Starting phenix.real_space_refine
on Thu Jul 31 13:34:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ld5_23282/07_2025/7ld5_23282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ld5_23282/07_2025/7ld5_23282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ld5_23282/07_2025/7ld5_23282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ld5_23282/07_2025/7ld5_23282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ld5_23282/07_2025/7ld5_23282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ld5_23282/07_2025/7ld5_23282.cif"
  }
  resolution = 3.07
  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=  -0.001 sd=   0.110
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: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      6      5.21       5
     S      54      5.16       5
     C    8451      2.51       5
     N    2358      2.21       5
     O    2664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 132 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13542
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4416
          Classifications: {'peptide': 587}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 555}
    Chain: "E"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 96
          Classifications: {'DNA': 1, 'RNA': 4}
          Modifications used: {'5*END': 2, 'rna3p_pur': 4}
          Link IDs: {'rna3p': 4}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    D, F, C, B
  Residues with excluded nonbonded symmetry interactions: 15
    residue:
      pdb=" O5'   A D   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A D   1 " occ=0.30
    residue:
      pdb=" P     A D   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   2 " occ=0.30
    residue:
      pdb=" P     A D   3 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   3 " occ=0.30
    residue:
      pdb=" P     A D   4 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   4 " occ=0.30
    residue:
      pdb=" C1'   A D   9 " occ=0.30
      ... (9 atoms not shown)
      pdb=" C4    A D   9 " occ=0.30
    residue:
      pdb=" O5'   A E   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A E   1 " occ=0.30
    residue:
      pdb=" P     A E   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   2 " occ=0.30
    residue:
      pdb=" P     A E   3 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   3 " occ=0.30
    residue:
      pdb=" P     A E   4 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   4 " occ=0.30
    residue:
      pdb=" C1'   A E   9 " occ=0.30
      ... (9 atoms not shown)
      pdb=" C4    A E   9 " occ=0.30
    residue:
      pdb=" O5'   A F   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A F   1 " occ=0.30
    residue:
      pdb=" P     A F   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A F   2 " occ=0.30
    ... (remaining 3 not shown)
  Time building chain proxies: 9.65, per 1000 atoms: 0.71
  Number of scatterers: 13542
  At special positions: 0
  Unit cell: (114.912, 122.36, 89.376, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P       9     15.00
     Mg      6     11.99
     O    2664      8.00
     N    2358      7.00
     C    8451      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=0, symmetry=0
  Time building additional restraints: 3.95
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 12 sheets defined
      37.8% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 97 through 112
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 138 through 153
      removed outlier: 4.043A  pdb=" N   ASN A 144 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A 153 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 224
    Processing helix  chain 'A' and resid 229 through 240
    Processing helix  chain 'A' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 314
    Processing helix  chain 'A' and resid 321 through 345
    Processing helix  chain 'A' and resid 390 through 394
    Processing helix  chain 'A' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 441
      removed outlier: 3.587A  pdb=" N   ILE A 433 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 447
    Processing helix  chain 'A' and resid 470 through 485
    Processing helix  chain 'A' and resid 523 through 527
      removed outlier: 3.594A  pdb=" N   ASP A 526 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 581
      removed outlier: 4.005A  pdb=" N   GLU A 579 " --> pdb=" O   ASP A 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA A 580 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE A 581 " --> pdb=" O   MET A 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 97 through 112
      Proline residue:  B 110  - end of helix
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 138 through 153
      removed outlier: 4.044A  pdb=" N   ASN B 144 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA B 153 " --> pdb=" O   SER B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 229 through 240
    Processing helix  chain 'B' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE B 244 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR B 276 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA B 286 " --> pdb=" O   VAL B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 314
    Processing helix  chain 'B' and resid 321 through 345
    Processing helix  chain 'B' and resid 390 through 394
    Processing helix  chain 'B' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 441
      removed outlier: 3.588A  pdb=" N   ILE B 433 " --> pdb=" O   LYS B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 447
    Processing helix  chain 'B' and resid 470 through 485
    Processing helix  chain 'B' and resid 523 through 527
      removed outlier: 3.595A  pdb=" N   ASP B 526 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 581
      removed outlier: 4.005A  pdb=" N   GLU B 579 " --> pdb=" O   ASP B 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA B 580 " --> pdb=" O   VAL B 576 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE B 581 " --> pdb=" O   MET B 577 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 83
    Processing helix  chain 'C' and resid 97 through 112
      Proline residue:  C 110  - end of helix
    Processing helix  chain 'C' and resid 113 through 115
      No H-bonds generated for 'chain 'C' and resid 113 through 115'
    Processing helix  chain 'C' and resid 138 through 153
      removed outlier: 4.043A  pdb=" N   ASN C 144 " --> pdb=" O   VAL C 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA C 153 " --> pdb=" O   SER C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 224
    Processing helix  chain 'C' and resid 229 through 240
    Processing helix  chain 'C' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE C 244 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR C 276 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA C 286 " --> pdb=" O   VAL C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 314
    Processing helix  chain 'C' and resid 321 through 345
    Processing helix  chain 'C' and resid 390 through 394
    Processing helix  chain 'C' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR C 419 " --> pdb=" O   PRO C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 441
      removed outlier: 3.588A  pdb=" N   ILE C 433 " --> pdb=" O   LYS C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 447
    Processing helix  chain 'C' and resid 470 through 485
    Processing helix  chain 'C' and resid 523 through 527
      removed outlier: 3.594A  pdb=" N   ASP C 526 " --> pdb=" O   GLY C 523 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 581
      removed outlier: 4.004A  pdb=" N   GLU C 579 " --> pdb=" O   ASP C 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA C 580 " --> pdb=" O   VAL C 576 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE C 581 " --> pdb=" O   MET C 577 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET A  51 " --> pdb=" O   MET A 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175
      removed outlier: 4.424A  pdb=" N   PHE A 187 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   VAL A 186 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   ALA A 213 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP A 188 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA A 211 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 190 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL A 209 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA A 192 " --> pdb=" O   MET A 207 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   MET A 207 " --> pdb=" O   THR A 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR A 543 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363
      removed outlier: 6.303A  pdb=" N   GLN A 381 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET A 409 " --> pdb=" O   GLN A 459 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   SER A 461 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS A 411 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ALA A 463 " --> pdb=" O   HIS A 411 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ASN A 413 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLY A 465 " --> pdb=" O   ASN A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET B  51 " --> pdb=" O   MET B 130 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175
      removed outlier: 4.425A  pdb=" N   PHE B 187 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   VAL B 186 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ALA B 213 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP B 188 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA B 211 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 190 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL B 209 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA B 192 " --> pdb=" O   MET B 207 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   MET B 207 " --> pdb=" O   THR B 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR B 543 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 363
      removed outlier: 6.303A  pdb=" N   GLN B 381 " --> pdb=" O   LEU B 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET B 409 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   SER B 461 " --> pdb=" O   MET B 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS B 411 " --> pdb=" O   SER B 461 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   ALA B 463 " --> pdb=" O   HIS B 411 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   ASN B 413 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLY B 465 " --> pdb=" O   ASN B 413 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 396
    Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET C  51 " --> pdb=" O   MET C 130 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 175
      removed outlier: 4.425A  pdb=" N   PHE C 187 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL C 186 " --> pdb=" O   ALA C 213 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ALA C 213 " --> pdb=" O   VAL C 186 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP C 188 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA C 211 " --> pdb=" O   ASP C 188 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL C 190 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL C 209 " --> pdb=" O   VAL C 190 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ALA C 192 " --> pdb=" O   MET C 207 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   MET C 207 " --> pdb=" O   THR C 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR C 543 " --> pdb=" O   ALA C 213 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 359 through 363
      removed outlier: 6.304A  pdb=" N   GLN C 381 " --> pdb=" O   LEU C 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET C 409 " --> pdb=" O   GLN C 459 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   SER C 461 " --> pdb=" O   MET C 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS C 411 " --> pdb=" O   SER C 461 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ALA C 463 " --> pdb=" O   HIS C 411 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ASN C 413 " --> pdb=" O   ALA C 463 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLY C 465 " --> pdb=" O   ASN C 413 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 395 through 396

    720 hydrogen bonds defined for protein.
    1980 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: 5.84

  Time building geometry restraints manager: 4.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4601
        1.34 -     1.45: 1539
        1.45 -     1.57: 7531
        1.57 -     1.69: 18
        1.69 -     1.80: 99
  Bond restraints: 13788
  Sorted by residual:
  bond pdb=" CB  GLU A 298 "
       pdb=" CG  GLU A 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.19e+00
  bond pdb=" CB  GLU C 298 "
       pdb=" CG  GLU C 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.16e+00
  bond pdb=" CB  GLU B 298 "
       pdb=" CG  GLU B 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.10e+00
  bond pdb=" CA  ILE C 366 "
       pdb=" CB  ILE C 366 "
    ideal  model  delta    sigma   weight residual
    1.537  1.523  0.014 1.29e-02 6.01e+03 1.25e+00
  bond pdb=" CA  ILE B 366 "
       pdb=" CB  ILE B 366 "
    ideal  model  delta    sigma   weight residual
    1.537  1.523  0.014 1.29e-02 6.01e+03 1.20e+00
  ... (remaining 13783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 18417
        1.88 -     3.77: 315
        3.77 -     5.65: 30
        5.65 -     7.53: 6
        7.53 -     9.42: 6
  Bond angle restraints: 18774
  Sorted by residual:
  angle pdb=" CA  GLU A 298 "
        pdb=" CB  GLU A 298 "
        pdb=" CG  GLU A 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.52   -9.42 2.00e+00 2.50e-01 2.22e+01
  angle pdb=" CA  GLU B 298 "
        pdb=" CB  GLU B 298 "
        pdb=" CG  GLU B 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.49   -9.39 2.00e+00 2.50e-01 2.21e+01
  angle pdb=" CA  GLU C 298 "
        pdb=" CB  GLU C 298 "
        pdb=" CG  GLU C 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.48   -9.38 2.00e+00 2.50e-01 2.20e+01
  angle pdb=" CG1 ILE B 293 "
        pdb=" CB  ILE B 293 "
        pdb=" CG2 ILE B 293 "
      ideal   model   delta    sigma   weight residual
     110.70  101.52    9.18 3.00e+00 1.11e-01 9.36e+00
  angle pdb=" CG1 ILE C 293 "
        pdb=" CB  ILE C 293 "
        pdb=" CG2 ILE C 293 "
      ideal   model   delta    sigma   weight residual
     110.70  101.54    9.16 3.00e+00 1.11e-01 9.31e+00
  ... (remaining 18769 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 7259
       16.59 -    33.19: 768
       33.19 -    49.78: 256
       49.78 -    66.38: 54
       66.38 -    82.97: 15
  Dihedral angle restraints: 8352
    sinusoidal: 3312
      harmonic: 5040
  Sorted by residual:
  dihedral pdb=" CA  VAL C 507 "
           pdb=" C   VAL C 507 "
           pdb=" N   ASP C 508 "
           pdb=" CA  ASP C 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.33  -17.67     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  VAL B 507 "
           pdb=" C   VAL B 507 "
           pdb=" N   ASP B 508 "
           pdb=" CA  ASP B 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  VAL A 507 "
           pdb=" C   VAL A 507 "
           pdb=" N   ASP A 508 "
           pdb=" CA  ASP A 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 8349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1553
       0.046 -    0.091: 483
       0.091 -    0.137: 136
       0.137 -    0.183: 9
       0.183 -    0.229: 3
  Chirality restraints: 2184
  Sorted by residual:
  chirality pdb=" CB  ILE B 293 "
            pdb=" CA  ILE B 293 "
            pdb=" CG1 ILE B 293 "
            pdb=" CG2 ILE B 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  ILE C 293 "
            pdb=" CA  ILE C 293 "
            pdb=" CG1 ILE C 293 "
            pdb=" CG2 ILE C 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  ILE A 293 "
            pdb=" CA  ILE A 293 "
            pdb=" CG1 ILE A 293 "
            pdb=" CG2 ILE A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 2181 not shown)

  Planarity restraints: 2439
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 444 "   -0.033 5.00e-02 4.00e+02   4.90e-02 3.84e+00
        pdb=" N   PRO C 445 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO C 445 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 445 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 444 "   -0.033 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO B 445 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 445 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 445 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 444 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.80e+00
        pdb=" N   PRO A 445 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 445 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 445 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2436 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 273
        2.66 -     3.22: 12389
        3.22 -     3.78: 19572
        3.78 -     4.34: 28398
        4.34 -     4.90: 48333
  Nonbonded interactions: 108965
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 418 "
            pdb=" O   ALA B 463 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OG  SER A 418 "
            pdb=" O   ALA A 463 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OG  SER C 418 "
            pdb=" O   ALA C 463 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" OE2 GLU C  77 "
            pdb=" OH  TYR C 138 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" OE2 GLU B  77 "
            pdb=" OH  TYR B 138 "
     model   vdw
     2.153 3.040
  ... (remaining 108960 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: 0.15
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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=0.99
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:             39.430
  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:          0.600
  Check model and map are aligned:         0.100
  Set scattering table:                    0.160
  Process input model:                     37.530
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   82.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  13788  Z= 0.262
  Angle     :  0.671   9.415  18774  Z= 0.375
  Chirality :  0.048   0.229   2184
  Planarity :  0.004   0.049   2439
  Dihedral  : 16.010  82.970   5112
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 15.84 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.18), residues: 1755
  helix: -0.76 (0.20), residues: 549
  sheet: -0.72 (0.23), residues: 444
  loop : -2.17 (0.21), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 173 
 HIS   0.001   0.000   HIS B 370 
 PHE   0.016   0.001   PHE A 157 
 TYR   0.011   0.002   TYR A  45 
 ARG   0.005   0.000   ARG B 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14108 (  720)
  hydrogen bonds       : angle       6.74148 ( 1980)
  covalent geometry    : bond        0.00629 (13788)
  covalent geometry    : angle       0.67138 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 193
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7378 (ptpt)
REVERT: A   79 MET cc_start: 0.8695 (tpp) cc_final: 0.8370 (tpp)
REVERT: A  130 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7981 (mtt)
REVERT: A  356 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7221 (mt)
REVERT: B   74 ASP cc_start: 0.7829 (m-30) cc_final: 0.7628 (m-30)
REVERT: B  329 PHE cc_start: 0.8412 (t80) cc_final: 0.8060 (t80)
REVERT: B  348 ILE cc_start: 0.8425 (pt) cc_final: 0.8210 (pt)
REVERT: B  356 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7440 (mt)
REVERT: B  397 ILE cc_start: 0.8574 (mm) cc_final: 0.8334 (mm)
REVERT: C   63 LYS cc_start: 0.7607 (ptpp) cc_final: 0.7272 (ptpp)
REVERT: C   95 ARG cc_start: 0.7801 (ptt180) cc_final: 0.7391 (ptm-80)
REVERT: C  122 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7202 (tm-30)
REVERT: C  130 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8290 (mtt)
REVERT: C  383 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8177 (tp)
  outliers start: 90
  outliers final: 49
  residues processed: 272
  average time/residue: 0.3271
  time to fit residues: 129.0916
Evaluate side-chains
  223 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 168
  time to evaluate  : 1.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  549 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   59 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  130 MET
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  449 SER
Chi-restraints excluded: chain C residue  471 SER
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:    7.9990
   chunk 131 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 136 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 82 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 158 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A  61 ASN
A 339 GLN
A 381 GLN
A 546 GLN
B  61 ASN
B 339 GLN
B 381 GLN
B 546 GLN
C  36 GLN
C  61 ASN
C 381 GLN
C 396 GLN
C 546 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.165984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.125640 restraints weight = 14368.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.94
r_work: 0.3349 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13788  Z= 0.129
  Angle     :  0.532   5.324  18774  Z= 0.280
  Chirality :  0.044   0.133   2184
  Planarity :  0.004   0.034   2439
  Dihedral  :  6.634  48.845   2123
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.93 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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: -0.54 (0.20), residues: 1755
  helix:  1.02 (0.21), residues: 558
  sheet: -0.23 (0.23), residues: 444
  loop : -1.48 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 173 
 HIS   0.001   0.000   HIS A 370 
 PHE   0.014   0.001   PHE A 157 
 TYR   0.012   0.001   TYR C  80 
 ARG   0.005   0.000   ARG C 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03735 (  720)
  hydrogen bonds       : angle       5.07297 ( 1980)
  covalent geometry    : bond        0.00302 (13788)
  covalent geometry    : angle       0.53224 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 182
  time to evaluate  : 1.939 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.7572 (ptpp) cc_final: 0.7015 (ptpt)
REVERT: A  122 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7581 (tm-30)
REVERT: A  330 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7418 (mtm-85)
REVERT: B   74 ASP cc_start: 0.8625 (m-30) cc_final: 0.8376 (m-30)
REVERT: B  330 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7292 (mtm-85)
REVERT: B  397 ILE cc_start: 0.8571 (mm) cc_final: 0.8281 (mm)
REVERT: C   63 LYS cc_start: 0.7734 (ptpp) cc_final: 0.7482 (ptpt)
REVERT: C  332 LEU cc_start: 0.8405 (tp) cc_final: 0.8196 (mp)
REVERT: C  470 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7931 (p)
  outliers start: 36
  outliers final: 26
  residues processed: 211
  average time/residue: 0.3491
  time to fit residues: 109.2976
Evaluate side-chains
  201 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 1.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  538 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0770
   chunk 83 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 142 optimal weight:    1.9990
   chunk 156 optimal weight:    1.9990
   overall best weight:    1.6146

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
C 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.161731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.121189 restraints weight = 14558.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.95
r_work: 0.3295 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13788  Z= 0.218
  Angle     :  0.597   6.332  18774  Z= 0.311
  Chirality :  0.046   0.146   2184
  Planarity :  0.004   0.036   2439
  Dihedral  :  6.062  49.103   2072
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 17.43 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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: -0.22 (0.20), residues: 1755
  helix:  1.27 (0.22), residues: 558
  sheet: -0.03 (0.24), residues: 444
  loop : -1.29 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 173 
 HIS   0.002   0.001   HIS C 410 
 PHE   0.019   0.002   PHE A 533 
 TYR   0.013   0.002   TYR C  80 
 ARG   0.005   0.000   ARG C 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (  720)
  hydrogen bonds       : angle       5.06661 ( 1980)
  covalent geometry    : bond        0.00542 (13788)
  covalent geometry    : angle       0.59730 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 177
  time to evaluate  : 2.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7654 (tm-30)
REVERT: A  397 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8238 (mm)
REVERT: B  314 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7695 (tp)
REVERT: B  330 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7349 (mtm-85)
REVERT: B  397 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8374 (mm)
REVERT: C   63 LYS cc_start: 0.7621 (ptpp) cc_final: 0.7411 (ptpt)
REVERT: C  330 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7438 (mtm110)
REVERT: C  397 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8161 (mm)
  outliers start: 61
  outliers final: 44
  residues processed: 224
  average time/residue: 0.3570
  time to fit residues: 120.4804
Evaluate side-chains
  222 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 173
  time to evaluate  : 2.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  397 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  498 MET
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 148 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 139 optimal weight:    0.8980
   chunk 80 optimal weight:    0.2980
   chunk 99 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0170
   chunk 67 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.168202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.127923 restraints weight = 14176.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.96
r_work: 0.3357 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13788  Z= 0.105
  Angle     :  0.488   4.819  18774  Z= 0.256
  Chirality :  0.042   0.133   2184
  Planarity :  0.004   0.034   2439
  Dihedral  :  5.412  48.607   2067
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.38 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.34 (0.20), residues: 1755
  helix:  1.77 (0.22), residues: 558
  sheet:  0.22 (0.23), residues: 444
  loop : -0.94 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 173 
 HIS   0.001   0.000   HIS A 370 
 PHE   0.013   0.001   PHE A 157 
 TYR   0.011   0.001   TYR C  80 
 ARG   0.004   0.000   ARG C 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03242 (  720)
  hydrogen bonds       : angle       4.65289 ( 1980)
  covalent geometry    : bond        0.00246 (13788)
  covalent geometry    : angle       0.48751 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 184
  time to evaluate  : 2.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7663 (tm-30)
REVERT: A  393 MET cc_start: 0.9249 (mmm) cc_final: 0.9025 (mmp)
REVERT: B   66 PHE cc_start: 0.7977 (m-80) cc_final: 0.7719 (m-80)
REVERT: B  397 ILE cc_start: 0.8548 (mm) cc_final: 0.8272 (mm)
REVERT: C   63 LYS cc_start: 0.7619 (ptpp) cc_final: 0.7309 (ptpt)
REVERT: C  111 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7693 (mp)
REVERT: C  314 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7925 (tp)
REVERT: C  330 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7521 (mtm180)
REVERT: C  332 LEU cc_start: 0.8400 (tp) cc_final: 0.8181 (mp)
REVERT: C  470 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7877 (p)
  outliers start: 37
  outliers final: 27
  residues processed: 211
  average time/residue: 0.3991
  time to fit residues: 126.3089
Evaluate side-chains
  204 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 173
  time to evaluate  : 2.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 81 optimal weight:    0.6980
   chunk 153 optimal weight:    2.9990
   chunk 151 optimal weight:    0.0370
   chunk 63 optimal weight:    7.9990
   chunk 76 optimal weight:    0.8980
   chunk 121 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.168770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.128679 restraints weight = 14348.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.95
r_work: 0.3356 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13788  Z= 0.112
  Angle     :  0.486   4.925  18774  Z= 0.253
  Chirality :  0.042   0.135   2184
  Planarity :  0.004   0.033   2439
  Dihedral  :  4.801  45.724   2055
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.73 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.64 (0.20), residues: 1755
  helix:  1.95 (0.22), residues: 558
  sheet:  0.47 (0.24), residues: 444
  loop : -0.75 (0.23), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 173 
 HIS   0.001   0.000   HIS C 370 
 PHE   0.013   0.001   PHE A 157 
 TYR   0.011   0.001   TYR C  80 
 ARG   0.004   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03278 (  720)
  hydrogen bonds       : angle       4.52207 ( 1980)
  covalent geometry    : bond        0.00266 (13788)
  covalent geometry    : angle       0.48551 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 182
  time to evaluate  : 2.639 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7673 (tm-30)
REVERT: A  330 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7531 (mtm-85)
REVERT: A  393 MET cc_start: 0.9290 (mmm) cc_final: 0.9047 (mmp)
REVERT: B  314 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7799 (tp)
REVERT: B  397 ILE cc_start: 0.8544 (mm) cc_final: 0.8270 (mm)
REVERT: C  111 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7698 (mp)
REVERT: C  314 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7981 (tp)
REVERT: C  330 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7452 (mtm180)
REVERT: C  332 LEU cc_start: 0.8403 (tp) cc_final: 0.8175 (mp)
REVERT: C  470 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7985 (p)
  outliers start: 54
  outliers final: 37
  residues processed: 220
  average time/residue: 0.2969
  time to fit residues: 97.7323
Evaluate side-chains
  217 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 175
  time to evaluate  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 162 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 165 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 147 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.160984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.120578 restraints weight = 14806.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.94
r_work: 0.3276 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063  13788  Z= 0.279
  Angle     :  0.641  12.391  18774  Z= 0.329
  Chirality :  0.048   0.174   2184
  Planarity :  0.005   0.044   2439
  Dihedral  :  5.246  51.864   2055
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 18.15 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.25 (0.20), residues: 1755
  helix:  1.49 (0.21), residues: 558
  sheet:  0.31 (0.24), residues: 450
  loop : -0.91 (0.22), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 173 
 HIS   0.003   0.001   HIS C 410 
 PHE   0.024   0.002   PHE A 533 
 TYR   0.015   0.002   TYR C  45 
 ARG   0.004   0.001   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04765 (  720)
  hydrogen bonds       : angle       4.98705 ( 1980)
  covalent geometry    : bond        0.00701 (13788)
  covalent geometry    : angle       0.64116 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 174
  time to evaluate  : 1.526 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7684 (tm-30)
REVERT: A  130 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8260 (mtt)
REVERT: A  330 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7521 (mtm-85)
REVERT: A  393 MET cc_start: 0.9274 (mmm) cc_final: 0.9023 (mmp)
REVERT: A  397 ILE cc_start: 0.8435 (mm) cc_final: 0.8176 (mm)
REVERT: B  314 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7902 (tp)
REVERT: B  330 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7338 (mtm-85)
REVERT: B  397 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8277 (mm)
REVERT: B  462 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7882 (mt-10)
REVERT: C   63 LYS cc_start: 0.7516 (ptpp) cc_final: 0.7230 (ptpt)
REVERT: C  111 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7873 (mp)
REVERT: C  330 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7330 (mtm110)
REVERT: C  332 LEU cc_start: 0.8401 (tp) cc_final: 0.8163 (mp)
REVERT: C  397 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8091 (mm)
  outliers start: 71
  outliers final: 51
  residues processed: 227
  average time/residue: 0.2395
  time to fit residues: 81.7784
Evaluate side-chains
  229 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 171
  time to evaluate  : 1.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  572 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  397 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  563 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 84 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 146 optimal weight:   20.0000
   chunk 72 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 164 optimal weight:    0.7980
   chunk 152 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 396 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.167577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.127062 restraints weight = 14419.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.97
r_work: 0.3333 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13788  Z= 0.125
  Angle     :  0.508  12.136  18774  Z= 0.262
  Chirality :  0.043   0.133   2184
  Planarity :  0.004   0.034   2439
  Dihedral  :  4.919  51.586   2055
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 19.74 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.20), residues: 1755
  helix:  1.86 (0.22), residues: 558
  sheet:  0.50 (0.24), residues: 444
  loop : -0.65 (0.23), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 173 
 HIS   0.001   0.000   HIS C 410 
 PHE   0.014   0.001   PHE A 157 
 TYR   0.012   0.001   TYR A 412 
 ARG   0.002   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  720)
  hydrogen bonds       : angle       4.62302 ( 1980)
  covalent geometry    : bond        0.00301 (13788)
  covalent geometry    : angle       0.50802 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 174
  time to evaluate  : 1.584 
Fit side-chains
REVERT: A   66 PHE cc_start: 0.8110 (m-80) cc_final: 0.7143 (t80)
REVERT: A  122 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7732 (tm-30)
REVERT: A  397 ILE cc_start: 0.8408 (mm) cc_final: 0.8166 (mm)
REVERT: A  462 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7955 (mm-30)
REVERT: B  314 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7955 (tp)
REVERT: B  397 ILE cc_start: 0.8562 (mm) cc_final: 0.8278 (mm)
REVERT: C   63 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7142 (ptpt)
REVERT: C  111 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7823 (mp)
REVERT: C  330 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7297 (mtm110)
REVERT: C  332 LEU cc_start: 0.8390 (tp) cc_final: 0.8157 (mp)
REVERT: C  462 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7928 (mm-30)
REVERT: C  470 THR cc_start: 0.8234 (p) cc_final: 0.7984 (p)
  outliers start: 52
  outliers final: 39
  residues processed: 213
  average time/residue: 0.2509
  time to fit residues: 80.1733
Evaluate side-chains
  216 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 171
  time to evaluate  : 1.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   63 LYS
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  563 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 89 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0030
   overall best weight:    0.9194

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

Flipped N/Q/H residues before XYZ refinement:
C  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.165053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.124457 restraints weight = 14475.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.96
r_work: 0.3331 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13788  Z= 0.140
  Angle     :  0.519  11.638  18774  Z= 0.267
  Chirality :  0.043   0.137   2184
  Planarity :  0.004   0.034   2439
  Dihedral  :  4.864  53.443   2055
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 19.67 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.77 (0.20), residues: 1755
  helix:  1.90 (0.22), residues: 561
  sheet:  0.59 (0.24), residues: 444
  loop : -0.58 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 173 
 HIS   0.001   0.000   HIS C 410 
 PHE   0.014   0.001   PHE A 157 
 TYR   0.011   0.001   TYR A 412 
 ARG   0.003   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  720)
  hydrogen bonds       : angle       4.59730 ( 1980)
  covalent geometry    : bond        0.00342 (13788)
  covalent geometry    : angle       0.51892 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 174
  time to evaluate  : 1.404 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8116 (m-80) cc_final: 0.7137 (t80)
REVERT: A  122 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7725 (tm-30)
REVERT: A  330 ARG cc_start: 0.7711 (mtm180) cc_final: 0.7249 (mtm-85)
REVERT: A  397 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8175 (mm)
REVERT: A  462 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7969 (mm-30)
REVERT: B   66 PHE cc_start: 0.7895 (m-80) cc_final: 0.7290 (t80)
REVERT: B  314 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8003 (tp)
REVERT: B  397 ILE cc_start: 0.8557 (mm) cc_final: 0.8288 (mm)
REVERT: B  462 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7773 (mt-10)
REVERT: C   63 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7155 (ptpt)
REVERT: C  111 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7800 (mp)
REVERT: C  330 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7293 (mtm110)
REVERT: C  332 LEU cc_start: 0.8413 (tp) cc_final: 0.8178 (mp)
REVERT: C  346 PHE cc_start: 0.7336 (m-80) cc_final: 0.7010 (m-80)
REVERT: C  462 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7923 (mm-30)
  outliers start: 58
  outliers final: 47
  residues processed: 216
  average time/residue: 0.2378
  time to fit residues: 76.3914
Evaluate side-chains
  226 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 171
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain C residue   63 LYS
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  563 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 163 optimal weight:    2.9990
   chunk 148 optimal weight:    6.9990
   chunk 80 optimal weight:    0.2980
   chunk 171 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.4386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.163316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.122810 restraints weight = 14458.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.95
r_work: 0.3308 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13788  Z= 0.193
  Angle     :  0.569  11.562  18774  Z= 0.291
  Chirality :  0.045   0.140   2184
  Planarity :  0.004   0.038   2439
  Dihedral  :  4.986  55.166   2055
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.23 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.62 (0.20), residues: 1755
  helix:  1.73 (0.22), residues: 561
  sheet:  0.52 (0.24), residues: 450
  loop : -0.66 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 173 
 HIS   0.002   0.000   HIS C 410 
 PHE   0.018   0.001   PHE A 533 
 TYR   0.012   0.002   TYR C  80 
 ARG   0.003   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04026 (  720)
  hydrogen bonds       : angle       4.74836 ( 1980)
  covalent geometry    : bond        0.00481 (13788)
  covalent geometry    : angle       0.56909 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 173
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.8083 (m-80) cc_final: 0.7102 (t80)
REVERT: A  122 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7674 (tm-30)
REVERT: A  130 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8140 (mtt)
REVERT: A  186 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7831 (m)
REVERT: A  330 ARG cc_start: 0.7707 (mtm180) cc_final: 0.7308 (mtm-85)
REVERT: A  397 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8181 (mm)
REVERT: A  462 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8023 (mm-30)
REVERT: B  314 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8065 (tp)
REVERT: B  330 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7363 (mtm-85)
REVERT: B  397 ILE cc_start: 0.8588 (mm) cc_final: 0.8299 (mm)
REVERT: B  462 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7817 (mt-10)
REVERT: C   63 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7318 (ptpt)
REVERT: C  111 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7890 (mp)
REVERT: C  330 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7318 (mtm110)
REVERT: C  332 LEU cc_start: 0.8445 (tp) cc_final: 0.8204 (mp)
REVERT: C  383 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7998 (tp)
REVERT: C  462 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8007 (mm-30)
  outliers start: 65
  outliers final: 50
  residues processed: 219
  average time/residue: 0.2420
  time to fit residues: 78.6867
Evaluate side-chains
  233 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 172
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain C residue   63 LYS
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  563 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 114 optimal weight:    0.6980
   chunk 5 optimal weight:    8.9990
   chunk 121 optimal weight:    0.9990
   chunk 150 optimal weight:    0.3980
   chunk 172 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 124 optimal weight:    0.0980
   chunk 112 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.168439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.128966 restraints weight = 14292.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.89
r_work: 0.3374 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13788  Z= 0.108
  Angle     :  0.501  11.336  18774  Z= 0.257
  Chirality :  0.042   0.139   2184
  Planarity :  0.004   0.033   2439
  Dihedral  :  4.760  54.346   2055
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.17 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 (0.20), residues: 1755
  helix:  2.07 (0.22), residues: 558
  sheet:  0.67 (0.24), residues: 444
  loop : -0.47 (0.23), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 173 
 HIS   0.002   0.000   HIS B 370 
 PHE   0.014   0.001   PHE A 157 
 TYR   0.011   0.001   TYR A 412 
 ARG   0.004   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03172 (  720)
  hydrogen bonds       : angle       4.48421 ( 1980)
  covalent geometry    : bond        0.00255 (13788)
  covalent geometry    : angle       0.50078 (18774)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 174
  time to evaluate  : 1.446 
Fit side-chains
REVERT: A   66 PHE cc_start: 0.8000 (m-80) cc_final: 0.7102 (t80)
REVERT: A  122 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7676 (tm-30)
REVERT: A  130 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8082 (mtt)
REVERT: A  330 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7224 (mtm-85)
REVERT: A  397 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8175 (mm)
REVERT: A  462 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7898 (mm-30)
REVERT: B   66 PHE cc_start: 0.7969 (m-80) cc_final: 0.7300 (t80)
REVERT: B  314 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8084 (tp)
REVERT: B  330 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7437 (mtm-85)
REVERT: B  397 ILE cc_start: 0.8544 (mm) cc_final: 0.8274 (mm)
REVERT: C   63 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7151 (ptpt)
REVERT: C  111 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7763 (mp)
REVERT: C  330 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7250 (mtm110)
REVERT: C  332 LEU cc_start: 0.8427 (tp) cc_final: 0.8188 (mp)
REVERT: C  346 PHE cc_start: 0.7311 (m-80) cc_final: 0.6980 (m-80)
REVERT: C  383 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7953 (tp)
REVERT: C  462 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7886 (mm-30)
  outliers start: 53
  outliers final: 42
  residues processed: 209
  average time/residue: 0.2541
  time to fit residues: 78.4615
Evaluate side-chains
  223 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 172
  time to evaluate  : 1.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   63 LYS
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  339 GLN
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 119 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 143 optimal weight:    6.9990
   chunk 142 optimal weight:    4.9990
   chunk 137 optimal weight:    2.9990
   chunk 150 optimal weight:    0.3980
   chunk 164 optimal weight:    0.3980
   chunk 28 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.165777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.125128 restraints weight = 14531.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.97
r_work: 0.3337 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13788  Z= 0.134
  Angle     :  0.518  11.206  18774  Z= 0.265
  Chirality :  0.043   0.138   2184
  Planarity :  0.004   0.033   2439
  Dihedral  :  4.776  55.225   2055
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.54 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.94 (0.20), residues: 1755
  helix:  2.00 (0.22), residues: 561
  sheet:  0.66 (0.24), residues: 444
  loop : -0.43 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 173 
 HIS   0.001   0.000   HIS C 410 
 PHE   0.014   0.001   PHE A 157 
 TYR   0.011   0.001   TYR A 412 
 ARG   0.004   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 (  720)
  hydrogen bonds       : angle       4.53636 ( 1980)
  covalent geometry    : bond        0.00326 (13788)
  covalent geometry    : angle       0.51777 (18774)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8875.19 seconds
wall clock time: 162 minutes 33.99 seconds (9753.99 seconds total)