Starting phenix.real_space_refine
on Sat Aug 23 11:10:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eoa_28332/08_2025/8eoa_28332.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eoa_28332/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eoa_28332/08_2025/8eoa_28332.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eoa_28332/08_2025/8eoa_28332.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eoa_28332/08_2025/8eoa_28332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eoa_28332/08_2025/8eoa_28332.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.007 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.76, per 1000 atoms: 0.24
  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: 1.07
  Conformation dependent library (CDL) restraints added in 657.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.34
  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: 1.60

  Time building geometry restraints manager: 1.44 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 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:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.200
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.420
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.000   ARG B  41 
 TYR   0.016   0.001   TYR B 211 
 PHE   0.009   0.001   PHE A 668 
 TRP   0.018   0.002   TRP A 312 
 HIS   0.004   0.001   HIS B 632 

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

*********************** 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  : 0.446 
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: 0.8243 (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: 0.8960 (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: 0.8596 (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: 0.8318 (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: 0.8499 (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: 0.1026
  time to fit residues: 53.8245
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  : 0.298 
-------------------------------------------------------------------------------
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 98 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0170
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.5224

-------------------------------------------------------------------------------
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  18 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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.066048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.051398 restraints weight = 49831.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.053407 restraints weight = 28069.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.054833 restraints weight = 18903.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.055850 restraints weight = 14186.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.056590 restraints weight = 11437.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11735  Z= 0.150
  Angle     :  0.626  11.420  15804  Z= 0.323
  Chirality :  0.042   0.216   1759
  Planarity :  0.004   0.053   2011
  Dihedral  :  7.962 172.415   1608
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.26 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.23), residues: 1411
  helix:  1.58 (0.22), residues: 560
  sheet:  0.47 (0.34), residues: 262
  loop : -0.62 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 583 
 TYR   0.013   0.002   TYR A 457 
 PHE   0.017   0.002   PHE B 133 
 TRP   0.014   0.002   TRP B 312 
 HIS   0.006   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11735)
  covalent geometry    : angle       0.62649 (15804)
  hydrogen bonds       : bond        0.03896 (  547)
  hydrogen bonds       : angle       4.65687 ( 1560)

*********************** 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
  243 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 224
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8848 (mm-40)
REVERT: A   42 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8391 (mm-30)
REVERT: A  114 MET cc_start: 0.9329 (tpp) cc_final: 0.8881 (tmm)
REVERT: A  200 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: A  441 ILE cc_start: 0.9635 (tp) cc_final: 0.9366 (pt)
REVERT: A  499 PHE cc_start: 0.9200 (m-80) cc_final: 0.8967 (m-10)
REVERT: A  513 MET cc_start: 0.8583 (mtt) cc_final: 0.8333 (mtt)
REVERT: A  602 MET cc_start: 0.9518 (tpp) cc_final: 0.9143 (tpp)
REVERT: A  603 GLU cc_start: 0.9544 (OUTLIER) cc_final: 0.9300 (tp30)
REVERT: A  606 MET cc_start: 0.9215 (ttm) cc_final: 0.8188 (tpp)
REVERT: A  621 MET cc_start: 0.8320 (mmm) cc_final: 0.7436 (mpp)
REVERT: A  672 ASP cc_start: 0.8988 (t70) cc_final: 0.8719 (p0)
REVERT: B   49 ASP cc_start: 0.9021 (m-30) cc_final: 0.8797 (m-30)
REVERT: B  203 LYS cc_start: 0.9600 (mmmt) cc_final: 0.8916 (tppt)
REVERT: B  311 ASP cc_start: 0.8796 (t0) cc_final: 0.8581 (t0)
REVERT: B  337 ARG cc_start: 0.8612 (mtp180) cc_final: 0.8141 (ttm110)
REVERT: B  362 ILE cc_start: 0.9610 (mm) cc_final: 0.9324 (tp)
REVERT: B  436 ASN cc_start: 0.9354 (m110) cc_final: 0.8655 (m-40)
REVERT: B  553 MET cc_start: 0.9357 (tmm) cc_final: 0.8849 (ppp)
REVERT: B  564 CYS cc_start: 0.9227 (m) cc_final: 0.9005 (m)
REVERT: B  566 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9018 (mt)
REVERT: B  567 MET cc_start: 0.9265 (mtm) cc_final: 0.8886 (mtm)
REVERT: B  627 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8308 (pm20)
REVERT: B  681 TYR cc_start: 0.9070 (m-10) cc_final: 0.8597 (m-80)
REVERT: B  685 LYS cc_start: 0.9307 (mttt) cc_final: 0.8999 (mmtt)
REVERT: C   45 MET cc_start: 0.9129 (mpp) cc_final: 0.8532 (mpp)
REVERT: C   95 ASP cc_start: 0.9047 (m-30) cc_final: 0.8713 (m-30)
REVERT: C  102 TYR cc_start: 0.9110 (t80) cc_final: 0.8690 (t80)
REVERT: C  143 ASP cc_start: 0.9685 (m-30) cc_final: 0.9481 (p0)
  outliers start: 19
  outliers final: 11
  residues processed: 236
  average time/residue: 0.0888
  time to fit residues: 30.7854
Evaluate side-chains
  193 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 180
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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 34 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0270
   overall best weight:    2.4044

-------------------------------------------------------------------------------
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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.065068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.050391 restraints weight = 50075.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.052421 restraints weight = 27702.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.053842 restraints weight = 18507.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.054851 restraints weight = 13823.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.055551 restraints weight = 11111.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    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 = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11735  Z= 0.140
  Angle     :  0.594   8.399  15804  Z= 0.305
  Chirality :  0.041   0.139   1759
  Planarity :  0.003   0.045   2011
  Dihedral  :  7.775 170.847   1607
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.03 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.23), residues: 1411
  helix:  1.49 (0.22), residues: 564
  sheet:  0.59 (0.33), residues: 262
  loop : -0.69 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 679 
 TYR   0.014   0.001   TYR A 373 
 PHE   0.016   0.001   PHE B 133 
 TRP   0.008   0.001   TRP A 157 
 HIS   0.011   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11735)
  covalent geometry    : angle       0.59397 (15804)
  hydrogen bonds       : bond        0.03421 (  547)
  hydrogen bonds       : angle       4.49625 ( 1560)

*********************** 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
  222 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 0.432 
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: 0.9423 (mm-40) cc_final: 0.9059 (mm-40)
REVERT: A   42 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8290 (mm-30)
REVERT: A   93 MET cc_start: 0.8086 (mtm) cc_final: 0.7778 (mtm)
REVERT: A  114 MET cc_start: 0.9303 (tpp) cc_final: 0.9047 (tmm)
REVERT: A  200 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8854 (tm-30)
REVERT: A  394 MET cc_start: 0.8733 (ptp) cc_final: 0.8395 (ptm)
REVERT: A  476 MET cc_start: 0.8486 (ttt) cc_final: 0.7841 (tpp)
REVERT: A  513 MET cc_start: 0.8617 (mtt) cc_final: 0.8254 (mtt)
REVERT: A  567 MET cc_start: 0.9199 (mmm) cc_final: 0.8851 (mmm)
REVERT: A  602 MET cc_start: 0.9435 (tpp) cc_final: 0.9155 (tpp)
REVERT: A  606 MET cc_start: 0.9170 (ttm) cc_final: 0.7976 (tpp)
REVERT: A  613 ASP cc_start: 0.8540 (t0) cc_final: 0.8259 (t0)
REVERT: A  617 MET cc_start: 0.7142 (mmm) cc_final: 0.6628 (mmm)
REVERT: A  671 GLU cc_start: 0.9009 (mp0) cc_final: 0.8744 (pm20)
REVERT: A  683 MET cc_start: 0.8906 (tmm) cc_final: 0.8512 (ppp)
REVERT: B   49 ASP cc_start: 0.9039 (m-30) cc_final: 0.8793 (m-30)
REVERT: B   93 MET cc_start: 0.8045 (ttm) cc_final: 0.7742 (tmm)
REVERT: B  311 ASP cc_start: 0.8805 (t0) cc_final: 0.8353 (t0)
REVERT: B  346 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8957 (p0)
REVERT: B  362 ILE cc_start: 0.9600 (mm) cc_final: 0.9273 (tp)
REVERT: B  365 SER cc_start: 0.8723 (t) cc_final: 0.8428 (p)
REVERT: B  385 ASP cc_start: 0.9166 (t0) cc_final: 0.8590 (p0)
REVERT: B  436 ASN cc_start: 0.9380 (m110) cc_final: 0.8955 (m110)
REVERT: B  553 MET cc_start: 0.9390 (tmm) cc_final: 0.8886 (ppp)
REVERT: B  564 CYS cc_start: 0.9232 (m) cc_final: 0.8989 (m)
REVERT: B  566 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9133 (mt)
REVERT: B  567 MET cc_start: 0.9318 (mtm) cc_final: 0.8928 (mtm)
REVERT: B  627 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8253 (pm20)
REVERT: B  681 TYR cc_start: 0.9083 (m-10) cc_final: 0.8566 (m-80)
REVERT: B  685 LYS cc_start: 0.9304 (mttt) cc_final: 0.8992 (mmtt)
REVERT: C   45 MET cc_start: 0.9133 (mpp) cc_final: 0.8576 (mpp)
REVERT: C   75 GLU cc_start: 0.8988 (pp20) cc_final: 0.8310 (mp0)
REVERT: C  102 TYR cc_start: 0.9065 (t80) cc_final: 0.8681 (t80)
  outliers start: 32
  outliers final: 15
  residues processed: 210
  average time/residue: 0.0789
  time to fit residues: 25.2002
Evaluate side-chains
  186 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue  126 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  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   20 THR
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 76 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 56 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 131 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 124 optimal weight:    0.0050
   chunk 89 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    5.2002

-------------------------------------------------------------------------------
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 101 ASN
B 154 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 ASN
B 609 GLN
C 146 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.063203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.048594 restraints weight = 50968.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.050553 restraints weight = 28467.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.051933 restraints weight = 19162.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.052896 restraints weight = 14371.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.053581 restraints weight = 11613.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    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 = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11735  Z= 0.233
  Angle     :  0.625   6.727  15804  Z= 0.328
  Chirality :  0.042   0.152   1759
  Planarity :  0.003   0.040   2011
  Dihedral  :  7.897 171.630   1604
  Min Nonbonded Distance : 1.747

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.64 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.23), residues: 1411
  helix:  1.42 (0.22), residues: 565
  sheet:  0.59 (0.33), residues: 261
  loop : -0.71 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 679 
 TYR   0.017   0.002   TYR B 137 
 PHE   0.015   0.002   PHE C  72 
 TRP   0.007   0.001   TRP A 598 
 HIS   0.007   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (11735)
  covalent geometry    : angle       0.62502 (15804)
  hydrogen bonds       : bond        0.03573 (  547)
  hydrogen bonds       : angle       4.68249 ( 1560)

*********************** 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
  201 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.9503 (mm-40) cc_final: 0.8994 (mm-40)
REVERT: A   42 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8378 (mm-30)
REVERT: A  114 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.9067 (tmm)
REVERT: A  200 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8848 (tm-30)
REVERT: A  394 MET cc_start: 0.8786 (ptp) cc_final: 0.8496 (ptm)
REVERT: A  430 TYR cc_start: 0.8617 (t80) cc_final: 0.8269 (t80)
REVERT: A  567 MET cc_start: 0.9475 (mmm) cc_final: 0.9054 (mmm)
REVERT: A  602 MET cc_start: 0.9452 (tpp) cc_final: 0.9157 (tpp)
REVERT: A  606 MET cc_start: 0.9177 (ttm) cc_final: 0.8793 (tpt)
REVERT: A  621 MET cc_start: 0.8277 (mmt) cc_final: 0.8025 (mpp)
REVERT: A  683 MET cc_start: 0.8917 (tmm) cc_final: 0.8648 (ppp)
REVERT: B   49 ASP cc_start: 0.9009 (m-30) cc_final: 0.8716 (m-30)
REVERT: B  311 ASP cc_start: 0.8855 (t0) cc_final: 0.8372 (t0)
REVERT: B  346 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8992 (p0)
REVERT: B  365 SER cc_start: 0.8828 (t) cc_final: 0.8446 (p)
REVERT: B  385 ASP cc_start: 0.9178 (t0) cc_final: 0.8498 (p0)
REVERT: B  466 MET cc_start: 0.9244 (mtp) cc_final: 0.9027 (mtp)
REVERT: B  513 MET cc_start: 0.7899 (mtm) cc_final: 0.7526 (mtm)
REVERT: B  553 MET cc_start: 0.9402 (tmm) cc_final: 0.8890 (ppp)
REVERT: B  564 CYS cc_start: 0.9284 (m) cc_final: 0.8943 (m)
REVERT: B  567 MET cc_start: 0.9362 (mtm) cc_final: 0.8986 (mtm)
REVERT: B  602 MET cc_start: 0.8989 (tpp) cc_final: 0.8702 (tpp)
REVERT: B  606 MET cc_start: 0.8962 (mmt) cc_final: 0.8736 (mmm)
REVERT: B  617 MET cc_start: 0.9354 (ttp) cc_final: 0.8988 (mmm)
REVERT: B  627 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8424 (pm20)
REVERT: B  681 TYR cc_start: 0.9164 (m-10) cc_final: 0.8647 (m-80)
REVERT: C   40 PHE cc_start: 0.9180 (p90) cc_final: 0.8757 (p90)
REVERT: C   45 MET cc_start: 0.9105 (mpp) cc_final: 0.8638 (mpp)
REVERT: C   72 PHE cc_start: 0.7126 (p90) cc_final: 0.6886 (p90)
REVERT: C   75 GLU cc_start: 0.9019 (pp20) cc_final: 0.8305 (mp0)
REVERT: C   84 MET cc_start: 0.8740 (tpp) cc_final: 0.8397 (tpp)
REVERT: C  102 TYR cc_start: 0.9106 (t80) cc_final: 0.8760 (t80)
REVERT: C  143 ASP cc_start: 0.9684 (m-30) cc_final: 0.9471 (p0)
  outliers start: 32
  outliers final: 19
  residues processed: 192
  average time/residue: 0.0788
  time to fit residues: 23.3597
Evaluate side-chains
  178 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  139 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  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  678 ASN
Chi-restraints excluded: chain C residue   53 VAL
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 2 optimal weight:    8.9990
   chunk 90 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 83 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 92 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 436 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.063399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.049188 restraints weight = 49848.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.051170 restraints weight = 27384.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.052577 restraints weight = 18269.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.053560 restraints weight = 13536.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.054342 restraints weight = 10799.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3042
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    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 = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3042
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11735  Z= 0.172
  Angle     :  0.586   8.020  15804  Z= 0.304
  Chirality :  0.041   0.150   1759
  Planarity :  0.003   0.044   2011
  Dihedral  :  7.817 171.210   1604
  Min Nonbonded Distance : 1.812

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.18 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.23), residues: 1411
  helix:  1.39 (0.23), residues: 565
  sheet:  0.69 (0.33), residues: 261
  loop : -0.73 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 583 
 TYR   0.016   0.002   TYR A 457 
 PHE   0.013   0.001   PHE C  72 
 TRP   0.007   0.001   TRP B 157 
 HIS   0.009   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (11735)
  covalent geometry    : angle       0.58590 (15804)
  hydrogen bonds       : bond        0.03390 (  547)
  hydrogen bonds       : angle       4.55214 ( 1560)

*********************** 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
  203 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 171
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8303 (mm-30)
REVERT: A   51 LEU cc_start: 0.9547 (mt) cc_final: 0.9324 (mt)
REVERT: A  114 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9038 (tmm)
REVERT: A  200 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8851 (tm-30)
REVERT: A  363 MET cc_start: 0.8609 (ppp) cc_final: 0.8228 (ppp)
REVERT: A  394 MET cc_start: 0.8806 (ptp) cc_final: 0.8528 (ptm)
REVERT: A  430 TYR cc_start: 0.8682 (t80) cc_final: 0.8313 (t80)
REVERT: A  499 PHE cc_start: 0.9399 (m-80) cc_final: 0.9101 (m-10)
REVERT: A  553 MET cc_start: 0.8563 (tpp) cc_final: 0.8300 (tmm)
REVERT: A  567 MET cc_start: 0.9573 (mmm) cc_final: 0.9007 (mmm)
REVERT: A  602 MET cc_start: 0.9476 (tpp) cc_final: 0.9170 (tpp)
REVERT: A  606 MET cc_start: 0.9161 (ttm) cc_final: 0.8725 (tpt)
REVERT: A  621 MET cc_start: 0.8230 (mmt) cc_final: 0.7810 (mpp)
REVERT: A  660 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8391 (mt-10)
REVERT: A  679 ARG cc_start: 0.8835 (ttm110) cc_final: 0.8398 (mtm-85)
REVERT: A  683 MET cc_start: 0.8951 (tmm) cc_final: 0.8742 (ppp)
REVERT: B   49 ASP cc_start: 0.9082 (m-30) cc_final: 0.8821 (m-30)
REVERT: B  311 ASP cc_start: 0.8885 (t0) cc_final: 0.8380 (t0)
REVERT: B  346 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8729 (p0)
REVERT: B  362 ILE cc_start: 0.9384 (mm) cc_final: 0.9136 (tp)
REVERT: B  365 SER cc_start: 0.8661 (t) cc_final: 0.8409 (p)
REVERT: B  385 ASP cc_start: 0.9157 (t0) cc_final: 0.8480 (p0)
REVERT: B  513 MET cc_start: 0.7845 (mtm) cc_final: 0.7502 (mtm)
REVERT: B  553 MET cc_start: 0.9391 (tmm) cc_final: 0.8865 (ppp)
REVERT: B  564 CYS cc_start: 0.9272 (m) cc_final: 0.8865 (m)
REVERT: B  567 MET cc_start: 0.9337 (mtm) cc_final: 0.8891 (mtm)
REVERT: B  590 CYS cc_start: 0.8286 (m) cc_final: 0.7411 (m)
REVERT: B  602 MET cc_start: 0.8979 (tpp) cc_final: 0.8593 (tpp)
REVERT: B  606 MET cc_start: 0.8869 (mmt) cc_final: 0.8619 (mmm)
REVERT: B  617 MET cc_start: 0.9328 (ttp) cc_final: 0.8967 (mmm)
REVERT: B  627 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8376 (pm20)
REVERT: B  681 TYR cc_start: 0.9119 (m-10) cc_final: 0.8580 (m-80)
REVERT: C   40 PHE cc_start: 0.9188 (p90) cc_final: 0.8760 (p90)
REVERT: C   45 MET cc_start: 0.9093 (mpp) cc_final: 0.8570 (mpp)
REVERT: C   95 ASP cc_start: 0.9140 (m-30) cc_final: 0.8689 (m-30)
REVERT: C  102 TYR cc_start: 0.9072 (t80) cc_final: 0.8717 (t80)
REVERT: C  143 ASP cc_start: 0.9673 (m-30) cc_final: 0.9446 (p0)
  outliers start: 32
  outliers final: 21
  residues processed: 198
  average time/residue: 0.0809
  time to fit residues: 24.7459
Evaluate side-chains
  185 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  459 THR
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  139 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  346 ASN
Chi-restraints excluded: chain B residue  348 LYS
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  139 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 114 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 117 optimal weight:    0.5980
   chunk 93 optimal weight:    0.0870
   chunk 133 optimal weight:    0.7980
   chunk 103 optimal weight:    9.9990
   chunk 78 optimal weight:   20.0000
   overall best weight:    1.6962

-------------------------------------------------------------------------------
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 101 ASN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 ASN
B 601 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.064499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.050204 restraints weight = 49448.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.052230 restraints weight = 27174.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.053673 restraints weight = 18084.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.054575 restraints weight = 13349.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.055387 restraints weight = 10879.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11735  Z= 0.116
  Angle     :  0.590  14.013  15804  Z= 0.296
  Chirality :  0.041   0.219   1759
  Planarity :  0.003   0.043   2011
  Dihedral  :  7.581 168.144   1603
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.97 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.23), residues: 1411
  helix:  1.46 (0.23), residues: 565
  sheet:  0.76 (0.33), residues: 268
  loop : -0.83 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 177 
 TYR   0.017   0.001   TYR A 457 
 PHE   0.015   0.001   PHE B 668 
 TRP   0.009   0.001   TRP B 157 
 HIS   0.008   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (11735)
  covalent geometry    : angle       0.59028 (15804)
  hydrogen bonds       : bond        0.03109 (  547)
  hydrogen bonds       : angle       4.37326 ( 1560)

*********************** 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
  217 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 0.510 
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: 0.9577 (mm-40) cc_final: 0.9348 (mt0)
REVERT: A   42 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8278 (mm-30)
REVERT: A   51 LEU cc_start: 0.9559 (mt) cc_final: 0.9325 (mt)
REVERT: A  114 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9092 (tmm)
REVERT: A  183 LEU cc_start: 0.9514 (mt) cc_final: 0.9016 (pp)
REVERT: A  200 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8836 (tm-30)
REVERT: A  207 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8931 (tm-30)
REVERT: A  394 MET cc_start: 0.8811 (ptp) cc_final: 0.8557 (ptm)
REVERT: A  499 PHE cc_start: 0.9383 (m-80) cc_final: 0.9146 (m-10)
REVERT: A  513 MET cc_start: 0.8305 (mtt) cc_final: 0.7803 (mtt)
REVERT: A  553 MET cc_start: 0.8489 (tpp) cc_final: 0.8257 (tmm)
REVERT: A  567 MET cc_start: 0.9588 (mmm) cc_final: 0.9028 (mmm)
REVERT: A  602 MET cc_start: 0.9476 (tpp) cc_final: 0.9163 (tpp)
REVERT: A  606 MET cc_start: 0.9159 (ttm) cc_final: 0.8608 (tpt)
REVERT: A  621 MET cc_start: 0.8044 (mmt) cc_final: 0.7639 (mpp)
REVERT: A  660 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8804 (mt-10)
REVERT: B   49 ASP cc_start: 0.9015 (m-30) cc_final: 0.8792 (m-30)
REVERT: B  125 MET cc_start: 0.8317 (mtm) cc_final: 0.7981 (mtm)
REVERT: B  311 ASP cc_start: 0.8860 (t0) cc_final: 0.8358 (t0)
REVERT: B  328 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: B  362 ILE cc_start: 0.9408 (mm) cc_final: 0.9130 (tp)
REVERT: B  365 SER cc_start: 0.8667 (t) cc_final: 0.8431 (p)
REVERT: B  385 ASP cc_start: 0.9092 (t0) cc_final: 0.8452 (p0)
REVERT: B  476 MET cc_start: 0.8442 (ttt) cc_final: 0.8155 (tpt)
REVERT: B  484 TYR cc_start: 0.9200 (m-80) cc_final: 0.8817 (m-10)
REVERT: B  513 MET cc_start: 0.7759 (mtm) cc_final: 0.7396 (mtm)
REVERT: B  553 MET cc_start: 0.9375 (tmm) cc_final: 0.8839 (ppp)
REVERT: B  563 LEU cc_start: 0.9438 (tp) cc_final: 0.9194 (tp)
REVERT: B  564 CYS cc_start: 0.9230 (m) cc_final: 0.8917 (m)
REVERT: B  567 MET cc_start: 0.9295 (mtm) cc_final: 0.8885 (ptp)
REVERT: B  590 CYS cc_start: 0.8366 (m) cc_final: 0.7562 (m)
REVERT: B  602 MET cc_start: 0.9065 (tpp) cc_final: 0.8667 (tpp)
REVERT: B  606 MET cc_start: 0.8869 (mmt) cc_final: 0.8604 (mmm)
REVERT: B  627 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8394 (pm20)
REVERT: B  685 LYS cc_start: 0.9341 (mttt) cc_final: 0.9033 (mmtt)
REVERT: C   21 ILE cc_start: 0.9167 (mm) cc_final: 0.8948 (mm)
REVERT: C   45 MET cc_start: 0.9064 (mpp) cc_final: 0.8595 (mpp)
REVERT: C   75 GLU cc_start: 0.9018 (pp20) cc_final: 0.8320 (mp0)
REVERT: C   84 MET cc_start: 0.8376 (tpp) cc_final: 0.8110 (tpp)
REVERT: C   95 ASP cc_start: 0.9061 (m-30) cc_final: 0.8561 (m-30)
REVERT: C  102 TYR cc_start: 0.9056 (t80) cc_final: 0.8687 (t80)
REVERT: C  139 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6198 (t80)
REVERT: C  143 ASP cc_start: 0.9664 (m-30) cc_final: 0.9411 (p0)
  outliers start: 28
  outliers final: 21
  residues processed: 208
  average time/residue: 0.0870
  time to fit residues: 27.9211
Evaluate side-chains
  191 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  139 VAL
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  688 LEU
Chi-restraints excluded: chain A residue  690 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  587 SER
Chi-restraints excluded: chain B residue  596 TYR
Chi-restraints excluded: chain B residue  678 ASN
Chi-restraints excluded: chain C residue   20 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 58 optimal weight:    0.0470
   chunk 72 optimal weight:    6.9990
   chunk 119 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 117 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.6084

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.065335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.050664 restraints weight = 49754.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.052666 restraints weight = 27862.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.054064 restraints weight = 18737.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055087 restraints weight = 14049.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.055833 restraints weight = 11302.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3072
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3072
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.4441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11735  Z= 0.114
  Angle     :  0.602  10.273  15804  Z= 0.302
  Chirality :  0.042   0.233   1759
  Planarity :  0.003   0.042   2011
  Dihedral  :  7.536 168.207   1603
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.20 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.23), residues: 1411
  helix:  1.42 (0.23), residues: 564
  sheet:  0.85 (0.33), residues: 267
  loop : -0.85 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 177 
 TYR   0.025   0.001   TYR A 457 
 PHE   0.020   0.001   PHE C  40 
 TRP   0.007   0.001   TRP B 157 
 HIS   0.003   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (11735)
  covalent geometry    : angle       0.60172 (15804)
  hydrogen bonds       : bond        0.03061 (  547)
  hydrogen bonds       : angle       4.31705 ( 1560)

*********************** 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
  208 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 177
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8375 (mm-30)
REVERT: A   51 LEU cc_start: 0.9541 (mt) cc_final: 0.9294 (mt)
REVERT: A   93 MET cc_start: 0.8385 (mtm) cc_final: 0.7599 (mpp)
REVERT: A  110 THR cc_start: 0.9323 (m) cc_final: 0.9050 (p)
REVERT: A  114 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.9095 (tmm)
REVERT: A  183 LEU cc_start: 0.9503 (mt) cc_final: 0.9032 (pp)
REVERT: A  200 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8836 (tm-30)
REVERT: A  207 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8856 (tm-30)
REVERT: A  304 PHE cc_start: 0.8884 (t80) cc_final: 0.8616 (t80)
REVERT: A  394 MET cc_start: 0.8820 (ptp) cc_final: 0.8558 (ptm)
REVERT: A  499 PHE cc_start: 0.9347 (m-80) cc_final: 0.9141 (m-10)
REVERT: A  513 MET cc_start: 0.8624 (mtt) cc_final: 0.8386 (mtt)
REVERT: A  553 MET cc_start: 0.8464 (tpp) cc_final: 0.8256 (tmm)
REVERT: A  567 MET cc_start: 0.9620 (mmm) cc_final: 0.9033 (mmm)
REVERT: A  602 MET cc_start: 0.9473 (tpp) cc_final: 0.9116 (tpp)
REVERT: A  605 ILE cc_start: 0.9474 (tp) cc_final: 0.9255 (tp)
REVERT: A  606 MET cc_start: 0.9124 (ttm) cc_final: 0.8526 (tpt)
REVERT: A  621 MET cc_start: 0.8045 (mmt) cc_final: 0.7842 (tpp)
REVERT: A  660 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8838 (mt-10)
REVERT: A  679 ARG cc_start: 0.9023 (ttm110) cc_final: 0.8475 (mtt-85)
REVERT: B   49 ASP cc_start: 0.8962 (m-30) cc_final: 0.8746 (m-30)
REVERT: B   93 MET cc_start: 0.8666 (tmm) cc_final: 0.8377 (tpp)
REVERT: B  125 MET cc_start: 0.8314 (mtm) cc_final: 0.7981 (mtm)
REVERT: B  311 ASP cc_start: 0.8860 (t0) cc_final: 0.8342 (t0)
REVERT: B  328 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: B  362 ILE cc_start: 0.9448 (mm) cc_final: 0.9227 (tp)
REVERT: B  365 SER cc_start: 0.8731 (t) cc_final: 0.8401 (p)
REVERT: B  385 ASP cc_start: 0.9083 (t0) cc_final: 0.8427 (p0)
REVERT: B  411 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8626 (tppt)
REVERT: B  466 MET cc_start: 0.9319 (mtp) cc_final: 0.8663 (tpp)
REVERT: B  476 MET cc_start: 0.8451 (ttt) cc_final: 0.8235 (tpt)
REVERT: B  484 TYR cc_start: 0.9193 (m-80) cc_final: 0.8784 (m-10)
REVERT: B  513 MET cc_start: 0.7764 (mtm) cc_final: 0.7456 (mtm)
REVERT: B  515 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8550 (mp0)
REVERT: B  553 MET cc_start: 0.9380 (tmm) cc_final: 0.8847 (ppp)
REVERT: B  561 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8729 (pm20)
REVERT: B  564 CYS cc_start: 0.9308 (m) cc_final: 0.8384 (m)
REVERT: B  567 MET cc_start: 0.9211 (mtm) cc_final: 0.8661 (mtm)
REVERT: B  590 CYS cc_start: 0.8345 (m) cc_final: 0.7549 (m)
REVERT: B  602 MET cc_start: 0.9118 (tpp) cc_final: 0.8589 (tpp)
REVERT: B  627 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8360 (pm20)
REVERT: B  681 TYR cc_start: 0.9161 (m-10) cc_final: 0.8589 (m-80)
REVERT: B  685 LYS cc_start: 0.9349 (mttt) cc_final: 0.9044 (mmtt)
REVERT: C   21 ILE cc_start: 0.9116 (mm) cc_final: 0.8882 (mm)
REVERT: C   40 PHE cc_start: 0.9142 (p90) cc_final: 0.8715 (p90)
REVERT: C   45 MET cc_start: 0.9080 (mpp) cc_final: 0.8563 (mpp)
REVERT: C   75 GLU cc_start: 0.8995 (pp20) cc_final: 0.8303 (mp0)
REVERT: C   84 MET cc_start: 0.8366 (tpp) cc_final: 0.8115 (tpp)
REVERT: C   95 ASP cc_start: 0.9154 (m-30) cc_final: 0.8725 (m-30)
REVERT: C  102 TYR cc_start: 0.9086 (t80) cc_final: 0.8758 (t80)
REVERT: C  139 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6195 (t80)
REVERT: C  143 ASP cc_start: 0.9657 (m-30) cc_final: 0.9399 (p0)
  outliers start: 31
  outliers final: 23
  residues processed: 201
  average time/residue: 0.0866
  time to fit residues: 27.1635
Evaluate side-chains
  196 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 170
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain A residue  599 THR
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   91 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  561 GLU
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    9 SER
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   53 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 99 optimal weight:    0.7980
   chunk 32 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 127 optimal weight:    4.9990
   chunk 118 optimal weight:    9.9990
   chunk 77 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9980
   overall best weight:    3.1586

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.064040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.049608 restraints weight = 50100.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.051568 restraints weight = 27902.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.052974 restraints weight = 18797.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.053931 restraints weight = 14002.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.054656 restraints weight = 11285.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    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 = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.4559

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= 0.158
  Angle     :  0.612  13.576  15804  Z= 0.313
  Chirality :  0.042   0.317   1759
  Planarity :  0.003   0.039   2011
  Dihedral  :  7.654 171.777   1603
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.59 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.23), residues: 1411
  helix:  1.34 (0.23), residues: 564
  sheet:  0.90 (0.34), residues: 267
  loop : -0.89 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 583 
 TYR   0.027   0.001   TYR A 457 
 PHE   0.020   0.001   PHE B 429 
 TRP   0.014   0.001   TRP A 598 
 HIS   0.005   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11735)
  covalent geometry    : angle       0.61243 (15804)
  hydrogen bonds       : bond        0.03211 (  547)
  hydrogen bonds       : angle       4.44708 ( 1560)

*********************** 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
  200 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8460 (mm-30)
REVERT: A   51 LEU cc_start: 0.9574 (mt) cc_final: 0.9317 (mt)
REVERT: A  125 MET cc_start: 0.9218 (pmm) cc_final: 0.8966 (pmm)
REVERT: A  183 LEU cc_start: 0.9503 (mt) cc_final: 0.8983 (pp)
REVERT: A  200 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8855 (tm-30)
REVERT: A  304 PHE cc_start: 0.8890 (t80) cc_final: 0.8615 (t80)
REVERT: A  394 MET cc_start: 0.8799 (ptp) cc_final: 0.8459 (ptm)
REVERT: A  430 TYR cc_start: 0.8477 (t80) cc_final: 0.8241 (t80)
REVERT: A  499 PHE cc_start: 0.9392 (m-80) cc_final: 0.9175 (m-10)
REVERT: A  553 MET cc_start: 0.8527 (tpp) cc_final: 0.8293 (tmm)
REVERT: A  567 MET cc_start: 0.9630 (mmm) cc_final: 0.9144 (mmm)
REVERT: A  602 MET cc_start: 0.9529 (tpp) cc_final: 0.9172 (tpp)
REVERT: A  606 MET cc_start: 0.9156 (ttm) cc_final: 0.8576 (tpt)
REVERT: A  660 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8596 (mt-10)
REVERT: A  676 HIS cc_start: 0.9634 (t70) cc_final: 0.9240 (t-90)
REVERT: A  679 ARG cc_start: 0.9084 (ttm110) cc_final: 0.8263 (mtm-85)
REVERT: B   49 ASP cc_start: 0.9001 (m-30) cc_final: 0.8758 (m-30)
REVERT: B   93 MET cc_start: 0.8686 (tmm) cc_final: 0.8299 (tmm)
REVERT: B  311 ASP cc_start: 0.8908 (t0) cc_final: 0.8397 (t0)
REVERT: B  328 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: B  362 ILE cc_start: 0.9402 (mm) cc_final: 0.9156 (tp)
REVERT: B  365 SER cc_start: 0.8838 (t) cc_final: 0.8480 (p)
REVERT: B  385 ASP cc_start: 0.9112 (t0) cc_final: 0.8556 (p0)
REVERT: B  476 MET cc_start: 0.8480 (ttt) cc_final: 0.8247 (tpt)
REVERT: B  513 MET cc_start: 0.7863 (mtm) cc_final: 0.7572 (mtm)
REVERT: B  515 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8465 (mp0)
REVERT: B  553 MET cc_start: 0.9410 (tmm) cc_final: 0.8886 (ppp)
REVERT: B  561 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8728 (pm20)
REVERT: B  564 CYS cc_start: 0.9302 (m) cc_final: 0.8940 (p)
REVERT: B  567 MET cc_start: 0.9346 (mtm) cc_final: 0.8973 (mtm)
REVERT: B  590 CYS cc_start: 0.8276 (m) cc_final: 0.7531 (m)
REVERT: B  602 MET cc_start: 0.9077 (tpp) cc_final: 0.8535 (tpp)
REVERT: B  627 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8372 (pm20)
REVERT: B  681 TYR cc_start: 0.9165 (m-10) cc_final: 0.8663 (m-80)
REVERT: C   21 ILE cc_start: 0.9111 (mm) cc_final: 0.8880 (mm)
REVERT: C   45 MET cc_start: 0.9087 (mpp) cc_final: 0.8867 (mpp)
REVERT: C   75 GLU cc_start: 0.8988 (pp20) cc_final: 0.8284 (mp0)
REVERT: C   84 MET cc_start: 0.8418 (tpp) cc_final: 0.8144 (tpp)
REVERT: C   95 ASP cc_start: 0.9179 (m-30) cc_final: 0.8731 (m-30)
REVERT: C  139 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.6202 (t80)
REVERT: C  143 ASP cc_start: 0.9655 (m-30) cc_final: 0.9383 (p0)
  outliers start: 29
  outliers final: 24
  residues processed: 193
  average time/residue: 0.0854
  time to fit residues: 25.5495
Evaluate side-chains
  181 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  575 VAL
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  688 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   91 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  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  561 GLU
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    9 SER
Chi-restraints excluded: chain C residue   20 THR
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 126 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 95 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0370
   chunk 65 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    5.0064

-------------------------------------------------------------------------------
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
B 101 ASN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.063063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.048535 restraints weight = 50818.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.050463 restraints weight = 28627.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.051807 restraints weight = 19336.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.052785 restraints weight = 14528.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.053436 restraints weight = 11728.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
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:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.4712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11735  Z= 0.229
  Angle     :  0.673  10.532  15804  Z= 0.348
  Chirality :  0.044   0.309   1759
  Planarity :  0.004   0.040   2011
  Dihedral  :  7.846 173.438   1603
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.22 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.23), residues: 1411
  helix:  1.16 (0.22), residues: 564
  sheet:  0.93 (0.34), residues: 264
  loop : -0.96 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 583 
 TYR   0.032   0.002   TYR A 457 
 PHE   0.023   0.002   PHE A 208 
 TRP   0.011   0.001   TRP A 598 
 HIS   0.005   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (11735)
  covalent geometry    : angle       0.67256 (15804)
  hydrogen bonds       : bond        0.03546 (  547)
  hydrogen bonds       : angle       4.69793 ( 1560)

*********************** 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
  182 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8452 (mm-30)
REVERT: A   51 LEU cc_start: 0.9544 (mt) cc_final: 0.9304 (mt)
REVERT: A  200 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8844 (tm-30)
REVERT: A  304 PHE cc_start: 0.8890 (t80) cc_final: 0.8609 (t80)
REVERT: A  394 MET cc_start: 0.8812 (ptp) cc_final: 0.8493 (ptm)
REVERT: A  430 TYR cc_start: 0.8509 (t80) cc_final: 0.8145 (t80)
REVERT: A  499 PHE cc_start: 0.9433 (m-80) cc_final: 0.9206 (m-10)
REVERT: A  553 MET cc_start: 0.8626 (tpp) cc_final: 0.8340 (tmm)
REVERT: A  567 MET cc_start: 0.9625 (mmm) cc_final: 0.9129 (mmm)
REVERT: A  602 MET cc_start: 0.9552 (tpp) cc_final: 0.9222 (tpp)
REVERT: A  606 MET cc_start: 0.9183 (ttm) cc_final: 0.8800 (tpt)
REVERT: A  660 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8608 (mt-10)
REVERT: A  676 HIS cc_start: 0.9623 (t70) cc_final: 0.9233 (t-90)
REVERT: A  679 ARG cc_start: 0.9027 (ttm110) cc_final: 0.8447 (mtm-85)
REVERT: B   93 MET cc_start: 0.8738 (tmm) cc_final: 0.8361 (tmm)
REVERT: B  311 ASP cc_start: 0.8951 (t0) cc_final: 0.8510 (t0)
REVERT: B  362 ILE cc_start: 0.9412 (mm) cc_final: 0.9155 (tp)
REVERT: B  365 SER cc_start: 0.8876 (t) cc_final: 0.8584 (p)
REVERT: B  385 ASP cc_start: 0.9133 (t0) cc_final: 0.8629 (p0)
REVERT: B  466 MET cc_start: 0.9310 (mtp) cc_final: 0.8848 (tpp)
REVERT: B  476 MET cc_start: 0.8461 (ttt) cc_final: 0.8072 (tpt)
REVERT: B  513 MET cc_start: 0.7928 (mtm) cc_final: 0.7565 (mtm)
REVERT: B  553 MET cc_start: 0.9411 (tmm) cc_final: 0.8887 (ppp)
REVERT: B  567 MET cc_start: 0.9239 (mtm) cc_final: 0.8759 (mtm)
REVERT: B  590 CYS cc_start: 0.8284 (m) cc_final: 0.7433 (m)
REVERT: B  602 MET cc_start: 0.9025 (tpp) cc_final: 0.8341 (tpt)
REVERT: B  617 MET cc_start: 0.9334 (ttp) cc_final: 0.8944 (mmm)
REVERT: B  627 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8260 (pm20)
REVERT: B  640 GLN cc_start: 0.9474 (mt0) cc_final: 0.9180 (tp-100)
REVERT: B  681 TYR cc_start: 0.9272 (m-10) cc_final: 0.8708 (m-80)
REVERT: C   45 MET cc_start: 0.9092 (mpp) cc_final: 0.8856 (mpp)
REVERT: C   95 ASP cc_start: 0.9205 (m-30) cc_final: 0.8763 (m-30)
REVERT: C  139 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.6179 (t80)
REVERT: C  143 ASP cc_start: 0.9651 (m-30) cc_final: 0.9368 (p0)
  outliers start: 28
  outliers final: 24
  residues processed: 178
  average time/residue: 0.0777
  time to fit residues: 21.7846
Evaluate side-chains
  175 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  575 VAL
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  688 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   91 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  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    9 SER
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 28 optimal weight:    0.0470
   chunk 123 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0670
   chunk 102 optimal weight:    4.9990
   overall best weight:    1.8222

-------------------------------------------------------------------------------
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
B 101 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.064964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.050236 restraints weight = 50080.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.052243 restraints weight = 28000.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.053651 restraints weight = 18752.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.054635 restraints weight = 14038.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.055368 restraints weight = 11326.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3057
|-occupancy refinement: start-------------------------------------------------|
| 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 |
|-----------------------------------------------------------------------------|
|-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: 0.8372
moved from start:          0.4782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11735  Z= 0.131
  Angle     :  0.677  12.938  15804  Z= 0.338
  Chirality :  0.044   0.324   1759
  Planarity :  0.003   0.053   2011
  Dihedral  :  7.679 170.049   1603
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.16 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.23), residues: 1411
  helix:  1.18 (0.22), residues: 565
  sheet:  0.95 (0.34), residues: 269
  loop : -0.99 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  85 
 TYR   0.029   0.001   TYR A 457 
 PHE   0.039   0.001   PHE A 208 
 TRP   0.009   0.001   TRP A 289 
 HIS   0.003   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (11735)
  covalent geometry    : angle       0.67664 (15804)
  hydrogen bonds       : bond        0.03373 (  547)
  hydrogen bonds       : angle       4.51757 ( 1560)

********************** 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
  189 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8470 (mm-30)
REVERT: A   51 LEU cc_start: 0.9520 (mt) cc_final: 0.9263 (mt)
REVERT: A  114 MET cc_start: 0.9208 (tpt) cc_final: 0.8911 (tpt)
REVERT: A  183 LEU cc_start: 0.9499 (mt) cc_final: 0.8966 (pp)
REVERT: A  200 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8844 (tm-30)
REVERT: A  304 PHE cc_start: 0.8879 (t80) cc_final: 0.8633 (t80)
REVERT: A  394 MET cc_start: 0.8802 (ptp) cc_final: 0.8472 (ptm)
REVERT: A  499 PHE cc_start: 0.9371 (m-80) cc_final: 0.9139 (m-10)
REVERT: A  553 MET cc_start: 0.8512 (tpp) cc_final: 0.8265 (tmm)
REVERT: A  567 MET cc_start: 0.9655 (mmm) cc_final: 0.9182 (mmm)
REVERT: A  584 LEU cc_start: 0.9105 (mp) cc_final: 0.8471 (tp)
REVERT: A  602 MET cc_start: 0.9579 (tpp) cc_final: 0.9269 (tpp)
REVERT: A  606 MET cc_start: 0.9179 (ttm) cc_final: 0.8807 (tpt)
REVERT: A  660 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8601 (mt-10)
REVERT: A  676 HIS cc_start: 0.9629 (t70) cc_final: 0.9268 (t-90)
REVERT: A  679 ARG cc_start: 0.9100 (ttm110) cc_final: 0.8382 (mtm-85)
REVERT: B   49 ASP cc_start: 0.8967 (m-30) cc_final: 0.8718 (t0)
REVERT: B  126 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.6612 (mt)
REVERT: B  311 ASP cc_start: 0.8940 (t0) cc_final: 0.8525 (t0)
REVERT: B  328 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: B  362 ILE cc_start: 0.9444 (mm) cc_final: 0.9222 (tp)
REVERT: B  365 SER cc_start: 0.8853 (t) cc_final: 0.8473 (p)
REVERT: B  384 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8243 (tp30)
REVERT: B  385 ASP cc_start: 0.9061 (t0) cc_final: 0.8581 (p0)
REVERT: B  466 MET cc_start: 0.9350 (mtp) cc_final: 0.8862 (tpp)
REVERT: B  476 MET cc_start: 0.8460 (ttt) cc_final: 0.8101 (tpt)
REVERT: B  484 TYR cc_start: 0.9096 (m-80) cc_final: 0.8807 (m-10)
REVERT: B  513 MET cc_start: 0.8037 (mtm) cc_final: 0.7757 (mtm)
REVERT: B  553 MET cc_start: 0.9350 (tmm) cc_final: 0.8812 (ppp)
REVERT: B  567 MET cc_start: 0.9174 (mtm) cc_final: 0.8673 (mtm)
REVERT: B  584 LEU cc_start: 0.8773 (mp) cc_final: 0.7654 (mt)
REVERT: B  590 CYS cc_start: 0.8378 (m) cc_final: 0.7662 (m)
REVERT: B  602 MET cc_start: 0.9025 (tpp) cc_final: 0.8436 (tpp)
REVERT: B  627 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8247 (pm20)
REVERT: B  640 GLN cc_start: 0.9455 (mt0) cc_final: 0.9169 (tp-100)
REVERT: B  681 TYR cc_start: 0.9231 (m-10) cc_final: 0.8707 (m-80)
REVERT: C   21 ILE cc_start: 0.9012 (mm) cc_final: 0.8729 (mm)
REVERT: C   45 MET cc_start: 0.9070 (mpp) cc_final: 0.8848 (mpp)
REVERT: C   75 GLU cc_start: 0.9018 (pp20) cc_final: 0.8334 (mp0)
REVERT: C   84 MET cc_start: 0.8519 (tpp) cc_final: 0.8089 (tpp)
REVERT: C   95 ASP cc_start: 0.9164 (m-30) cc_final: 0.8707 (m-30)
REVERT: C  139 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6154 (t80)
REVERT: C  143 ASP cc_start: 0.9653 (m-30) cc_final: 0.9378 (p0)
  outliers start: 24
  outliers final: 20
  residues processed: 184
  average time/residue: 0.0792
  time to fit residues: 22.8740
Evaluate side-chains
  180 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   91 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  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  624 LYS
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 33 optimal weight:    9.9990
   chunk 71 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    0.3980
   chunk 91 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   chunk 109 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    2.6788

-------------------------------------------------------------------------------
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 = 0.3285 r_free = 0.3285 target = 0.064575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.049943 restraints weight = 50281.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.051905 restraints weight = 28200.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.053288 restraints weight = 18969.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.054238 restraints weight = 14187.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.054979 restraints weight = 11507.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    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 = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11735  Z= 0.150
  Angle     :  0.671  11.844  15804  Z= 0.338
  Chirality :  0.044   0.323   1759
  Planarity :  0.003   0.047   2011
  Dihedral  :  7.692 172.419   1601
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.16 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.23), residues: 1411
  helix:  1.14 (0.22), residues: 565
  sheet:  1.00 (0.34), residues: 264
  loop : -1.01 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  85 
 TYR   0.030   0.001   TYR A 457 
 PHE   0.040   0.001   PHE A 208 
 TRP   0.007   0.001   TRP B 157 
 HIS   0.003   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11735)
  covalent geometry    : angle       0.67095 (15804)
  hydrogen bonds       : bond        0.03284 (  547)
  hydrogen bonds       : angle       4.55126 ( 1560)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1854.81 seconds
wall clock time: 33 minutes 3.99 seconds (1983.99 seconds total)