Starting phenix.real_space_refine
on Wed May 14 10:00:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eoa_28332/05_2025/8eoa_28332.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eoa_28332/05_2025/8eoa_28332.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eoa_28332/05_2025/8eoa_28332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eoa_28332/05_2025/8eoa_28332.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eoa_28332/05_2025/8eoa_28332.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eoa_28332/05_2025/8eoa_28332.cif"
  }
  resolution = 3.9
  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=  -0.007 sd=   0.728
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       6      5.49       5
     Mg      2      5.21       5
     S      56      5.16       5
     C    7298      2.51       5
     N    1939      2.21       5
     O    2234      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11535
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 629, 5092
          Classifications: {'peptide': 629}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 611}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 5072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 5072
          Classifications: {'peptide': 627}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 609}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 1307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1307
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 7, 'TRANS': 157}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   ASP C   7 " occ=0.93
      ... (6 atoms not shown)
      pdb=" OD2 ASP C   7 " occ=0.93
    residue:
      pdb=" N   LEU C  10 " occ=0.93
      ... (6 atoms not shown)
      pdb=" CD2 LEU C  10 " occ=0.93
    residue:
      pdb=" N   LEU C  11 " occ=0.93
      ... (6 atoms not shown)
      pdb=" CD2 LEU C  11 " occ=0.93
    residue:
      pdb=" N   LEU C  12 " occ=0.93
      ... (6 atoms not shown)
      pdb=" CD2 LEU C  12 " occ=0.93
  Time building chain proxies: 6.98, per 1000 atoms: 0.61
  Number of scatterers: 11535
  At special positions: 0
  Unit cell: (94.848, 114.816, 131.04, 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      56     16.00
     P       6     15.00
     Mg      2     11.99
     O    2234      8.00
     N    1939      7.00
     C    7298      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: 2.87
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2696

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      43.7% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 31
    Processing helix  chain 'A' and resid 35 through 37
      No H-bonds generated for 'chain 'A' and resid 35 through 37'
    Processing helix  chain 'A' and resid 38 through 60
      removed outlier: 3.810A  pdb=" N   ILE A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR A  60 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 94 through 101
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 132 through 138
    Processing helix  chain 'A' and resid 190 through 193
    Processing helix  chain 'A' and resid 194 through 205
    Processing helix  chain 'A' and resid 287 through 291
      removed outlier: 3.868A  pdb=" N   THR A 290 " --> pdb=" O   PRO A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 310
    Processing helix  chain 'A' and resid 371 through 375
    Processing helix  chain 'A' and resid 397 through 420
      removed outlier: 4.105A  pdb=" N   LEU A 401 " --> pdb=" O   GLN A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 444
      removed outlier: 6.466A  pdb=" N   LYS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ASN A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 454
      removed outlier: 3.786A  pdb=" N   LEU A 451 " --> pdb=" O   ASN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 476
    Processing helix  chain 'A' and resid 490 through 496
    Processing helix  chain 'A' and resid 500 through 506
    Processing helix  chain 'A' and resid 516 through 525
      removed outlier: 4.249A  pdb=" N   TYR A 520 " --> pdb=" O   PRO A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 560
    Processing helix  chain 'A' and resid 560 through 571
    Processing helix  chain 'A' and resid 599 through 607
    Processing helix  chain 'A' and resid 613 through 618
      removed outlier: 3.733A  pdb=" N   GLY A 618 " --> pdb=" O   ASN A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 645
    Processing helix  chain 'A' and resid 648 through 666
    Processing helix  chain 'A' and resid 672 through 689
      removed outlier: 3.924A  pdb=" N   HIS A 676 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 31
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'B' and resid 38 through 60
      removed outlier: 4.066A  pdb=" N   THR B  60 " --> pdb=" O   TYR B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 66
    Processing helix  chain 'B' and resid 94 through 101
    Processing helix  chain 'B' and resid 108 through 116
      removed outlier: 3.681A  pdb=" N   ALA B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 138
    Processing helix  chain 'B' and resid 190 through 193
    Processing helix  chain 'B' and resid 194 through 206
    Processing helix  chain 'B' and resid 297 through 310
    Processing helix  chain 'B' and resid 371 through 375
    Processing helix  chain 'B' and resid 397 through 420
      removed outlier: 3.905A  pdb=" N   LEU B 401 " --> pdb=" O   GLN B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 444
      removed outlier: 6.444A  pdb=" N   LYS B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   ASN B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 452
    Processing helix  chain 'B' and resid 469 through 476
    Processing helix  chain 'B' and resid 490 through 496
    Processing helix  chain 'B' and resid 499 through 506
      removed outlier: 4.669A  pdb=" N   VAL B 503 " --> pdb=" O   PHE B 499 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS B 505 " --> pdb=" O   GLU B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 525
      removed outlier: 4.343A  pdb=" N   TYR B 520 " --> pdb=" O   PRO B 516 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLN B 524 " --> pdb=" O   TYR B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 571
      removed outlier: 5.397A  pdb=" N   ASN B 562 " --> pdb=" O   ALA B 558 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   LEU B 563 " --> pdb=" O   LYS B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 608
    Processing helix  chain 'B' and resid 616 through 621
      removed outlier: 3.819A  pdb=" N   MET B 620 " --> pdb=" O   THR B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 645
    Processing helix  chain 'B' and resid 648 through 667
      removed outlier: 3.514A  pdb=" N   GLY B 667 " --> pdb=" O   LEU B 663 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 689
      removed outlier: 3.775A  pdb=" N   HIS B 676 " --> pdb=" O   ASP B 672 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 61
    Processing helix  chain 'C' and resid 74 through 83
      removed outlier: 3.689A  pdb=" N   THR C  82 " --> pdb=" O   GLU C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 112
      removed outlier: 3.656A  pdb=" N   LEU C 105 " --> pdb=" O   VAL C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 133
    Processing helix  chain 'C' and resid 139 through 147
      removed outlier: 3.604A  pdb=" N   LYS C 147 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 3.652A  pdb=" N   LYS B 142 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ILE B  73 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   TYR B 216 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE B  75 " --> pdb=" O   TYR B 216 " (cutoff:3.500A)
      removed outlier: 8.304A  pdb=" N   GLU B 218 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19
      removed outlier: 6.748A  pdb=" N   GLN A  18 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215
      removed outlier: 6.416A  pdb=" N   ILE A  73 " --> pdb=" O   THR A 214 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS A 142 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105
    Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 219
    Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 323
      removed outlier: 3.764A  pdb=" N   ALA A 317 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS A 354 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ILE A 353 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   ASP A 364 " --> pdb=" O   ILE A 353 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   LEU A 355 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 468
      removed outlier: 3.939A  pdb=" N   HIS A 458 " --> pdb=" O   TYR A 512 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   ILE A 483 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 577 through 580
    Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 323
      removed outlier: 7.457A  pdb=" N   ILE B 353 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   ASP B 364 " --> pdb=" O   ILE B 353 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   LEU B 355 " --> pdb=" O   ILE B 362 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 468
      removed outlier: 3.804A  pdb=" N   HIS B 458 " --> pdb=" O   TYR B 512 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ILE B 483 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 577 through 580
    Processing sheet with id=AB3, first strand: chain 'C' and resid 17 through 21
      removed outlier: 3.805A  pdb=" N   LEU C 152 " --> pdb=" O   CYS C  94 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL C 153 " --> pdb=" O   MET C  45 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   THR C  39 " --> pdb=" O   LEU C 159 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   VAL C 161 " --> pdb=" O   ARG C  37 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ARG C  37 " --> pdb=" O   VAL C 161 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   LYS C  46 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   VAL C  53 " --> pdb=" O   LYS C  46 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 21
      removed outlier: 3.805A  pdb=" N   LEU C 152 " --> pdb=" O   CYS C  94 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL C 153 " --> pdb=" O   MET C  45 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   THR C  39 " --> pdb=" O   LEU C 159 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   VAL C 161 " --> pdb=" O   ARG C  37 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ARG C  37 " --> pdb=" O   VAL C 161 " (cutoff:3.500A)

    562 hydrogen bonds defined for protein.
    1560 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: 3.55

  Time building geometry restraints manager: 3.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3772
        1.34 -     1.46: 2432
        1.46 -     1.58: 5426
        1.58 -     1.69: 8
        1.69 -     1.81: 97
  Bond restraints: 11735
  Sorted by residual:
  bond pdb=" O3A ANP A 801 "
       pdb=" PB  ANP A 801 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" O3A ANP B 801 "
       pdb=" PB  ANP B 801 "
    ideal  model  delta    sigma   weight residual
    1.700  1.553  0.147 2.00e-02 2.50e+03 5.38e+01
  bond pdb=" N3B ANP A 801 "
       pdb=" PG  ANP A 801 "
    ideal  model  delta    sigma   weight residual
    1.795  1.688  0.107 2.00e-02 2.50e+03 2.89e+01
  bond pdb=" N3B ANP B 801 "
       pdb=" PG  ANP B 801 "
    ideal  model  delta    sigma   weight residual
    1.795  1.688  0.107 2.00e-02 2.50e+03 2.86e+01
  bond pdb=" O5' ANP A 801 "
       pdb=" PA  ANP A 801 "
    ideal  model  delta    sigma   weight residual
    1.655  1.573  0.082 2.00e-02 2.50e+03 1.67e+01
  ... (remaining 11730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.71: 15758
        3.71 -     7.42: 36
        7.42 -    11.13: 8
       11.13 -    14.83: 0
       14.83 -    18.54: 2
  Bond angle restraints: 15804
  Sorted by residual:
  angle pdb=" PB  ANP A 801 "
        pdb=" N3B ANP A 801 "
        pdb=" PG  ANP A 801 "
      ideal   model   delta    sigma   weight residual
     126.95  108.41   18.54 3.00e+00 1.11e-01 3.82e+01
  angle pdb=" PB  ANP B 801 "
        pdb=" N3B ANP B 801 "
        pdb=" PG  ANP B 801 "
      ideal   model   delta    sigma   weight residual
     126.95  110.11   16.84 3.00e+00 1.11e-01 3.15e+01
  angle pdb=" C   ASN B  46 "
        pdb=" CA  ASN B  46 "
        pdb=" CB  ASN B  46 "
      ideal   model   delta    sigma   weight residual
     110.92  105.37    5.55 1.59e+00 3.96e-01 1.22e+01
  angle pdb=" N   ASN B  46 "
        pdb=" CA  ASN B  46 "
        pdb=" C   ASN B  46 "
      ideal   model   delta    sigma   weight residual
     111.02  107.02    4.00 1.22e+00 6.72e-01 1.08e+01
  angle pdb=" O1B ANP A 801 "
        pdb=" PB  ANP A 801 "
        pdb=" O2B ANP A 801 "
      ideal   model   delta    sigma   weight residual
     120.08  110.25    9.83 3.00e+00 1.11e-01 1.07e+01
  ... (remaining 15799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.84: 7164
       34.84 -    69.68: 74
       69.68 -   104.52: 5
      104.52 -   139.35: 0
      139.35 -   174.19: 1
  Dihedral angle restraints: 7244
    sinusoidal: 3081
      harmonic: 4163
  Sorted by residual:
  dihedral pdb=" O1B ANP B 801 "
           pdb=" N3B ANP B 801 "
           pdb=" PB  ANP B 801 "
           pdb=" PG  ANP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15 -150.66 -174.19     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C   ASN B  46 "
           pdb=" N   ASN B  46 "
           pdb=" CA  ASN B  46 "
           pdb=" CB  ASN B  46 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.21   -8.39     0      2.50e+00 1.60e-01 1.13e+01
  dihedral pdb=" CA  ALA C 133 "
           pdb=" C   ALA C 133 "
           pdb=" N   TYR C 134 "
           pdb=" CA  TYR C 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.98  -16.02     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 7241 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1520
       0.056 -    0.112: 223
       0.112 -    0.168: 13
       0.168 -    0.224: 0
       0.224 -    0.280: 3
  Chirality restraints: 1759
  Sorted by residual:
  chirality pdb=" C3' ANP B 801 "
            pdb=" C2' ANP B 801 "
            pdb=" C4' ANP B 801 "
            pdb=" O3' ANP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" C3' ANP A 801 "
            pdb=" C2' ANP A 801 "
            pdb=" C4' ANP A 801 "
            pdb=" O3' ANP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  ASN B  46 "
            pdb=" N   ASN B  46 "
            pdb=" C   ASN B  46 "
            pdb=" CB  ASN B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1756 not shown)

  Planarity restraints: 2011
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 370 "   -0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO B 371 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 371 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 371 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 517 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   ILE A 517 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE A 517 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A 518 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 370 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A 371 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 371 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 371 "    0.024 5.00e-02 4.00e+02
  ... (remaining 2008 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.35: 17
        2.35 -     2.99: 6299
        2.99 -     3.63: 16858
        3.63 -     4.26: 25190
        4.26 -     4.90: 42571
  Nonbonded interactions: 90935
  Sorted by model distance:
  nonbonded pdb=" O2A ANP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.718 2.170
  nonbonded pdb=" N3B ANP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.887 2.250
  nonbonded pdb=" PG  ANP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.112 2.530
  nonbonded pdb=" N3B ANP A 801 "
            pdb=" O2A ANP A 801 "
     model   vdw
     2.122 3.120
  nonbonded pdb=" O3G ANP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.125 2.170
  ... (remaining 90930 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 11 through 220 or resid 275 through 691 or resid 801 throu \ 
gh 802))
  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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     27.590
  Find NCS groups from input model:        0.370
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
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      :  0.004   0.150  11735  Z= 0.197
  Angle     :  0.584  18.543  15804  Z= 0.287
  Chirality :  0.040   0.280   1759
  Planarity :  0.003   0.044   2011
  Dihedral  : 11.607 174.192   4548
  Min Nonbonded Distance : 1.718

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  7.04 %
    Favored  : 91.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.23), residues: 1411
  helix:  1.31 (0.23), residues: 568
  sheet:  0.07 (0.33), residues: 258
  loop : -0.86 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 312 
 HIS   0.004   0.001   HIS B 632 
 PHE   0.009   0.001   PHE A 668 
 TYR   0.016   0.001   TYR B 211 
 ARG   0.005   0.000   ARG B  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14279 (  547)
  hydrogen bonds       : angle       6.16189 ( 1560)
  covalent geometry    : bond        0.00394 (11735)
  covalent geometry    : angle       0.58427 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  387 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 366
  time to evaluate  : 1.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 MET cc_start: 0.8536 (tpp) cc_final: 0.7945 (tmm)
REVERT: A  606 MET cc_start: 0.8543 (ttm) cc_final: 0.8244 (tpp)
REVERT: A  611 LEU cc_start: 0.9302 (mm) cc_final: 0.8687 (tp)
REVERT: A  621 MET cc_start: 0.8701 (mmm) cc_final: 0.8458 (mmt)
REVERT: A  626 LEU cc_start: 0.9202 (tp) cc_final: 0.8961 (tp)
REVERT: B   25 MET cc_start: 0.8724 (tpp) cc_final: 0.8415 (tpp)
REVERT: B   49 ASP cc_start: 0.8465 (m-30) cc_final: 0.8134 (m-30)
REVERT: B  114 MET cc_start: 0.8558 (tpp) cc_final: 0.7980 (tpt)
REVERT: B  311 ASP cc_start: 0.8560 (t0) cc_final: 0.8198 (t0)
REVERT: B  362 ILE cc_start: 0.9469 (mm) cc_final: 0.9219 (tp)
REVERT: B  436 ASN cc_start: 0.9027 (m110) cc_final: 0.8595 (m-40)
REVERT: B  564 CYS cc_start: 0.9126 (m) cc_final: 0.8449 (m)
REVERT: B  606 MET cc_start: 0.8595 (mmt) cc_final: 0.8312 (mmt)
REVERT: B  681 TYR cc_start: 0.8381 (m-10) cc_final: 0.8081 (m-80)
REVERT: C    5 HIS cc_start: 0.6998 (m90) cc_final: 0.6354 (m170)
REVERT: C   40 PHE cc_start: 0.8601 (p90) cc_final: 0.7880 (p90)
REVERT: C   45 MET cc_start: 0.9074 (mpp) cc_final: 0.8498 (mpp)
REVERT: C   95 ASP cc_start: 0.8931 (m-30) cc_final: 0.8669 (m-30)
REVERT: C  139 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.5880 (t80)
REVERT: C  150 GLN cc_start: 0.7908 (mp10) cc_final: 0.7279 (mp-120)
  outliers start: 21
  outliers final: 6
  residues processed: 381
  average time/residue: 0.2538
  time to fit residues: 132.9138
Evaluate side-chains
  222 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 215
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 106 optimal weight:   10.0000
   chunk 58 optimal weight:   30.0000
   chunk 36 optimal weight:    0.8980
   chunk 71 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   chunk 109 optimal weight:    0.1980
   chunk 42 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 127 optimal weight:    8.9990
   overall best weight:    2.6184

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 640 GLN
B  80 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 352 ASN
B 407 ASN
B 609 GLN
C 146 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.066025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.051371 restraints weight = 49692.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.053390 restraints weight = 28084.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.054779 restraints weight = 18947.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3057
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11735  Z= 0.150
  Angle     :  0.627  11.608  15804  Z= 0.323
  Chirality :  0.042   0.187   1759
  Planarity :  0.004   0.052   2011
  Dihedral  :  7.985 173.152   1608
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.03 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1411
  helix:  1.56 (0.22), residues: 560
  sheet:  0.44 (0.33), residues: 263
  loop : -0.62 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 312 
 HIS   0.006   0.001   HIS A 676 
 PHE   0.017   0.001   PHE B 133 
 TYR   0.013   0.002   TYR A 457 
 ARG   0.003   0.000   ARG B 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03859 (  547)
  hydrogen bonds       : angle       4.64240 ( 1560)
  covalent geometry    : bond        0.00325 (11735)
  covalent geometry    : angle       0.62739 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 223
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.9382 (mm-40) cc_final: 0.8879 (mm-40)
REVERT: A   42 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8395 (mm-30)
REVERT: A  111 LYS cc_start: 0.9562 (ttmm) cc_final: 0.9341 (ttpt)
REVERT: A  114 MET cc_start: 0.9399 (tpp) cc_final: 0.8959 (tmm)
REVERT: A  200 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8929 (tm-30)
REVERT: A  441 ILE cc_start: 0.9628 (tp) cc_final: 0.9366 (pt)
REVERT: A  499 PHE cc_start: 0.9195 (m-80) cc_final: 0.8967 (m-10)
REVERT: A  602 MET cc_start: 0.9508 (tpp) cc_final: 0.9137 (tpp)
REVERT: A  603 GLU cc_start: 0.9554 (OUTLIER) cc_final: 0.9306 (tp30)
REVERT: A  606 MET cc_start: 0.9220 (ttm) cc_final: 0.8185 (tpp)
REVERT: A  621 MET cc_start: 0.8289 (mmm) cc_final: 0.7440 (mpp)
REVERT: B   49 ASP cc_start: 0.9078 (m-30) cc_final: 0.8806 (m-30)
REVERT: B  125 MET cc_start: 0.8154 (mtm) cc_final: 0.7946 (mtm)
REVERT: B  203 LYS cc_start: 0.9598 (mmmt) cc_final: 0.8923 (tppt)
REVERT: B  311 ASP cc_start: 0.8798 (t0) cc_final: 0.8583 (t0)
REVERT: B  337 ARG cc_start: 0.8614 (mtp180) cc_final: 0.8186 (ttm110)
REVERT: B  362 ILE cc_start: 0.9615 (mm) cc_final: 0.9316 (tp)
REVERT: B  436 ASN cc_start: 0.9373 (m110) cc_final: 0.8674 (m-40)
REVERT: B  471 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9231 (mt-10)
REVERT: B  564 CYS cc_start: 0.9245 (m) cc_final: 0.8989 (m)
REVERT: B  566 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8994 (mt)
REVERT: B  567 MET cc_start: 0.9309 (mtm) cc_final: 0.8920 (mtm)
REVERT: B  627 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8324 (pm20)
REVERT: B  681 TYR cc_start: 0.9099 (m-10) cc_final: 0.8621 (m-80)
REVERT: B  685 LYS cc_start: 0.9346 (mttt) cc_final: 0.9034 (mmtt)
REVERT: C   45 MET cc_start: 0.9158 (mpp) cc_final: 0.8526 (mpp)
REVERT: C   64 MET cc_start: 0.9070 (tmm) cc_final: 0.8865 (ppp)
REVERT: C   75 GLU cc_start: 0.9037 (pp20) cc_final: 0.8396 (mp0)
REVERT: C   84 MET cc_start: 0.8854 (tpp) cc_final: 0.8437 (tpp)
REVERT: C   95 ASP cc_start: 0.9043 (m-30) cc_final: 0.8731 (m-30)
REVERT: C  102 TYR cc_start: 0.9136 (t80) cc_final: 0.8716 (t80)
REVERT: C  143 ASP cc_start: 0.9688 (m-30) cc_final: 0.9486 (p0)
  outliers start: 19
  outliers final: 11
  residues processed: 235
  average time/residue: 0.2209
  time to fit residues: 75.3951
Evaluate side-chains
  194 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 181
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  566 LEU
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 112 optimal weight:   10.0000
   chunk 78 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 128 optimal weight:    9.9990
   chunk 101 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 127 optimal weight:   20.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.062612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.048156 restraints weight = 51432.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.050063 restraints weight = 28701.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.051440 restraints weight = 19316.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  11735  Z= 0.275
  Angle     :  0.674   7.222  15804  Z= 0.355
  Chirality :  0.042   0.141   1759
  Planarity :  0.004   0.044   2011
  Dihedral  :  8.233 174.357   1607
  Min Nonbonded Distance : 1.723

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.73 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.23), residues: 1411
  helix:  1.25 (0.22), residues: 565
  sheet:  0.52 (0.33), residues: 257
  loop : -0.74 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 312 
 HIS   0.012   0.001   HIS C   5 
 PHE   0.018   0.002   PHE B 429 
 TYR   0.017   0.002   TYR B 426 
 ARG   0.009   0.001   ARG B 679 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03963 (  547)
  hydrogen bonds       : angle       4.94144 ( 1560)
  covalent geometry    : bond        0.00574 (11735)
  covalent geometry    : angle       0.67442 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 178
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9062 (mt0)
REVERT: A   42 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8377 (mm-30)
REVERT: A  111 LYS cc_start: 0.9612 (ttmm) cc_final: 0.9365 (ttpt)
REVERT: A  114 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.9085 (tmm)
REVERT: A  200 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8872 (tm-30)
REVERT: A  394 MET cc_start: 0.8793 (ptp) cc_final: 0.8484 (ptm)
REVERT: A  567 MET cc_start: 0.9260 (mmm) cc_final: 0.8922 (mmm)
REVERT: A  602 MET cc_start: 0.9438 (tpp) cc_final: 0.9162 (tpp)
REVERT: A  606 MET cc_start: 0.9230 (ttm) cc_final: 0.8846 (tpt)
REVERT: A  617 MET cc_start: 0.7630 (mmm) cc_final: 0.7354 (mmm)
REVERT: A  683 MET cc_start: 0.8935 (tmm) cc_final: 0.8626 (ppp)
REVERT: B   49 ASP cc_start: 0.9068 (m-30) cc_final: 0.8807 (m-30)
REVERT: B  125 MET cc_start: 0.8309 (mtm) cc_final: 0.8077 (mtm)
REVERT: B  200 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: B  311 ASP cc_start: 0.8864 (t0) cc_final: 0.8400 (t0)
REVERT: B  385 ASP cc_start: 0.9201 (t0) cc_final: 0.8679 (p0)
REVERT: B  513 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7775 (mtm)
REVERT: B  553 MET cc_start: 0.8969 (ppp) cc_final: 0.8470 (ppp)
REVERT: B  564 CYS cc_start: 0.9285 (m) cc_final: 0.9077 (m)
REVERT: B  567 MET cc_start: 0.9344 (mtm) cc_final: 0.9000 (mtm)
REVERT: B  616 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8179 (p)
REVERT: B  627 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8335 (pm20)
REVERT: B  681 TYR cc_start: 0.9158 (m-10) cc_final: 0.8781 (m-80)
REVERT: C   45 MET cc_start: 0.9154 (mpp) cc_final: 0.8609 (mpp)
REVERT: C   62 GLN cc_start: 0.9481 (tp-100) cc_final: 0.9243 (tp-100)
REVERT: C  102 TYR cc_start: 0.9141 (t80) cc_final: 0.8770 (t80)
  outliers start: 33
  outliers final: 21
  residues processed: 200
  average time/residue: 0.1957
  time to fit residues: 60.1129
Evaluate side-chains
  183 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  678 ASN
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  294 ASP
Chi-restraints excluded: chain B residue  346 ASN
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  513 MET
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain B residue  616 THR
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 108 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 99 optimal weight:    7.9990
   chunk 133 optimal weight:    3.9990
   chunk 56 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  18 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 ASN
B 436 ASN
C 146 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.064003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.049458 restraints weight = 49769.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.051449 restraints weight = 27586.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.052856 restraints weight = 18499.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.4017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11735  Z= 0.154
  Angle     :  0.596   8.998  15804  Z= 0.309
  Chirality :  0.041   0.153   1759
  Planarity :  0.003   0.045   2011
  Dihedral  :  7.925 170.632   1607
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.65 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.23), residues: 1411
  helix:  1.28 (0.22), residues: 570
  sheet:  0.62 (0.33), residues: 263
  loop : -0.80 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 312 
 HIS   0.007   0.001   HIS C   5 
 PHE   0.016   0.001   PHE C  72 
 TYR   0.012   0.001   TYR A 596 
 ARG   0.006   0.000   ARG B 679 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  547)
  hydrogen bonds       : angle       4.62575 ( 1560)
  covalent geometry    : bond        0.00333 (11735)
  covalent geometry    : angle       0.59640 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 180
  time to evaluate  : 1.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8396 (mm-30)
REVERT: A  111 LYS cc_start: 0.9592 (ttmm) cc_final: 0.9363 (ttpt)
REVERT: A  114 MET cc_start: 0.9347 (tpp) cc_final: 0.9110 (tmm)
REVERT: A  200 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8872 (tm-30)
REVERT: A  394 MET cc_start: 0.8802 (ptp) cc_final: 0.8511 (ptm)
REVERT: A  481 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9120 (mtmm)
REVERT: A  567 MET cc_start: 0.9514 (mmm) cc_final: 0.9052 (mmm)
REVERT: A  602 MET cc_start: 0.9449 (tpp) cc_final: 0.9148 (tpp)
REVERT: A  606 MET cc_start: 0.9165 (ttm) cc_final: 0.8730 (tpt)
REVERT: A  660 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8763 (mt-10)
REVERT: A  679 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8256 (mtt-85)
REVERT: B   49 ASP cc_start: 0.8968 (m-30) cc_final: 0.8699 (m-30)
REVERT: B   93 MET cc_start: 0.7929 (ttp) cc_final: 0.7472 (tmm)
REVERT: B  200 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8644 (tm-30)
REVERT: B  311 ASP cc_start: 0.8895 (t0) cc_final: 0.8440 (t0)
REVERT: B  362 ILE cc_start: 0.9401 (mm) cc_final: 0.9040 (tp)
REVERT: B  365 SER cc_start: 0.8736 (t) cc_final: 0.8513 (p)
REVERT: B  385 ASP cc_start: 0.9235 (t0) cc_final: 0.8495 (p0)
REVERT: B  476 MET cc_start: 0.8465 (ttt) cc_final: 0.7951 (tpt)
REVERT: B  553 MET cc_start: 0.9041 (ppp) cc_final: 0.8545 (ppp)
REVERT: B  564 CYS cc_start: 0.9293 (m) cc_final: 0.8973 (m)
REVERT: B  567 MET cc_start: 0.9350 (mtm) cc_final: 0.8934 (mtm)
REVERT: B  584 LEU cc_start: 0.8835 (mp) cc_final: 0.8231 (mp)
REVERT: B  590 CYS cc_start: 0.8297 (m) cc_final: 0.7767 (m)
REVERT: B  627 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8188 (pm20)
REVERT: B  653 ASP cc_start: 0.8378 (p0) cc_final: 0.8118 (m-30)
REVERT: B  681 TYR cc_start: 0.9272 (m-10) cc_final: 0.8748 (m-80)
REVERT: B  685 LYS cc_start: 0.9382 (mttt) cc_final: 0.9073 (mmtt)
REVERT: C   40 PHE cc_start: 0.9199 (p90) cc_final: 0.8809 (p90)
REVERT: C   45 MET cc_start: 0.9149 (mpp) cc_final: 0.8608 (mpp)
REVERT: C   62 GLN cc_start: 0.9482 (tp-100) cc_final: 0.9248 (tp-100)
REVERT: C   75 GLU cc_start: 0.9066 (pp20) cc_final: 0.8359 (mp0)
REVERT: C  102 TYR cc_start: 0.9096 (t80) cc_final: 0.8732 (t80)
REVERT: C  143 ASP cc_start: 0.9690 (m-30) cc_final: 0.9476 (p0)
  outliers start: 34
  outliers final: 21
  residues processed: 205
  average time/residue: 0.2005
  time to fit residues: 62.4772
Evaluate side-chains
  182 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  481 LYS
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  678 ASN
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  346 ASN
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 117 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 104 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 131 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 609 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.062251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.047796 restraints weight = 51099.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.049660 restraints weight = 28984.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.050977 restraints weight = 19694.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  11735  Z= 0.289
  Angle     :  0.690  12.085  15804  Z= 0.361
  Chirality :  0.043   0.161   1759
  Planarity :  0.004   0.045   2011
  Dihedral  :  8.134 172.855   1605
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.89 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.23), residues: 1411
  helix:  0.96 (0.22), residues: 572
  sheet:  0.65 (0.34), residues: 252
  loop : -0.92 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 312 
 HIS   0.005   0.001   HIS A 315 
 PHE   0.014   0.002   PHE A 361 
 TYR   0.019   0.002   TYR A 457 
 ARG   0.006   0.001   ARG B 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03863 (  547)
  hydrogen bonds       : angle       4.99662 ( 1560)
  covalent geometry    : bond        0.00601 (11735)
  covalent geometry    : angle       0.68974 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 160
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8385 (mm-30)
REVERT: A  111 LYS cc_start: 0.9615 (ttmm) cc_final: 0.9357 (ttpt)
REVERT: A  114 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9134 (tmm)
REVERT: A  200 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8865 (tm-30)
REVERT: A  394 MET cc_start: 0.8806 (ptp) cc_final: 0.8463 (ptm)
REVERT: A  481 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9088 (mtmm)
REVERT: A  567 MET cc_start: 0.9633 (mmm) cc_final: 0.9027 (mmm)
REVERT: A  602 MET cc_start: 0.9468 (tpp) cc_final: 0.9186 (tpp)
REVERT: A  606 MET cc_start: 0.9239 (ttm) cc_final: 0.8887 (tpt)
REVERT: A  621 MET cc_start: 0.8447 (mmt) cc_final: 0.8191 (mmt)
REVERT: A  660 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8854 (mt-10)
REVERT: B   49 ASP cc_start: 0.9037 (m-30) cc_final: 0.8778 (m-30)
REVERT: B   93 MET cc_start: 0.8362 (ttp) cc_final: 0.7585 (tmm)
REVERT: B  114 MET cc_start: 0.8843 (tpt) cc_final: 0.8616 (tpt)
REVERT: B  125 MET cc_start: 0.8442 (mtm) cc_final: 0.7957 (mtm)
REVERT: B  200 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8687 (tm-30)
REVERT: B  311 ASP cc_start: 0.8932 (t0) cc_final: 0.8452 (t0)
REVERT: B  513 MET cc_start: 0.7872 (mtm) cc_final: 0.7567 (mtm)
REVERT: B  553 MET cc_start: 0.8987 (ppp) cc_final: 0.8496 (ppp)
REVERT: B  564 CYS cc_start: 0.9367 (m) cc_final: 0.8722 (m)
REVERT: B  567 MET cc_start: 0.9385 (mtm) cc_final: 0.8936 (mtm)
REVERT: B  584 LEU cc_start: 0.8797 (mp) cc_final: 0.8237 (tp)
REVERT: B  590 CYS cc_start: 0.8364 (m) cc_final: 0.7638 (m)
REVERT: B  602 MET cc_start: 0.9004 (tpp) cc_final: 0.8739 (tpp)
REVERT: B  617 MET cc_start: 0.9024 (mtp) cc_final: 0.8475 (mmm)
REVERT: B  627 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8421 (pm20)
REVERT: B  660 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8694 (pt0)
REVERT: B  681 TYR cc_start: 0.9364 (m-10) cc_final: 0.8710 (m-80)
REVERT: B  685 LYS cc_start: 0.9419 (mttt) cc_final: 0.9106 (mmtt)
REVERT: C   45 MET cc_start: 0.9133 (mpp) cc_final: 0.8659 (mpp)
REVERT: C   62 GLN cc_start: 0.9495 (tp-100) cc_final: 0.9261 (tp-100)
REVERT: C   84 MET cc_start: 0.8687 (tpp) cc_final: 0.8480 (tpp)
REVERT: C  102 TYR cc_start: 0.9159 (t80) cc_final: 0.8782 (t80)
REVERT: C  139 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.6139 (t80)
  outliers start: 42
  outliers final: 28
  residues processed: 194
  average time/residue: 0.1874
  time to fit residues: 55.4151
Evaluate side-chains
  180 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  481 LYS
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  678 ASN
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  294 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  346 ASN
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain B residue  596 TYR
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 124 optimal weight:    0.0270
   chunk 15 optimal weight:    5.9990
   chunk 120 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 132 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   overall best weight:    2.2046

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.064197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.049562 restraints weight = 50142.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.051537 restraints weight = 28108.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.052931 restraints weight = 18893.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2995
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2995
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11735  Z= 0.132
  Angle     :  0.613  14.802  15804  Z= 0.309
  Chirality :  0.041   0.178   1759
  Planarity :  0.003   0.041   2011
  Dihedral  :  7.789 169.736   1605
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.67 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.23), residues: 1411
  helix:  1.17 (0.22), residues: 570
  sheet:  0.74 (0.34), residues: 259
  loop : -0.89 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 312 
 HIS   0.009   0.001   HIS C   5 
 PHE   0.016   0.001   PHE C  42 
 TYR   0.015   0.001   TYR A 457 
 ARG   0.002   0.000   ARG B 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03341 (  547)
  hydrogen bonds       : angle       4.56931 ( 1560)
  covalent geometry    : bond        0.00291 (11735)
  covalent geometry    : angle       0.61252 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 1.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LYS cc_start: 0.9593 (ttmm) cc_final: 0.9254 (ttpt)
REVERT: A  200 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8860 (tm-30)
REVERT: A  207 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8878 (tm-30)
REVERT: A  333 LEU cc_start: 0.9636 (mt) cc_final: 0.9429 (mp)
REVERT: A  394 MET cc_start: 0.8807 (ptp) cc_final: 0.8448 (ptm)
REVERT: A  481 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9058 (mtmm)
REVERT: A  567 MET cc_start: 0.9649 (mmm) cc_final: 0.9126 (mmm)
REVERT: A  602 MET cc_start: 0.9448 (tpp) cc_final: 0.9131 (tpp)
REVERT: A  606 MET cc_start: 0.9159 (ttm) cc_final: 0.8644 (tpt)
REVERT: A  621 MET cc_start: 0.8072 (mmt) cc_final: 0.7860 (mpp)
REVERT: A  660 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8856 (mt-10)
REVERT: A  679 ARG cc_start: 0.8875 (ttm110) cc_final: 0.8239 (mtt-85)
REVERT: B   49 ASP cc_start: 0.9078 (m-30) cc_final: 0.8662 (m-30)
REVERT: B   93 MET cc_start: 0.8144 (ttp) cc_final: 0.7405 (tmm)
REVERT: B  125 MET cc_start: 0.8270 (mtm) cc_final: 0.7762 (mtm)
REVERT: B  126 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7589 (mt)
REVERT: B  200 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8697 (tm-30)
REVERT: B  311 ASP cc_start: 0.8912 (t0) cc_final: 0.8400 (t0)
REVERT: B  328 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: B  362 ILE cc_start: 0.9432 (mm) cc_final: 0.9117 (tp)
REVERT: B  385 ASP cc_start: 0.9239 (t0) cc_final: 0.8589 (p0)
REVERT: B  476 MET cc_start: 0.8468 (ttt) cc_final: 0.8075 (tpt)
REVERT: B  513 MET cc_start: 0.7903 (mtm) cc_final: 0.7601 (mtm)
REVERT: B  553 MET cc_start: 0.9068 (ppp) cc_final: 0.8762 (ppp)
REVERT: B  563 LEU cc_start: 0.9509 (tp) cc_final: 0.9223 (tp)
REVERT: B  564 CYS cc_start: 0.9287 (m) cc_final: 0.8990 (m)
REVERT: B  567 MET cc_start: 0.9358 (mtm) cc_final: 0.8951 (ptp)
REVERT: B  584 LEU cc_start: 0.8937 (mp) cc_final: 0.8413 (mt)
REVERT: B  590 CYS cc_start: 0.8382 (m) cc_final: 0.7068 (m)
REVERT: B  617 MET cc_start: 0.8984 (mtp) cc_final: 0.8498 (mmm)
REVERT: B  627 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8290 (pm20)
REVERT: B  660 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8664 (pt0)
REVERT: B  681 TYR cc_start: 0.9271 (m-10) cc_final: 0.8615 (m-80)
REVERT: B  685 LYS cc_start: 0.9384 (mttt) cc_final: 0.9069 (mmtt)
REVERT: C   21 ILE cc_start: 0.9292 (mm) cc_final: 0.9075 (mm)
REVERT: C   45 MET cc_start: 0.9140 (mpp) cc_final: 0.8643 (mpp)
REVERT: C   62 GLN cc_start: 0.9463 (tp-100) cc_final: 0.9244 (tp-100)
REVERT: C   73 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9123 (pttt)
REVERT: C   75 GLU cc_start: 0.9048 (pp20) cc_final: 0.8353 (mp0)
REVERT: C   84 MET cc_start: 0.8536 (tpp) cc_final: 0.8260 (tpp)
REVERT: C   95 ASP cc_start: 0.9140 (m-30) cc_final: 0.8675 (m-30)
REVERT: C  102 TYR cc_start: 0.9119 (t80) cc_final: 0.8740 (t80)
REVERT: C  139 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.6096 (t80)
REVERT: C  143 ASP cc_start: 0.9685 (m-30) cc_final: 0.9446 (p0)
  outliers start: 32
  outliers final: 20
  residues processed: 203
  average time/residue: 0.1992
  time to fit residues: 61.9337
Evaluate side-chains
  179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  481 LYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  678 ASN
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain B residue  596 TYR
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 126 optimal weight:   10.0000
   chunk 111 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 136 optimal weight:   50.0000
   chunk 117 optimal weight:   20.0000
   chunk 125 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 601 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.063327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.048857 restraints weight = 51176.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.050763 restraints weight = 28659.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.052114 restraints weight = 19406.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11735  Z= 0.180
  Angle     :  0.632  12.933  15804  Z= 0.324
  Chirality :  0.043   0.285   1759
  Planarity :  0.003   0.040   2011
  Dihedral  :  7.790 172.680   1603
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.06 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.23), residues: 1411
  helix:  1.11 (0.22), residues: 571
  sheet:  0.74 (0.34), residues: 262
  loop : -0.99 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 312 
 HIS   0.007   0.001   HIS B 458 
 PHE   0.025   0.002   PHE C  40 
 TYR   0.016   0.001   TYR A 457 
 ARG   0.003   0.000   ARG B 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03436 (  547)
  hydrogen bonds       : angle       4.65348 ( 1560)
  covalent geometry    : bond        0.00386 (11735)
  covalent geometry    : angle       0.63250 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 159
  time to evaluate  : 1.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8772 (pmm)
REVERT: A  200 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8885 (tm-30)
REVERT: A  394 MET cc_start: 0.8815 (ptp) cc_final: 0.8473 (ptm)
REVERT: A  481 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9090 (mtmm)
REVERT: A  567 MET cc_start: 0.9658 (mmm) cc_final: 0.9159 (mmm)
REVERT: A  602 MET cc_start: 0.9482 (tpp) cc_final: 0.9045 (tpp)
REVERT: A  606 MET cc_start: 0.9182 (ttm) cc_final: 0.8727 (tpt)
REVERT: A  621 MET cc_start: 0.8416 (mmt) cc_final: 0.8034 (mmt)
REVERT: A  660 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8871 (mt-10)
REVERT: A  679 ARG cc_start: 0.8877 (ttm110) cc_final: 0.8251 (mtt-85)
REVERT: B   49 ASP cc_start: 0.9062 (m-30) cc_final: 0.8758 (m-30)
REVERT: B   93 MET cc_start: 0.8176 (ttp) cc_final: 0.7379 (tmm)
REVERT: B  125 MET cc_start: 0.8211 (mtm) cc_final: 0.7682 (mtm)
REVERT: B  311 ASP cc_start: 0.8958 (t0) cc_final: 0.8420 (t0)
REVERT: B  328 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8240 (tm-30)
REVERT: B  362 ILE cc_start: 0.9446 (mm) cc_final: 0.9139 (tp)
REVERT: B  385 ASP cc_start: 0.9218 (t0) cc_final: 0.8575 (p0)
REVERT: B  476 MET cc_start: 0.8447 (ttt) cc_final: 0.7890 (tpt)
REVERT: B  513 MET cc_start: 0.7929 (mtm) cc_final: 0.7597 (mtm)
REVERT: B  553 MET cc_start: 0.9002 (ppp) cc_final: 0.8695 (ppp)
REVERT: B  564 CYS cc_start: 0.9310 (m) cc_final: 0.8415 (m)
REVERT: B  567 MET cc_start: 0.9311 (mtm) cc_final: 0.8824 (mtm)
REVERT: B  584 LEU cc_start: 0.8936 (mp) cc_final: 0.8466 (mt)
REVERT: B  590 CYS cc_start: 0.8404 (m) cc_final: 0.6977 (m)
REVERT: B  617 MET cc_start: 0.8978 (mtp) cc_final: 0.8499 (mmm)
REVERT: B  627 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8186 (pm20)
REVERT: B  660 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8702 (pt0)
REVERT: B  685 LYS cc_start: 0.9405 (mttt) cc_final: 0.9102 (mmtt)
REVERT: C   21 ILE cc_start: 0.9162 (mm) cc_final: 0.8906 (mm)
REVERT: C   45 MET cc_start: 0.9152 (mpp) cc_final: 0.8670 (mpp)
REVERT: C   62 GLN cc_start: 0.9465 (tp-100) cc_final: 0.9248 (tp-100)
REVERT: C   75 GLU cc_start: 0.9045 (pp20) cc_final: 0.8341 (mp0)
REVERT: C   84 MET cc_start: 0.8549 (tpp) cc_final: 0.8263 (tpp)
REVERT: C   95 ASP cc_start: 0.9148 (m-30) cc_final: 0.8708 (m-30)
REVERT: C  102 TYR cc_start: 0.9160 (t80) cc_final: 0.8797 (t80)
REVERT: C  139 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6066 (t80)
  outliers start: 39
  outliers final: 23
  residues processed: 190
  average time/residue: 0.2045
  time to fit residues: 59.4553
Evaluate side-chains
  175 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  481 LYS
Chi-restraints excluded: chain A residue  555 GLU
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  678 ASN
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain B residue  596 TYR
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 94 optimal weight:    5.9990
   chunk 124 optimal weight:    6.9990
   chunk 139 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   chunk 104 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 101 optimal weight:    8.9990
   chunk 114 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0670
   chunk 116 optimal weight:    2.9990
   overall best weight:    1.8126

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.064891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.050217 restraints weight = 49928.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.052218 restraints weight = 27915.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.053615 restraints weight = 18777.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.4685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11735  Z= 0.121
  Angle     :  0.639  14.333  15804  Z= 0.317
  Chirality :  0.043   0.261   1759
  Planarity :  0.003   0.041   2011
  Dihedral  :  7.619 169.438   1601
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.00 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.23), residues: 1411
  helix:  1.16 (0.22), residues: 570
  sheet:  0.84 (0.34), residues: 262
  loop : -1.03 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 598 
 HIS   0.007   0.001   HIS B 458 
 PHE   0.021   0.001   PHE A 208 
 TYR   0.015   0.001   TYR A 457 
 ARG   0.002   0.000   ARG B 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03230 (  547)
  hydrogen bonds       : angle       4.50481 ( 1560)
  covalent geometry    : bond        0.00272 (11735)
  covalent geometry    : angle       0.63889 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 173
  time to evaluate  : 1.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.8332 (mtm) cc_final: 0.7813 (mpp)
REVERT: A  111 LYS cc_start: 0.9564 (ttmm) cc_final: 0.9338 (ttpt)
REVERT: A  125 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8797 (pmm)
REVERT: A  200 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8874 (tm-30)
REVERT: A  394 MET cc_start: 0.8799 (ptp) cc_final: 0.8454 (ptm)
REVERT: A  553 MET cc_start: 0.8554 (tpp) cc_final: 0.8296 (tmm)
REVERT: A  567 MET cc_start: 0.9703 (mmm) cc_final: 0.9223 (mmm)
REVERT: A  602 MET cc_start: 0.9508 (tpp) cc_final: 0.9103 (tpp)
REVERT: A  606 MET cc_start: 0.9176 (ttm) cc_final: 0.8565 (tpt)
REVERT: A  621 MET cc_start: 0.8105 (mmt) cc_final: 0.7724 (tpp)
REVERT: A  660 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9002 (mt-10)
REVERT: A  676 HIS cc_start: 0.9563 (t70) cc_final: 0.9339 (t-90)
REVERT: A  679 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8213 (mtt-85)
REVERT: B   49 ASP cc_start: 0.8984 (m-30) cc_final: 0.8763 (m-30)
REVERT: B  125 MET cc_start: 0.8114 (mtm) cc_final: 0.7610 (mtm)
REVERT: B  311 ASP cc_start: 0.8919 (t0) cc_final: 0.8417 (t0)
REVERT: B  328 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: B  362 ILE cc_start: 0.9448 (mm) cc_final: 0.9134 (tp)
REVERT: B  384 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8333 (tp30)
REVERT: B  385 ASP cc_start: 0.9142 (t0) cc_final: 0.8463 (p0)
REVERT: B  476 MET cc_start: 0.8425 (ttt) cc_final: 0.7887 (tpt)
REVERT: B  484 TYR cc_start: 0.9119 (m-80) cc_final: 0.8787 (m-10)
REVERT: B  513 MET cc_start: 0.7928 (mtm) cc_final: 0.7590 (mtm)
REVERT: B  553 MET cc_start: 0.9105 (ppp) cc_final: 0.8798 (ppp)
REVERT: B  563 LEU cc_start: 0.9467 (tp) cc_final: 0.9159 (tp)
REVERT: B  564 CYS cc_start: 0.9332 (m) cc_final: 0.8980 (p)
REVERT: B  567 MET cc_start: 0.9363 (mtm) cc_final: 0.8950 (ptp)
REVERT: B  584 LEU cc_start: 0.8927 (mp) cc_final: 0.8424 (mt)
REVERT: B  590 CYS cc_start: 0.8426 (m) cc_final: 0.7211 (m)
REVERT: B  606 MET cc_start: 0.8963 (mmt) cc_final: 0.8558 (mmp)
REVERT: B  617 MET cc_start: 0.8958 (mtp) cc_final: 0.8510 (mmm)
REVERT: B  627 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8218 (pm20)
REVERT: B  660 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8692 (pt0)
REVERT: B  685 LYS cc_start: 0.9373 (mttt) cc_final: 0.9050 (mmtt)
REVERT: C   21 ILE cc_start: 0.9183 (mm) cc_final: 0.8945 (mm)
REVERT: C   45 MET cc_start: 0.9161 (mpp) cc_final: 0.8802 (mpp)
REVERT: C   62 GLN cc_start: 0.9472 (tp-100) cc_final: 0.9265 (tp-100)
REVERT: C   64 MET cc_start: 0.9483 (ppp) cc_final: 0.9253 (ppp)
REVERT: C   75 GLU cc_start: 0.9018 (pp20) cc_final: 0.8315 (mp0)
REVERT: C   84 MET cc_start: 0.8501 (tpp) cc_final: 0.8198 (tpp)
REVERT: C   95 ASP cc_start: 0.9147 (m-30) cc_final: 0.8696 (m-30)
REVERT: C  102 TYR cc_start: 0.9161 (t80) cc_final: 0.8811 (t80)
REVERT: C  139 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.6102 (t80)
REVERT: C  143 ASP cc_start: 0.9660 (m-30) cc_final: 0.9410 (p0)
  outliers start: 29
  outliers final: 21
  residues processed: 196
  average time/residue: 0.1989
  time to fit residues: 58.5253
Evaluate side-chains
  185 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  678 ASN
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain B residue  596 TYR
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 58 optimal weight:    0.1980
   chunk 103 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 135 optimal weight:    3.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  23 GLN
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.065583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.050946 restraints weight = 49720.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.052969 restraints weight = 27696.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.054388 restraints weight = 18592.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.4800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11735  Z= 0.112
  Angle     :  0.658  12.424  15804  Z= 0.323
  Chirality :  0.043   0.343   1759
  Planarity :  0.003   0.039   2011
  Dihedral  :  7.509 167.793   1601
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.09 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.23), residues: 1411
  helix:  1.16 (0.22), residues: 570
  sheet:  0.97 (0.34), residues: 262
  loop : -1.04 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 598 
 HIS   0.006   0.001   HIS B 458 
 PHE   0.027   0.001   PHE C 154 
 TYR   0.019   0.001   TYR A 373 
 ARG   0.002   0.000   ARG B 679 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03157 (  547)
  hydrogen bonds       : angle       4.45039 ( 1560)
  covalent geometry    : bond        0.00254 (11735)
  covalent geometry    : angle       0.65756 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 171
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8471 (pt0)
REVERT: A  111 LYS cc_start: 0.9550 (ttmm) cc_final: 0.9329 (ttpt)
REVERT: A  125 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8682 (pmm)
REVERT: A  183 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9064 (pp)
REVERT: A  200 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8873 (tm-30)
REVERT: A  394 MET cc_start: 0.8843 (ptp) cc_final: 0.8597 (ptm)
REVERT: A  466 MET cc_start: 0.9490 (mmm) cc_final: 0.9160 (mmm)
REVERT: A  553 MET cc_start: 0.8505 (tpp) cc_final: 0.8284 (tmm)
REVERT: A  567 MET cc_start: 0.9719 (mmm) cc_final: 0.9243 (mmm)
REVERT: A  602 MET cc_start: 0.9522 (tpp) cc_final: 0.9071 (tpp)
REVERT: A  606 MET cc_start: 0.9134 (ttm) cc_final: 0.8497 (tpt)
REVERT: A  621 MET cc_start: 0.8012 (mmt) cc_final: 0.7565 (tpp)
REVERT: A  671 GLU cc_start: 0.8936 (mp0) cc_final: 0.8525 (pm20)
REVERT: B   33 TYR cc_start: 0.8917 (m-80) cc_final: 0.8476 (m-80)
REVERT: B   49 ASP cc_start: 0.8946 (m-30) cc_final: 0.8742 (m-30)
REVERT: B   93 MET cc_start: 0.8627 (ttp) cc_final: 0.7785 (tmm)
REVERT: B  125 MET cc_start: 0.7999 (mtm) cc_final: 0.7438 (mtm)
REVERT: B  311 ASP cc_start: 0.8909 (t0) cc_final: 0.8411 (t0)
REVERT: B  328 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: B  362 ILE cc_start: 0.9441 (mm) cc_final: 0.9145 (tp)
REVERT: B  364 ASP cc_start: 0.8717 (t0) cc_final: 0.8424 (t0)
REVERT: B  385 ASP cc_start: 0.9120 (t0) cc_final: 0.8386 (p0)
REVERT: B  476 MET cc_start: 0.8352 (ttt) cc_final: 0.7982 (tpt)
REVERT: B  484 TYR cc_start: 0.9168 (m-80) cc_final: 0.8807 (m-10)
REVERT: B  513 MET cc_start: 0.7825 (mtm) cc_final: 0.7535 (mtm)
REVERT: B  515 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8602 (mp0)
REVERT: B  553 MET cc_start: 0.9081 (ppp) cc_final: 0.8765 (ppp)
REVERT: B  564 CYS cc_start: 0.9288 (m) cc_final: 0.8705 (m)
REVERT: B  567 MET cc_start: 0.9199 (mtm) cc_final: 0.8661 (mtm)
REVERT: B  584 LEU cc_start: 0.8965 (mp) cc_final: 0.8454 (mt)
REVERT: B  590 CYS cc_start: 0.8392 (m) cc_final: 0.7198 (m)
REVERT: B  606 MET cc_start: 0.8954 (mmt) cc_final: 0.8604 (mmm)
REVERT: B  617 MET cc_start: 0.8963 (mtp) cc_final: 0.8484 (mmm)
REVERT: B  627 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8213 (pm20)
REVERT: B  640 GLN cc_start: 0.9466 (mt0) cc_final: 0.9162 (tp-100)
REVERT: B  660 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8697 (pt0)
REVERT: B  685 LYS cc_start: 0.9390 (mttt) cc_final: 0.9058 (mmtt)
REVERT: C   21 ILE cc_start: 0.9123 (mm) cc_final: 0.8806 (mm)
REVERT: C   45 MET cc_start: 0.9150 (mpp) cc_final: 0.8771 (mpp)
REVERT: C   75 GLU cc_start: 0.9012 (pp20) cc_final: 0.8305 (mp0)
REVERT: C   84 MET cc_start: 0.8504 (tpp) cc_final: 0.8097 (tpp)
REVERT: C   95 ASP cc_start: 0.9149 (m-30) cc_final: 0.8710 (m-30)
REVERT: C  102 TYR cc_start: 0.9142 (t80) cc_final: 0.8820 (t80)
REVERT: C  139 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.6181 (t80)
REVERT: C  143 ASP cc_start: 0.9659 (m-30) cc_final: 0.9406 (p0)
  outliers start: 19
  outliers final: 14
  residues processed: 185
  average time/residue: 0.1954
  time to fit residues: 55.0638
Evaluate side-chains
  178 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 160
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLN
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 120 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 118 optimal weight:    5.9990
   chunk 110 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 104 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0010
   overall best weight:    6.1994

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.062869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.048250 restraints weight = 51893.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.050145 restraints weight = 29559.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.051503 restraints weight = 20100.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2953
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.4920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  11735  Z= 0.274
  Angle     :  0.729  13.462  15804  Z= 0.376
  Chirality :  0.045   0.303   1759
  Planarity :  0.004   0.038   2011
  Dihedral  :  7.883 174.454   1601
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.09 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.23), residues: 1411
  helix:  1.02 (0.22), residues: 570
  sheet:  0.83 (0.34), residues: 262
  loop : -1.13 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 598 
 HIS   0.006   0.001   HIS C   5 
 PHE   0.031   0.002   PHE A 208 
 TYR   0.026   0.002   TYR A 457 
 ARG   0.004   0.001   ARG B 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 (  547)
  hydrogen bonds       : angle       4.89421 ( 1560)
  covalent geometry    : bond        0.00579 (11735)
  covalent geometry    : angle       0.72909 (15804)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 1.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LYS cc_start: 0.9601 (ttmm) cc_final: 0.9381 (ttpt)
REVERT: A  125 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8733 (pmm)
REVERT: A  200 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8885 (tm-30)
REVERT: A  394 MET cc_start: 0.8825 (ptp) cc_final: 0.8501 (ptm)
REVERT: A  567 MET cc_start: 0.9692 (mmm) cc_final: 0.9163 (mmm)
REVERT: A  602 MET cc_start: 0.9528 (tpp) cc_final: 0.9230 (tpp)
REVERT: A  606 MET cc_start: 0.9202 (ttm) cc_final: 0.8898 (tpt)
REVERT: A  619 TYR cc_start: 0.7458 (m-10) cc_final: 0.7080 (m-80)
REVERT: A  621 MET cc_start: 0.8475 (mmt) cc_final: 0.7954 (mpp)
REVERT: B   25 MET cc_start: 0.9551 (tpp) cc_final: 0.9298 (tpp)
REVERT: B   49 ASP cc_start: 0.9088 (m-30) cc_final: 0.8785 (m-30)
REVERT: B   93 MET cc_start: 0.8772 (ttp) cc_final: 0.8097 (tmm)
REVERT: B  125 MET cc_start: 0.8182 (mtm) cc_final: 0.7626 (mtm)
REVERT: B  311 ASP cc_start: 0.8988 (t0) cc_final: 0.8548 (t0)
REVERT: B  362 ILE cc_start: 0.9432 (mm) cc_final: 0.9215 (tp)
REVERT: B  385 ASP cc_start: 0.9214 (t0) cc_final: 0.8655 (p0)
REVERT: B  513 MET cc_start: 0.8023 (mtm) cc_final: 0.7678 (mtm)
REVERT: B  515 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8523 (mp0)
REVERT: B  553 MET cc_start: 0.8987 (ppp) cc_final: 0.8670 (ppp)
REVERT: B  567 MET cc_start: 0.9302 (mtm) cc_final: 0.8850 (mtm)
REVERT: B  590 CYS cc_start: 0.8314 (m) cc_final: 0.7772 (m)
REVERT: B  606 MET cc_start: 0.8934 (mmt) cc_final: 0.8583 (mmm)
REVERT: B  617 MET cc_start: 0.8944 (mtp) cc_final: 0.8446 (mmm)
REVERT: B  627 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8303 (mt-10)
REVERT: B  660 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8753 (pt0)
REVERT: B  685 LYS cc_start: 0.9433 (mttt) cc_final: 0.9110 (mmtt)
REVERT: C   45 MET cc_start: 0.9037 (mpp) cc_final: 0.8536 (mpp)
REVERT: C   95 ASP cc_start: 0.9186 (m-30) cc_final: 0.8710 (m-30)
REVERT: C  102 TYR cc_start: 0.9246 (t80) cc_final: 0.8918 (t80)
REVERT: C  139 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.6109 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 164
  average time/residue: 0.1868
  time to fit residues: 47.6291
Evaluate side-chains
  161 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 1.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  678 ASN
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain B residue  596 TYR
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  139 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 131 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0980
   chunk 40 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.065096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.050520 restraints weight = 50085.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.052524 restraints weight = 27988.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.053891 restraints weight = 18766.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.4973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11735  Z= 0.127
  Angle     :  0.697  13.648  15804  Z= 0.345
  Chirality :  0.044   0.310   1759
  Planarity :  0.003   0.039   2011
  Dihedral  :  7.650 169.993   1601
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 21.19 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.23), residues: 1411
  helix:  1.07 (0.22), residues: 570
  sheet:  1.00 (0.34), residues: 265
  loop : -1.12 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 598 
 HIS   0.006   0.001   HIS B 458 
 PHE   0.029   0.001   PHE C 154 
 TYR   0.032   0.001   TYR A 457 
 ARG   0.002   0.000   ARG B 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  547)
  hydrogen bonds       : angle       4.65708 ( 1560)
  covalent geometry    : bond        0.00288 (11735)
  covalent geometry    : angle       0.69743 (15804)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3483.20 seconds
wall clock time: 62 minutes 11.47 seconds (3731.47 seconds total)