb=" N   ARG B 266 " --> pdb=" O   ASP B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 312
    Processing helix  chain 'B' and resid 397 through 412
      removed outlier: 3.809A  pdb=" N   ARG B 405 " --> pdb=" O   ILE B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 454
    Processing helix  chain 'B' and resid 482 through 489
      removed outlier: 4.003A  pdb=" N   HIS B 487 " --> pdb=" O   GLY B 483 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU B 488 " --> pdb=" O   ASP B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 541
      removed outlier: 3.510A  pdb=" N   MET B 519 " --> pdb=" O   THR B 515 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLN B 539 " --> pdb=" O   GLY B 535 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ALA B 540 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ILE B 541 " --> pdb=" O   MET B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 569
    Processing helix  chain 'B' and resid 570 through 572
      No H-bonds generated for 'chain 'B' and resid 570 through 572'
    Processing helix  chain 'B' and resid 573 through 584
    Processing helix  chain 'B' and resid 601 through 616
    Processing helix  chain 'B' and resid 650 through 654
    Processing helix  chain 'B' and resid 661 through 665
    Processing helix  chain 'B' and resid 689 through 695
      removed outlier: 4.077A  pdb=" N   GLU B 694 " --> pdb=" O   LYS B 690 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 100
      Proline residue:  C  98  - end of helix
    Processing helix  chain 'C' and resid 125 through 142
      removed outlier: 4.381A  pdb=" N   VAL C 129 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY C 142 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 173
      removed outlier: 3.837A  pdb=" N   GLU C 172 " --> pdb=" O   ASP C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 227
      removed outlier: 5.101A  pdb=" N   VAL C 214 " --> pdb=" O   GLU C 210 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   VAL C 215 " --> pdb=" O   GLN C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 260
      removed outlier: 3.705A  pdb=" N   LEU C 249 " --> pdb=" O   ARG C 245 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   ALA C 252 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ARG C 253 " --> pdb=" O   LEU C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 262 through 285
      removed outlier: 3.703A  pdb=" N   ARG C 266 " --> pdb=" O   ASP C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 312
    Processing helix  chain 'C' and resid 358 through 362
      removed outlier: 3.541A  pdb=" N   ALA C 362 " --> pdb=" O   ALA C 359 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 413
      removed outlier: 3.937A  pdb=" N   ARG C 405 " --> pdb=" O   ILE C 401 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ALA C 413 " --> pdb=" O   ARG C 409 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 437 through 454
      removed outlier: 3.534A  pdb=" N   ALA C 441 " --> pdb=" O   SER C 437 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 482 through 489
      removed outlier: 3.512A  pdb=" N   LEU C 488 " --> pdb=" O   ASP C 484 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 515 through 541
      removed outlier: 3.831A  pdb=" N   ALA C 540 " --> pdb=" O   VAL C 536 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE C 541 " --> pdb=" O   MET C 537 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 561 through 570
      removed outlier: 3.956A  pdb=" N   LYS C 566 " --> pdb=" O   PRO C 562 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 573 through 584
    Processing helix  chain 'C' and resid 601 through 617
      removed outlier: 3.960A  pdb=" N   ILE C 615 " --> pdb=" O   ARG C 611 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 689 through 695
      removed outlier: 4.466A  pdb=" N   GLN C 695 " --> pdb=" O   GLU C 691 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 3.551A  pdb=" N   GLU A  19 " --> pdb=" O   MET A  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163
    Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 331
      removed outlier: 3.533A  pdb=" N   ALA A 350 " --> pdb=" O   PHE A 343 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 433 " --> pdb=" O   GLN A 349 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU A 351 " --> pdb=" O   ILE A 431 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   ILE A 431 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   THR A 353 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   SER A 429 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   THR A 355 " --> pdb=" O   VAL A 427 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   VAL A 427 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU A 377 " --> pdb=" O   VAL A 427 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   SER A 429 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   HIS A 379 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   ILE A 431 " --> pdb=" O   HIS A 379 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   ASN A 381 " --> pdb=" O   ILE A 431 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   GLU A 433 " --> pdb=" O   ASN A 381 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 366
    Processing sheet with id=AA5, first strand: chain 'A' and resid 462 through 464
      removed outlier: 3.642A  pdb=" N   ALA A 462 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 478
      removed outlier: 3.661A  pdb=" N   LEU A 478 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY A 467 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 559
    Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 633
      removed outlier: 3.730A  pdb=" N   THR A 630 " --> pdb=" O   PHE A 638 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   PHE A 638 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE A 632 " --> pdb=" O   GLY A 636 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   GLY A 636 " --> pdb=" O   ILE A 632 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 648
      removed outlier: 3.987A  pdb=" N   LEU A 648 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 5 through 10
      removed outlier: 6.659A  pdb=" N   ALA B  39 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 5 through 10
      removed outlier: 6.659A  pdb=" N   ALA B  39 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 150 through 151
      removed outlier: 3.789A  pdb=" N   GLY B 150 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 155 through 157
    Processing sheet with id=AB5, first strand: chain 'B' and resid 327 through 331
      removed outlier: 3.536A  pdb=" N   ARG B 330 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   GLN B 349 " --> pdb=" O   THR B 432 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LEU B 377 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   SER B 429 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   HIS B 379 " --> pdb=" O   SER B 429 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ILE B 431 " --> pdb=" O   HIS B 379 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASN B 381 " --> pdb=" O   ILE B 431 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   GLU B 433 " --> pdb=" O   ASN B 381 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 363 through 365
    Processing sheet with id=AB7, first strand: chain 'B' and resid 462 through 464
      removed outlier: 3.520A  pdb=" N   ALA B 462 " --> pdb=" O   GLY B 497 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 462 through 464
      removed outlier: 3.520A  pdb=" N   ALA B 462 " --> pdb=" O   GLY B 497 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLN B 506 " --> pdb=" O   LYS B 494 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 554 through 559
      removed outlier: 3.636A  pdb=" N   ALA B 598 " --> pdb=" O   THR B 586 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 5 through 8
      removed outlier: 3.640A  pdb=" N   GLU C  19 " --> pdb=" O   MET C  32 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   THR C  60 " --> pdb=" O   VAL C 113 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 5 through 8
      removed outlier: 3.640A  pdb=" N   GLU C  19 " --> pdb=" O   MET C  32 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   PHE C  41 " --> pdb=" O   VAL C 117 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   VAL C 117 " --> pdb=" O   PHE C  41 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   THR C  43 " --> pdb=" O   ALA C 115 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   ALA C 115 " --> pdb=" O   THR C  43 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   GLN C  64 " --> pdb=" O   VAL C 117 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   SER C 119 " --> pdb=" O   GLN C  64 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 160 through 163
      removed outlier: 3.506A  pdb=" N   GLY C 181 " --> pdb=" O   GLY C 150 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 327 through 331
      removed outlier: 3.735A  pdb=" N   GLU C 433 " --> pdb=" O   GLN C 349 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LEU C 351 " --> pdb=" O   ILE C 431 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE C 431 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   THR C 353 " --> pdb=" O   SER C 429 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   SER C 429 " --> pdb=" O   THR C 353 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   THR C 355 " --> pdb=" O   VAL C 427 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   VAL C 427 " --> pdb=" O   THR C 355 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU C 377 " --> pdb=" O   VAL C 427 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   SER C 429 " --> pdb=" O   LEU C 377 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   HIS C 379 " --> pdb=" O   SER C 429 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   ILE C 431 " --> pdb=" O   HIS C 379 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   ASN C 381 " --> pdb=" O   ILE C 431 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   GLU C 433 " --> pdb=" O   ASN C 381 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 363 through 366
    Processing sheet with id=AC6, first strand: chain 'C' and resid 474 through 479
      removed outlier: 3.624A  pdb=" N   ALA C 462 " --> pdb=" O   GLY C 497 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL C 495 " --> pdb=" O   ILE C 464 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 554 through 559
      removed outlier: 3.559A  pdb=" N   ALA C 599 " --> pdb=" O   ARG C 554 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 631 through 633
      removed outlier: 4.910A  pdb=" N   ARG C 631 " --> pdb=" O   PHE C 638 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE C 638 " --> pdb=" O   ARG C 631 " (cutoff:3.500A)

    782 hydrogen bonds defined for protein.
    2187 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: 5.81

  Time building geometry restraints manager: 4.93 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2848
        1.31 -     1.43: 3854
        1.43 -     1.56: 9707
        1.56 -     1.68: 31
        1.68 -     1.81: 129
  Bond restraints: 16569
  Sorted by residual:
  bond pdb=" C   PRO A 148 "
       pdb=" O   PRO A 148 "
    ideal  model  delta    sigma   weight residual
    1.234  1.180  0.054 1.14e-02 7.69e+03 2.21e+01
  bond pdb=" C   PRO B 148 "
       pdb=" O   PRO B 148 "
    ideal  model  delta    sigma   weight residual
    1.234  1.185  0.048 1.14e-02 7.69e+03 1.79e+01
  bond pdb=" C   PRO C 148 "
       pdb=" O   PRO C 148 "
    ideal  model  delta    sigma   weight residual
    1.234  1.187  0.047 1.14e-02 7.69e+03 1.70e+01
  bond pdb=" N   PRO B 148 "
       pdb=" CA  PRO B 148 "
    ideal  model  delta    sigma   weight residual
    1.466  1.427  0.038 1.19e-02 7.06e+03 1.05e+01
  bond pdb=" N   ILE A 149 "
       pdb=" CA  ILE A 149 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.19e-02 7.06e+03 1.00e+01
  ... (remaining 16564 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 22196
        2.88 -     5.76: 266
        5.76 -     8.64: 21
        8.64 -    11.52: 3
       11.52 -    14.41: 2
  Bond angle restraints: 22488
  Sorted by residual:
  angle pdb=" C3' 8GM E   4 "
        pdb=" O3' 8GM E   4 "
        pdb=" P   8GM E   5 "
      ideal   model   delta    sigma   weight residual
     120.20  105.79   14.41 1.50e+00 4.44e-01 9.22e+01
  angle pdb=" C3'   C D   2 "
        pdb=" O3'   C D   2 "
        pdb=" P     A D   3 "
      ideal   model   delta    sigma   weight residual
     120.20  106.88   13.32 1.50e+00 4.44e-01 7.88e+01
  angle pdb=" C3'   C F   2 "
        pdb=" O3'   C F   2 "
        pdb=" P     A F   3 "
      ideal   model   delta    sigma   weight residual
     120.20  108.88   11.32 1.50e+00 4.44e-01 5.70e+01
  angle pdb=" C3' 8GM D   4 "
        pdb=" O3' 8GM D   4 "
        pdb=" P   8GM D   5 "
      ideal   model   delta    sigma   weight residual
     120.20  110.44    9.76 1.50e+00 4.44e-01 4.23e+01
  angle pdb=" C3'   C E   2 "
        pdb=" O3'   C E   2 "
        pdb=" P     A E   3 "
      ideal   model   delta    sigma   weight residual
     120.20  110.50    9.70 1.50e+00 4.44e-01 4.18e+01
  ... (remaining 22483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.05: 9063
       24.05 -    48.09: 873
       48.09 -    72.14: 218
       72.14 -    96.18: 48
       96.18 -   120.23: 4
  Dihedral angle restraints: 10206
    sinusoidal: 4287
      harmonic: 5919
  Sorted by residual:
  dihedral pdb=" C2' 8GM D   5 "
           pdb=" C3' 8GM D   5 "
           pdb=" C4' 8GM D   5 "
           pdb=" O4' 8GM D   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -34.87   58.87     1      8.00e+00 1.56e-02 7.24e+01
  dihedral pdb=" O4'   C F   2 "
           pdb=" C1'   C F   2 "
           pdb=" N1    C F   2 "
           pdb=" C2    C F   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   79.77  120.23     1      1.50e+01 4.44e-03 6.41e+01
  dihedral pdb=" C1' 8GM D   5 "
           pdb=" C2' 8GM D   5 "
           pdb=" C3' 8GM D   5 "
           pdb=" C4' 8GM D   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   20.07  -55.07     1      8.00e+00 1.56e-02 6.41e+01
  ... (remaining 10203 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 2535
       0.112 -    0.224: 85
       0.224 -    0.336: 4
       0.336 -    0.448: 3
       0.448 -    0.559: 3
  Chirality restraints: 2630
  Sorted by residual:
  chirality pdb=" P     C D   2 "
            pdb=" OP1   C D   2 "
            pdb=" OP2   C D   2 "
            pdb=" O5'   C D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.97   -0.56 2.00e-01 2.50e+01 7.83e+00
  chirality pdb=" P     C F   2 "
            pdb=" OP1   C F   2 "
            pdb=" OP2   C F   2 "
            pdb=" O5'   C F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.96   -0.55 2.00e-01 2.50e+01 7.67e+00
  chirality pdb=" P     C E   2 "
            pdb=" OP1   C E   2 "
            pdb=" OP2   C E   2 "
            pdb=" O5'   C E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.95   -0.54 2.00e-01 2.50e+01 7.28e+00
  ... (remaining 2627 not shown)

  Planarity restraints: 2895
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 208 "   -0.022 2.00e-02 2.50e+03   4.26e-02 1.81e+01
        pdb=" C   GLY A 208 "    0.074 2.00e-02 2.50e+03
        pdb=" O   GLY A 208 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   HIS A 209 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C 144 "    0.021 2.00e-02 2.50e+03   4.09e-02 1.67e+01
        pdb=" C   PRO C 144 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   PRO C 144 "    0.026 2.00e-02 2.50e+03
        pdb=" N   PHE C 145 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 144 "   -0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   PRO A 144 "    0.062 2.00e-02 2.50e+03
        pdb=" O   PRO A 144 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PHE A 145 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 2892 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 116
        2.49 -     3.09: 12472
        3.09 -     3.69: 24758
        3.69 -     4.30: 33809
        4.30 -     4.90: 56485
  Nonbonded interactions: 127640
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG C  93 "
            pdb=" OP1 8GM F   4 "
     model   vdw
     1.887 2.496
  nonbonded pdb=" OE2 GLU B 430 "
            pdb=" OH  TYR C  68 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OH  TYR C 258 "
            pdb=" OE2 GLU C 301 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   SER C 429 "
            pdb=" OG  SER C 429 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O   THR C 424 "
            pdb=" OG1 THR C 424 "
     model   vdw
     2.204 3.040
  ... (remaining 127635 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.720
  Check model and map are aligned:         0.120
  Set scattering table:                    0.170
  Process input model:                     39.780
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.080
  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:             0.010
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.775  16576  Z= 0.970
  Angle     :  0.805  14.406  22488  Z= 0.480
  Chirality :  0.055   0.559   2630
  Planarity :  0.005   0.056   2895
  Dihedral  : 19.958 120.231   6408
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  8.89 %
    Allowed  : 16.37 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.17), residues: 2079
  helix: -0.26 (0.18), residues: 670
  sheet: -1.93 (0.23), residues: 486
  loop : -1.18 (0.19), residues: 923

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 231 
 HIS   0.008   0.001   HIS A 338 
 PHE   0.016   0.002   PHE A 145 
 TYR   0.019   0.002   TYR A 385 
 ARG   0.009   0.001   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18384 (  739)
  hydrogen bonds       : angle       7.34516 ( 2187)
  covalent geometry    : bond        0.00759 (16569)
  covalent geometry    : angle       0.80509 (22488)
  Misc. bond           : bond        0.43953 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 151
    poor density    : 73
  time to evaluate  : 2.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8638 (ptp)
REVERT: A  274 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7984 (pptt)
REVERT: A  414 VAL cc_start: 0.9529 (OUTLIER) cc_final: 0.9320 (p)
REVERT: A  493 PHE cc_start: 0.7573 (m-80) cc_final: 0.7177 (m-80)
REVERT: A  623 ARG cc_start: 0.2345 (OUTLIER) cc_final: 0.2019 (ptt180)
REVERT: B  176 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.7961 (p0)
REVERT: B  191 SER cc_start: 0.9176 (m) cc_final: 0.8957 (p)
REVERT: B  369 MET cc_start: 0.8869 (mmm) cc_final: 0.8299 (mmm)
REVERT: B  466 MET cc_start: 0.8660 (mmm) cc_final: 0.8447 (mmp)
REVERT: B  486 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8295 (p0)
REVERT: B  668 MET cc_start: 0.5355 (mmp) cc_final: 0.5135 (mmp)
REVERT: C  323 MET cc_start: 0.8382 (mtp) cc_final: 0.8157 (mtp)
REVERT: C  369 MET cc_start: 0.8529 (mmm) cc_final: 0.7853 (mmm)
REVERT: C  566 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8829 (tptt)
REVERT: C  629 VAL cc_start: 0.3771 (OUTLIER) cc_final: 0.3530 (p)
REVERT: C  668 MET cc_start: 0.7772 (mmp) cc_final: 0.7387 (mmp)
  outliers start: 151
  outliers final: 93
  residues processed: 213
  average time/residue: 0.2507
  time to fit residues: 84.1707
Evaluate side-chains
  172 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 71
  time to evaluate  : 1.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 HIS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   26 GLN
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  429 SER
Chi-restraints excluded: chain A residue  440 MET
Chi-restraints excluded: chain A residue  447 SER
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  576 ILE
Chi-restraints excluded: chain A residue  614 GLU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  663 THR
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  355 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  399 ARG
Chi-restraints excluded: chain B residue  434 SER
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  533 ILE
Chi-restraints excluded: chain B residue  534 LEU
Chi-restraints excluded: chain B residue  549 SER
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  293 LEU
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain C residue  337 THR
Chi-restraints excluded: chain C residue  355 THR
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  401 ILE
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  430 GLU
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  486 ASP
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  511 ILE
Chi-restraints excluded: chain C residue  515 THR
Chi-restraints excluded: chain C residue  523 LEU
Chi-restraints excluded: chain C residue  536 VAL
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Chi-restraints excluded: chain C residue  629 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 174 optimal weight:    2.9990
   chunk 156 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 105 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 162 optimal weight:   10.0000
   chunk 62 optimal weight:   30.0000
   chunk 98 optimal weight:    7.9990
   chunk 120 optimal weight:    0.5980
   chunk 187 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN
A 403 HIS
A 506 GLN
B 164 ASN
B 200 GLN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 520 GLN
B 653 GLN
C 212 GLN
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.088500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.052765 restraints weight = 51568.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 4.84
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
r_final: 0.2825
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16576  Z= 0.143
  Angle     :  0.610   9.293  22488  Z= 0.320
  Chirality :  0.045   0.168   2630
  Planarity :  0.004   0.053   2895
  Dihedral  : 15.803 114.847   2728
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 19.85 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.19), residues: 2079
  helix:  1.22 (0.19), residues: 690
  sheet: -1.10 (0.24), residues: 471
  loop : -0.48 (0.21), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP C 231 
 HIS   0.008   0.001   HIS B 487 
 PHE   0.011   0.001   PHE C 103 
 TYR   0.016   0.002   TYR C 385 
 ARG   0.009   0.001   ARG A 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05126 (  739)
  hydrogen bonds       : angle       5.10074 ( 2187)
  covalent geometry    : bond        0.00303 (16569)
  covalent geometry    : angle       0.61017 (22488)
  Misc. bond           : bond        0.00296 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 80
  time to evaluate  : 1.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8886 (m110)
REVERT: A  188 MET cc_start: 0.8467 (tmm) cc_final: 0.7814 (tmm)
REVERT: B  164 ASN cc_start: 0.9335 (OUTLIER) cc_final: 0.9093 (t0)
REVERT: B  176 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8317 (p0)
REVERT: B  191 SER cc_start: 0.9290 (m) cc_final: 0.9031 (p)
REVERT: B  369 MET cc_start: 0.8486 (mmm) cc_final: 0.7775 (mmm)
REVERT: B  399 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7682 (ptm160)
REVERT: C  175 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8450 (tp)
REVERT: C  323 MET cc_start: 0.8118 (mtp) cc_final: 0.7714 (mtp)
REVERT: C  358 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8712 (t)
REVERT: C  369 MET cc_start: 0.8707 (mmm) cc_final: 0.8012 (mmm)
REVERT: C  430 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8714 (mt-10)
REVERT: C  433 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7636 (mt-10)
REVERT: C  451 MET cc_start: 0.9140 (mmm) cc_final: 0.8838 (tpt)
REVERT: C  507 MET cc_start: 0.8180 (mtp) cc_final: 0.7969 (mtm)
REVERT: C  566 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9020 (tptt)
REVERT: C  629 VAL cc_start: 0.7253 (OUTLIER) cc_final: 0.7022 (p)
  outliers start: 93
  outliers final: 55
  residues processed: 167
  average time/residue: 0.2369
  time to fit residues: 64.2031
Evaluate side-chains
  141 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 77
  time to evaluate  : 1.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLN
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  167 GLN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  355 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  399 ARG
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  327 LEU
Chi-restraints excluded: chain C residue  355 THR
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  430 GLU
Chi-restraints excluded: chain C residue  486 ASP
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  523 LEU
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Chi-restraints excluded: chain C residue  629 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 172 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 139 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 125 optimal weight:   10.0000
   chunk 113 optimal weight:    0.7980
   chunk 203 optimal weight:    0.0470
   chunk 105 optimal weight:    8.9990
   overall best weight:    1.7682

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

Flipped N/Q/H residues before XYZ refinement:
A  26 GLN
A 164 ASN
A 200 GLN
A 349 GLN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** 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 = 0.3704 r_free = 0.3704 target = 0.087086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.051303 restraints weight = 51478.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 4.72
r_work: 0.2618 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2591 r_free = 0.2591    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2590 r_free = 0.2590    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.2590
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16576  Z= 0.167
  Angle     :  0.566   7.912  22488  Z= 0.293
  Chirality :  0.044   0.210   2630
  Planarity :  0.004   0.053   2895
  Dihedral  : 15.039 114.246   2651
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.08 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.19), residues: 2079
  helix:  1.69 (0.20), residues: 690
  sheet: -0.65 (0.25), residues: 466
  loop : -0.15 (0.21), residues: 923

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 231 
 HIS   0.005   0.001   HIS C 607 
 PHE   0.012   0.001   PHE A  41 
 TYR   0.012   0.002   TYR A 380 
 ARG   0.003   0.000   ARG B 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04585 (  739)
  hydrogen bonds       : angle       4.69362 ( 2187)
  covalent geometry    : bond        0.00372 (16569)
  covalent geometry    : angle       0.56646 (22488)
  Misc. bond           : bond        0.00180 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 75
  time to evaluate  : 1.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 MET cc_start: 0.8933 (ttp) cc_final: 0.8605 (ptm)
REVERT: A  164 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.8933 (m110)
REVERT: A  360 ARG cc_start: 0.9099 (tmm-80) cc_final: 0.8795 (ttp80)
REVERT: A  392 MET cc_start: 0.8676 (tmm) cc_final: 0.8417 (tmm)
REVERT: A  451 MET cc_start: 0.9251 (ttm) cc_final: 0.8897 (mtp)
REVERT: B    1 MET cc_start: 0.7777 (ppp) cc_final: 0.7450 (ppp)
REVERT: B  176 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8451 (p0)
REVERT: B  191 SER cc_start: 0.9392 (m) cc_final: 0.9177 (p)
REVERT: B  369 MET cc_start: 0.8613 (mmm) cc_final: 0.8032 (mmm)
REVERT: B  417 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.7826 (p0)
REVERT: B  507 MET cc_start: 0.8262 (ptp) cc_final: 0.8013 (ptp)
REVERT: C  175 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8596 (tp)
REVERT: C  323 MET cc_start: 0.8293 (mtp) cc_final: 0.7942 (mtp)
REVERT: C  348 THR cc_start: 0.9755 (OUTLIER) cc_final: 0.9471 (p)
REVERT: C  358 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8840 (t)
REVERT: C  369 MET cc_start: 0.8668 (mmm) cc_final: 0.8060 (mmm)
REVERT: C  430 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8855 (mt-10)
REVERT: C  451 MET cc_start: 0.9382 (mmm) cc_final: 0.9061 (tpt)
REVERT: C  466 MET cc_start: 0.8638 (mtp) cc_final: 0.8143 (mtt)
REVERT: C  566 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9002 (tptt)
  outliers start: 91
  outliers final: 63
  residues processed: 162
  average time/residue: 0.2212
  time to fit residues: 59.4253
Evaluate side-chains
  146 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 75
  time to evaluate  : 1.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  355 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  586 THR
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  348 THR
Chi-restraints excluded: chain C residue  355 THR
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  430 GLU
Chi-restraints excluded: chain C residue  443 VAL
Chi-restraints excluded: chain C residue  486 ASP
Chi-restraints excluded: chain C residue  491 MET
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  515 THR
Chi-restraints excluded: chain C residue  533 ILE
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  555 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  662 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 132 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 185 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 88 optimal weight:    8.9990
   chunk 194 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 435 ASN
** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 650 HIS
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** 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 = 0.3663 r_free = 0.3663 target = 0.084691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.049034 restraints weight = 52338.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 4.68
r_work: 0.2557 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2557
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2532 r_free = 0.2532    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2532 r_free = 0.2532    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.2532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  16576  Z= 0.318
  Angle     :  0.636  10.196  22488  Z= 0.329
  Chirality :  0.044   0.185   2630
  Planarity :  0.004   0.060   2895
  Dihedral  : 14.712 112.324   2635
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 21.91 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.19), residues: 2079
  helix:  1.80 (0.20), residues: 689
  sheet: -0.51 (0.25), residues: 483
  loop :  0.02 (0.22), residues: 907

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 233 
 HIS   0.006   0.001   HIS A 338 
 PHE   0.015   0.001   PHE B  41 
 TYR   0.017   0.002   TYR B 380 
 ARG   0.005   0.000   ARG C 611 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04801 (  739)
  hydrogen bonds       : angle       4.73105 ( 2187)
  covalent geometry    : bond        0.00716 (16569)
  covalent geometry    : angle       0.63634 (22488)
  Misc. bond           : bond        0.00143 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 72
  time to evaluate  : 1.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 MET cc_start: 0.9129 (ttp) cc_final: 0.8733 (ptm)
REVERT: A  360 ARG cc_start: 0.9178 (tmm-80) cc_final: 0.8858 (ttp80)
REVERT: A  392 MET cc_start: 0.8787 (tmm) cc_final: 0.8479 (tmm)
REVERT: A  506 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8695 (tt0)
REVERT: B    1 MET cc_start: 0.8002 (ppp) cc_final: 0.7560 (ppp)
REVERT: B  176 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8543 (p0)
REVERT: B  369 MET cc_start: 0.8932 (mmm) cc_final: 0.8290 (mmm)
REVERT: B  415 MET cc_start: 0.9499 (ttm) cc_final: 0.9096 (tpp)
REVERT: B  417 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.7851 (p0)
REVERT: B  507 MET cc_start: 0.8407 (ptp) cc_final: 0.8158 (ptp)
REVERT: C  175 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8657 (tp)
REVERT: C  313 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8117 (tm-30)
REVERT: C  323 MET cc_start: 0.8385 (mtp) cc_final: 0.7989 (mtp)
REVERT: C  348 THR cc_start: 0.9761 (OUTLIER) cc_final: 0.9516 (p)
REVERT: C  358 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8830 (t)
REVERT: C  369 MET cc_start: 0.8751 (mmm) cc_final: 0.8063 (mmm)
REVERT: C  415 MET cc_start: 0.9585 (mmm) cc_final: 0.9324 (mmm)
REVERT: C  430 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8816 (mt-10)
REVERT: C  451 MET cc_start: 0.9437 (mmm) cc_final: 0.9026 (mmm)
REVERT: C  466 MET cc_start: 0.8653 (mtp) cc_final: 0.8180 (mtt)
REVERT: C  566 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9050 (tptt)
  outliers start: 96
  outliers final: 67
  residues processed: 165
  average time/residue: 0.2488
  time to fit residues: 68.0463
Evaluate side-chains
  147 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 71
  time to evaluate  : 1.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   23 MET
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  355 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  447 SER
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  586 THR
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  633 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  313 GLU
Chi-restraints excluded: chain C residue  319 ARG
Chi-restraints excluded: chain C residue  348 THR
Chi-restraints excluded: chain C residue  355 THR
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  430 GLU
Chi-restraints excluded: chain C residue  443 VAL
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  486 ASP
Chi-restraints excluded: chain C residue  491 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  515 THR
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  555 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Chi-restraints excluded: chain C residue  662 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 182 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0770
   chunk 131 optimal weight:   30.0000
   chunk 59 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A 487 HIS
B 218 ASN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.087044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.050658 restraints weight = 52440.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 4.87
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  16576  Z= 0.118
  Angle     :  0.524   9.510  22488  Z= 0.268
  Chirality :  0.043   0.165   2630
  Planarity :  0.004   0.055   2895
  Dihedral  : 14.272 109.119   2630
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.79 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.19), residues: 2079
  helix:  2.10 (0.20), residues: 689
  sheet: -0.24 (0.25), residues: 477
  loop :  0.09 (0.22), residues: 913

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 231 
 HIS   0.004   0.001   HIS A 338 
 PHE   0.017   0.001   PHE B  41 
 TYR   0.014   0.001   TYR C 385 
 ARG   0.003   0.000   ARG A 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  739)
  hydrogen bonds       : angle       4.30910 ( 2187)
  covalent geometry    : bond        0.00247 (16569)
  covalent geometry    : angle       0.52383 (22488)
  Misc. bond           : bond        0.00117 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 73
  time to evaluate  : 2.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 MET cc_start: 0.8760 (ttp) cc_final: 0.8494 (ptm)
REVERT: A  360 ARG cc_start: 0.8971 (tmm-80) cc_final: 0.8625 (ttp80)
REVERT: A  392 MET cc_start: 0.8218 (tmm) cc_final: 0.7937 (tmm)
REVERT: B    1 MET cc_start: 0.7760 (ppp) cc_final: 0.7369 (ppp)
REVERT: B  176 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8467 (p0)
REVERT: B  369 MET cc_start: 0.8624 (mmm) cc_final: 0.8112 (mmm)
REVERT: B  415 MET cc_start: 0.9339 (ttm) cc_final: 0.8967 (tpp)
REVERT: B  417 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7689 (p0)
REVERT: B  451 MET cc_start: 0.9273 (tpt) cc_final: 0.9031 (mmm)
REVERT: B  466 MET cc_start: 0.8743 (mmp) cc_final: 0.8485 (mmm)
REVERT: B  491 MET cc_start: 0.7582 (tmm) cc_final: 0.7008 (tmm)
REVERT: B  507 MET cc_start: 0.7830 (ptp) cc_final: 0.7579 (ptp)
REVERT: C  323 MET cc_start: 0.8114 (mtp) cc_final: 0.7705 (mtp)
REVERT: C  358 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8578 (t)
REVERT: C  369 MET cc_start: 0.8626 (mmm) cc_final: 0.8039 (mmm)
REVERT: C  430 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8525 (mt-10)
REVERT: C  451 MET cc_start: 0.9308 (mmm) cc_final: 0.8773 (mmm)
REVERT: C  466 MET cc_start: 0.7920 (mtp) cc_final: 0.7713 (mtt)
REVERT: C  566 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9024 (tptt)
  outliers start: 69
  outliers final: 51
  residues processed: 140
  average time/residue: 0.3017
  time to fit residues: 69.1787
Evaluate side-chains
  128 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 72
  time to evaluate  : 1.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 HIS
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  663 THR
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  355 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  586 THR
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  633 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  313 GLU
Chi-restraints excluded: chain C residue  319 ARG
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  430 GLU
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  515 THR
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  555 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 184 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 125 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   chunk 191 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 487 HIS
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.086623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.049887 restraints weight = 52106.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 4.90
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.2774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16576  Z= 0.149
  Angle     :  0.520   9.100  22488  Z= 0.266
  Chirality :  0.042   0.157   2630
  Planarity :  0.003   0.057   2895
  Dihedral  : 13.988 107.389   2620
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 24.26 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.20), residues: 2079
  helix:  2.22 (0.20), residues: 689
  sheet: -0.10 (0.25), residues: 476
  loop :  0.16 (0.22), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 231 
 HIS   0.004   0.001   HIS A 338 
 PHE   0.016   0.001   PHE B  41 
 TYR   0.014   0.001   TYR A  68 
 ARG   0.002   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03854 (  739)
  hydrogen bonds       : angle       4.20614 ( 2187)
  covalent geometry    : bond        0.00332 (16569)
  covalent geometry    : angle       0.51968 (22488)
  Misc. bond           : bond        0.00112 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 73
  time to evaluate  : 1.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7903 (tmm) cc_final: 0.7618 (tmm)
REVERT: A  188 MET cc_start: 0.8492 (tmm) cc_final: 0.8215 (tmm)
REVERT: A  360 ARG cc_start: 0.9014 (tmm-80) cc_final: 0.8783 (tmm-80)
REVERT: A  392 MET cc_start: 0.8236 (tmm) cc_final: 0.7950 (tmm)
REVERT: B    1 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7463 (ppp)
REVERT: B  369 MET cc_start: 0.8655 (mmm) cc_final: 0.8156 (mmm)
REVERT: B  415 MET cc_start: 0.9360 (ttm) cc_final: 0.9044 (tpp)
REVERT: B  466 MET cc_start: 0.8814 (mmp) cc_final: 0.8579 (mmm)
REVERT: B  491 MET cc_start: 0.7729 (tmm) cc_final: 0.7337 (tmm)
REVERT: B  507 MET cc_start: 0.7846 (ptp) cc_final: 0.7481 (ptp)
REVERT: C  323 MET cc_start: 0.8174 (mtp) cc_final: 0.7743 (mtp)
REVERT: C  348 THR cc_start: 0.9720 (OUTLIER) cc_final: 0.9397 (p)
REVERT: C  358 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8514 (t)
REVERT: C  369 MET cc_start: 0.8677 (mmm) cc_final: 0.8082 (mmm)
REVERT: C  415 MET cc_start: 0.9514 (mmm) cc_final: 0.9286 (mmm)
REVERT: C  430 GLU cc_start: 0.8876 (pt0) cc_final: 0.8411 (mt-10)
REVERT: C  451 MET cc_start: 0.9291 (mmm) cc_final: 0.8734 (mmm)
REVERT: C  566 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9041 (tptt)
  outliers start: 70
  outliers final: 61
  residues processed: 139
  average time/residue: 0.2318
  time to fit residues: 52.5982
Evaluate side-chains
  137 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 72
  time to evaluate  : 1.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  663 THR
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   23 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  355 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  533 ILE
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  586 THR
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  633 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  313 GLU
Chi-restraints excluded: chain C residue  319 ARG
Chi-restraints excluded: chain C residue  348 THR
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  491 MET
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  512 GLU
Chi-restraints excluded: chain C residue  515 THR
Chi-restraints excluded: chain C residue  533 ILE
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  555 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 193 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 196 optimal weight:   10.0000
   chunk 161 optimal weight:    2.9990
   chunk 127 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 167 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN
A 487 HIS
** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** 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 = 0.3647 r_free = 0.3647 target = 0.084609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.048196 restraints weight = 52549.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.2726 rms_B_bonded: 4.87
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  16576  Z= 0.287
  Angle     :  0.599   8.986  22488  Z= 0.309
  Chirality :  0.044   0.199   2630
  Planarity :  0.004   0.064   2895
  Dihedral  : 13.910 104.940   2615
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 23.50 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.19), residues: 2079
  helix:  2.10 (0.20), residues: 689
  sheet: -0.15 (0.25), residues: 478
  loop :  0.22 (0.22), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 233 
 HIS   0.004   0.001   HIS A 338 
 PHE   0.016   0.001   PHE B  41 
 TYR   0.017   0.002   TYR B 380 
 ARG   0.004   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04483 (  739)
  hydrogen bonds       : angle       4.41482 ( 2187)
  covalent geometry    : bond        0.00646 (16569)
  covalent geometry    : angle       0.59927 (22488)
  Misc. bond           : bond        0.00104 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 72
  time to evaluate  : 1.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.8934 (m110)
REVERT: A  188 MET cc_start: 0.8570 (tmm) cc_final: 0.8288 (tmm)
REVERT: A  360 ARG cc_start: 0.9050 (tmm-80) cc_final: 0.8826 (tmm-80)
REVERT: A  392 MET cc_start: 0.8279 (tmm) cc_final: 0.8042 (tmm)
REVERT: B    1 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7669 (ppp)
REVERT: B  188 MET cc_start: 0.8588 (tmm) cc_final: 0.8315 (tmm)
REVERT: B  369 MET cc_start: 0.8945 (mmm) cc_final: 0.8395 (mmm)
REVERT: B  466 MET cc_start: 0.8824 (mmp) cc_final: 0.8465 (mmm)
REVERT: B  491 MET cc_start: 0.7897 (tmm) cc_final: 0.7459 (tmm)
REVERT: B  507 MET cc_start: 0.8137 (ptp) cc_final: 0.7749 (ptp)
REVERT: C  323 MET cc_start: 0.8388 (mtp) cc_final: 0.7953 (mtp)
REVERT: C  348 THR cc_start: 0.9727 (OUTLIER) cc_final: 0.9481 (p)
REVERT: C  358 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8613 (m)
REVERT: C  369 MET cc_start: 0.8853 (mmm) cc_final: 0.8196 (mmm)
REVERT: C  415 MET cc_start: 0.9510 (mmm) cc_final: 0.9237 (mmm)
REVERT: C  430 GLU cc_start: 0.8885 (pt0) cc_final: 0.8427 (mt-10)
REVERT: C  451 MET cc_start: 0.9367 (mmm) cc_final: 0.8756 (mmm)
REVERT: C  566 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9045 (tptt)
  outliers start: 83
  outliers final: 70
  residues processed: 149
  average time/residue: 0.2301
  time to fit residues: 56.0523
Evaluate side-chains
  146 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 71
  time to evaluate  : 1.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 HIS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  663 THR
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   23 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  355 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  447 SER
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain B residue  586 THR
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  633 VAL
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  313 GLU
Chi-restraints excluded: chain C residue  319 ARG
Chi-restraints excluded: chain C residue  348 THR
Chi-restraints excluded: chain C residue  355 THR
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  491 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  512 GLU
Chi-restraints excluded: chain C residue  515 THR
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  555 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 155 optimal weight:    4.9990
   chunk 157 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 111 optimal weight:    0.8980
   chunk 147 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 167 optimal weight:    4.9990
   chunk 107 optimal weight:    0.0030
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN
A 487 HIS
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** 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 = 0.3696 r_free = 0.3696 target = 0.086837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.050239 restraints weight = 52086.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 4.84
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2785
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2785 r_free = 0.2785    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2785 r_free = 0.2785    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.2785
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  16576  Z= 0.108
  Angle     :  0.520   9.100  22488  Z= 0.264
  Chirality :  0.043   0.155   2630
  Planarity :  0.004   0.060   2895
  Dihedral  : 13.706 100.980   2615
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 24.79 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.20), residues: 2079
  helix:  2.24 (0.20), residues: 691
  sheet:  0.02 (0.25), residues: 475
  loop :  0.23 (0.22), residues: 913

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 233 
 HIS   0.003   0.001   HIS B 532 
 PHE   0.016   0.001   PHE B  41 
 TYR   0.015   0.001   TYR A  68 
 ARG   0.003   0.000   ARG B 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  739)
  hydrogen bonds       : angle       4.07320 ( 2187)
  covalent geometry    : bond        0.00229 (16569)
  covalent geometry    : angle       0.51960 (22488)
  Misc. bond           : bond        0.00089 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 73
  time to evaluate  : 1.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.9007 (m-40)
REVERT: A  188 MET cc_start: 0.8509 (tmm) cc_final: 0.8233 (tmm)
REVERT: A  360 ARG cc_start: 0.9074 (tmm-80) cc_final: 0.8697 (ttp80)
REVERT: A  392 MET cc_start: 0.8303 (tmm) cc_final: 0.8000 (tmm)
REVERT: A  451 MET cc_start: 0.8772 (mtp) cc_final: 0.8410 (mmm)
REVERT: B    1 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7630 (ppp)
REVERT: B  188 MET cc_start: 0.8514 (tmm) cc_final: 0.8228 (tmm)
REVERT: B  417 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7670 (p0)
REVERT: B  466 MET cc_start: 0.8772 (mmp) cc_final: 0.8537 (mmm)
REVERT: B  491 MET cc_start: 0.7934 (tmm) cc_final: 0.7456 (tmm)
REVERT: B  507 MET cc_start: 0.7961 (ptp) cc_final: 0.7633 (ptp)
REVERT: C  319 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8423 (mtm-85)
REVERT: C  323 MET cc_start: 0.8126 (mtp) cc_final: 0.7783 (mtp)
REVERT: C  358 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8457 (m)
REVERT: C  369 MET cc_start: 0.8624 (mmm) cc_final: 0.8085 (mmm)
REVERT: C  390 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9374 (t)
REVERT: C  415 MET cc_start: 0.9511 (mmm) cc_final: 0.9259 (mmm)
REVERT: C  430 GLU cc_start: 0.8852 (pt0) cc_final: 0.8440 (mt-10)
REVERT: C  451 MET cc_start: 0.9297 (mmm) cc_final: 0.8675 (mmm)
REVERT: C  566 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9116 (tptt)
  outliers start: 66
  outliers final: 49
  residues processed: 135
  average time/residue: 0.2306
  time to fit residues: 50.7962
Evaluate side-chains
  129 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 73
  time to evaluate  : 1.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  447 SER
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain B residue  586 THR
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  633 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  313 GLU
Chi-restraints excluded: chain C residue  319 ARG
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  491 MET
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  512 GLU
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 184 optimal weight:    7.9990
   chunk 161 optimal weight:    6.9990
   chunk 189 optimal weight:    4.9990
   chunk 87 optimal weight:    0.5980
   chunk 155 optimal weight:    3.9990
   chunk 138 optimal weight:    0.8980
   chunk 64 optimal weight:   50.0000
   chunk 34 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 112 optimal weight:    6.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN
A 487 HIS
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** 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 = 0.3694 r_free = 0.3694 target = 0.086692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.049969 restraints weight = 52155.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 4.98
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.2781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16576  Z= 0.122
  Angle     :  0.511   9.216  22488  Z= 0.260
  Chirality :  0.042   0.154   2630
  Planarity :  0.003   0.056   2895
  Dihedral  : 13.590  99.256   2612
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.62 %
    Favored  : 71.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.20), residues: 2079
  helix:  2.29 (0.20), residues: 691
  sheet:  0.07 (0.25), residues: 475
  loop :  0.27 (0.22), residues: 913

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 231 
 HIS   0.003   0.001   HIS A 338 
 PHE   0.017   0.001   PHE B  41 
 TYR   0.013   0.001   TYR A  68 
 ARG   0.002   0.000   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03615 (  739)
  hydrogen bonds       : angle       4.01428 ( 2187)
  covalent geometry    : bond        0.00267 (16569)
  covalent geometry    : angle       0.51136 (22488)
  Misc. bond           : bond        0.00087 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 76
  time to evaluate  : 1.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8962 (m110)
REVERT: A  188 MET cc_start: 0.8556 (tmm) cc_final: 0.8271 (tmm)
REVERT: A  360 ARG cc_start: 0.9084 (tmm-80) cc_final: 0.8701 (ttp80)
REVERT: A  392 MET cc_start: 0.8301 (tmm) cc_final: 0.8007 (tmm)
REVERT: A  451 MET cc_start: 0.8781 (mtp) cc_final: 0.8370 (mmm)
REVERT: B    1 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7617 (ppp)
REVERT: B  188 MET cc_start: 0.8511 (tmm) cc_final: 0.8230 (tmm)
REVERT: B  369 MET cc_start: 0.9031 (mmm) cc_final: 0.8773 (mmm)
REVERT: B  415 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9031 (tpp)
REVERT: B  417 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7526 (p0)
REVERT: B  451 MET cc_start: 0.9239 (tpt) cc_final: 0.8858 (tpt)
REVERT: B  466 MET cc_start: 0.8796 (mmp) cc_final: 0.8575 (mmm)
REVERT: B  491 MET cc_start: 0.7937 (tmm) cc_final: 0.7459 (tmm)
REVERT: B  507 MET cc_start: 0.7965 (ptp) cc_final: 0.7647 (ptp)
REVERT: C  313 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8233 (tm-30)
REVERT: C  323 MET cc_start: 0.8187 (mtp) cc_final: 0.7726 (mtp)
REVERT: C  348 THR cc_start: 0.9711 (OUTLIER) cc_final: 0.9391 (p)
REVERT: C  358 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8504 (m)
REVERT: C  369 MET cc_start: 0.8695 (mmm) cc_final: 0.8112 (mmm)
REVERT: C  390 THR cc_start: 0.9603 (OUTLIER) cc_final: 0.9400 (t)
REVERT: C  415 MET cc_start: 0.9526 (mmm) cc_final: 0.9262 (mmm)
REVERT: C  430 GLU cc_start: 0.8818 (pt0) cc_final: 0.8424 (mt-10)
REVERT: C  451 MET cc_start: 0.9295 (mmm) cc_final: 0.8679 (mmm)
REVERT: C  566 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9115 (tptt)
  outliers start: 67
  outliers final: 50
  residues processed: 139
  average time/residue: 0.2488
  time to fit residues: 56.3468
Evaluate side-chains
  132 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 73
  time to evaluate  : 1.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain B residue  586 THR
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  633 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  313 GLU
Chi-restraints excluded: chain C residue  319 ARG
Chi-restraints excluded: chain C residue  348 THR
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  491 MET
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  512 GLU
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 179 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 125 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 123 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 138 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 200 optimal weight:   30.0000
   chunk 96 optimal weight:    0.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 487 HIS
** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.084375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.048051 restraints weight = 52507.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.2726 rms_B_bonded: 4.77
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  16576  Z= 0.299
  Angle     :  0.620   9.416  22488  Z= 0.317
  Chirality :  0.044   0.175   2630
  Planarity :  0.004   0.060   2895
  Dihedral  : 13.646  98.826   2612
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.85 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.19), residues: 2079
  helix:  2.27 (0.20), residues: 683
  sheet: -0.06 (0.25), residues: 476
  loop :  0.28 (0.22), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 233 
 HIS   0.004   0.001   HIS C  14 
 PHE   0.018   0.001   PHE B  41 
 TYR   0.018   0.002   TYR B 380 
 ARG   0.004   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04413 (  739)
  hydrogen bonds       : angle       4.32753 ( 2187)
  covalent geometry    : bond        0.00675 (16569)
  covalent geometry    : angle       0.62028 (22488)
  Misc. bond           : bond        0.00088 (    7)

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

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

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4158 Ramachandran restraints generated.
    2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 71
  time to evaluate  : 2.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.8637 (tmm) cc_final: 0.8337 (tmm)
REVERT: A  360 ARG cc_start: 0.9112 (tmm-80) cc_final: 0.8749 (ttp80)
REVERT: A  392 MET cc_start: 0.8290 (tmm) cc_final: 0.8041 (tmm)
REVERT: A  451 MET cc_start: 0.8933 (mtp) cc_final: 0.8375 (mmm)
REVERT: B    1 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7815 (ppp)
REVERT: B  188 MET cc_start: 0.8496 (tmm) cc_final: 0.8200 (tmm)
REVERT: B  369 MET cc_start: 0.9215 (mmm) cc_final: 0.8563 (mmm)
REVERT: B  417 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7644 (p0)
REVERT: B  491 MET cc_start: 0.8045 (tmm) cc_final: 0.7551 (tmm)
REVERT: B  507 MET cc_start: 0.8125 (ptp) cc_final: 0.7778 (ptp)
REVERT: C  323 MET cc_start: 0.8343 (mtp) cc_final: 0.7895 (mtp)
REVERT: C  348 THR cc_start: 0.9717 (OUTLIER) cc_final: 0.9477 (p)
REVERT: C  358 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8596 (m)
REVERT: C  369 MET cc_start: 0.8885 (mmm) cc_final: 0.8230 (mmm)
REVERT: C  415 MET cc_start: 0.9557 (mmm) cc_final: 0.9299 (mmm)
REVERT: C  451 MET cc_start: 0.9367 (mmm) cc_final: 0.8906 (mmm)
REVERT: C  466 MET cc_start: 0.8287 (mtp) cc_final: 0.7528 (mtt)
REVERT: C  566 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.9125 (tptt)
  outliers start: 67
  outliers final: 57
  residues processed: 134
  average time/residue: 0.3480
  time to fit residues: 78.4003
Evaluate side-chains
  132 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 70
  time to evaluate  : 3.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  374 ASP
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  417 ASP
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  515 THR
Chi-restraints excluded: chain B residue  566 LYS
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain B residue  586 THR
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  633 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  313 GLU
Chi-restraints excluded: chain C residue  319 ARG
Chi-restraints excluded: chain C residue  348 THR
Chi-restraints excluded: chain C residue  358 THR
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  390 THR
Chi-restraints excluded: chain C residue  417 ASP
Chi-restraints excluded: chain C residue  429 SER
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  491 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  512 GLU
Chi-restraints excluded: chain C residue  515 THR
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  561 ASN
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  566 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 207
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 199 optimal weight:    4.9990
   chunk 189 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 206 optimal weight:   20.0000
   chunk 203 optimal weight:   40.0000
   chunk 135 optimal weight:    2.9990
   chunk 146 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN
A 487 HIS
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 561 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.085731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.049235 restraints weight = 52385.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 4.84
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  16576  Z= 0.163
  Angle     :  0.534   9.498  22488  Z= 0.272
  Chirality :  0.043   0.158   2630
  Planarity :  0.003   0.059   2895
  Dihedral  : 13.547  99.792   2610
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 25.21 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.20), residues: 2079
  helix:  2.32 (0.20), residues: 685
  sheet:  0.04 (0.25), residues: 475
  loop :  0.31 (0.22), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 233 
 HIS   0.004   0.001   HIS A 338 
 PHE   0.015   0.001   PHE B  41 
 TYR   0.011   0.001   TYR A  68 
 ARG   0.003   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  739)
  hydrogen bonds       : angle       4.12200 ( 2187)
  covalent geometry    : bond        0.00365 (16569)
  covalent geometry    : angle       0.53432 (22488)
  Misc. bond           : bond        0.00079 (    7)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8368.79 seconds
wall clock time: 148 minutes 59.78 seconds (8939.78 seconds total)