Starting phenix.real_space_refine
on Sat Sep 12 21:15:12 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6r25_4710/09_2026/6r25_4710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r25_4710/09_2026/6r25_4710.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r25_4710/09_2026/6r25_4710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r25_4710/09_2026/6r25_4710.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6r25_4710/09_2026/6r25_4710.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6r25_4710/09_2026/6r25_4710.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6r25_4710/09_2026/6r25_4710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r25_4710/09_2026/6r25_4710.map"
  }
  resolution = 4.61
  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=   0.000 sd=   0.003
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
     Zn      3      6.06       5
     P     296      5.49       5
     S      54      5.16       5
     C   10651      2.51       5
     N    3358      2.21       5
     O    4292      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 18654
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "K"
      Number of atoms: 5837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 737, 5837
          Classifications: {'peptide': 737}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 698}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 105
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
    Chain: "M"
      Number of atoms: 193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 193
          Classifications: {'peptide': 26}
          Link IDs: {'PTRANS': 1, 'TRANS': 24}
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 633
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 804
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 766
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 820
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 870
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 5, 'TRANS': 107}
    Chain: "H"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 775
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 356
          Unusual residues: {' ZN': 3, 'FAD': 1}
          Classifications: {'undetermined': 4, 'water': 300}
          Link IDs: {None: 303}
    Chain: "L"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "M"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM     36  SG  CYS K  53      55.670  53.110  19.749  1.00 48.02           S
  ATOM     69  SG  CYS K  58      52.551  50.397  19.415  1.00 47.27           S
  ATOM    114  SG  CYS K  65      49.904  64.512  19.360  1.00 37.13           S
  ATOM    173  SG  CYS K  73      49.674  67.112  16.618  1.00 40.55           S
  ATOM    331  SG  CYS K  92      53.559  65.891  17.690  1.00 37.37           S
  ATOM    354  SG  CYS K  95      51.378  68.058  19.886  1.00 36.80           S
  ATOM    761  SG  CYS K 142      25.258  54.078  23.619  1.00 35.45           S
  ATOM    799  SG  CYS K 147      26.048  51.692  20.812  1.00 37.39           S
  ATOM    992  SG  CYS K 169      27.431  55.303  20.820  1.00 34.97           S
  ATOM   1043  SG  CYS K 185      23.515  54.522  20.136  1.00 38.56           S

  Time building chain proxies: 4.03, per 1000 atoms: 0.22
  Number of scatterers: 18654
  At special positions: 0
  Unit cell: (134.62, 155.82, 118.72, 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)
     Zn      3     29.99
     S      54     16.00
     P     296     15.00
     O    4292      8.00
     N    3358      7.00
     C   10651      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
      
  Atom "ATOM  16378  O5'  DC J -20 .*.     O  " rejected from bonding due to valence issues.
  Atom "ATOM  16378  O5'  DC J -20 .*.     O  " rejected from bonding due to valence issues.
  Atom "ATOM  16378  O5'  DC J -20 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.77
  Conformation dependent library (CDL) restraints added in 635.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 902 "
        pdb="ZN    ZN K 902 " - pdb=" NE2 HIS K  90 "
        pdb="ZN    ZN K 902 " - pdb=" SG  CYS K  58 "
        pdb="ZN    ZN K 902 " - pdb=" ND1 HIS K  84 "
        pdb="ZN    ZN K 902 " - pdb=" SG  CYS K  53 "
      pdb="  ZN K 903 "
        pdb="ZN    ZN K 903 " - pdb=" SG  CYS K  95 "
        pdb="ZN    ZN K 903 " - pdb=" SG  CYS K  65 "
        pdb="ZN    ZN K 903 " - pdb=" SG  CYS K  73 "
        pdb="ZN    ZN K 903 " - pdb=" SG  CYS K  92 "
      pdb="  ZN K 904 "
        pdb="ZN    ZN K 904 " - pdb=" SG  CYS K 147 "
        pdb="ZN    ZN K 904 " - pdb=" SG  CYS K 142 "
        pdb="ZN    ZN K 904 " - pdb=" SG  CYS K 185 "
        pdb="ZN    ZN K 904 " - pdb=" SG  CYS K 169 "
      Number of angles added : 13


  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2884

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 16 sheets defined
      55.6% alpha, 6.0% beta
      142 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 2.86
  Creating SS restraints...
    Processing helix  chain 'K' and resid 93 through 101
    Processing helix  chain 'K' and resid 106 through 117
    Processing helix  chain 'K' and resid 126 through 135
    Processing helix  chain 'K' and resid 160 through 167
    Processing helix  chain 'K' and resid 183 through 187
    Processing helix  chain 'K' and resid 191 through 196
      removed outlier: 3.945A  pdb=" N   GLU K 195 " --> pdb=" O   LEU K 191 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL K 196 " --> pdb=" O   ARG K 192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 191 through 196'
    Processing helix  chain 'K' and resid 198 through 204
      removed outlier: 4.047A  pdb=" N   TYR K 202 " --> pdb=" O   ASN K 198 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   SER K 203 " --> pdb=" O   HIS K 199 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 216 through 220
    Processing helix  chain 'K' and resid 224 through 228
    Processing helix  chain 'K' and resid 290 through 297
    Processing helix  chain 'K' and resid 298 through 301
    Processing helix  chain 'K' and resid 304 through 321
    Processing helix  chain 'K' and resid 327 through 332
    Processing helix  chain 'K' and resid 333 through 335
      No H-bonds generated for 'chain 'K' and resid 333 through 335'
    Processing helix  chain 'K' and resid 340 through 359
      removed outlier: 3.591A  pdb=" N   ARG K 344 " --> pdb=" O   LEU K 340 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   GLU K 350 " --> pdb=" O   VAL K 346 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   ARG K 351 " --> pdb=" O   GLN K 347 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 377 through 381
    Processing helix  chain 'K' and resid 391 through 405
    Processing helix  chain 'K' and resid 445 through 455
    Processing helix  chain 'K' and resid 476 through 498
    Processing helix  chain 'K' and resid 499 through 501
      No H-bonds generated for 'chain 'K' and resid 499 through 501'
    Processing helix  chain 'K' and resid 502 through 506
    Processing helix  chain 'K' and resid 508 through 524
    Processing helix  chain 'K' and resid 529 through 548
    Processing helix  chain 'K' and resid 560 through 565
    Processing helix  chain 'K' and resid 579 through 588
    Processing helix  chain 'K' and resid 628 through 635
    Processing helix  chain 'K' and resid 644 through 653
    Processing helix  chain 'K' and resid 671 through 676
    Processing helix  chain 'K' and resid 715 through 721
      removed outlier: 4.196A  pdb=" N   ALA K 719 " --> pdb=" O   GLY K 715 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 725 through 741
    Processing helix  chain 'K' and resid 756 through 760
    Processing helix  chain 'K' and resid 776 through 784
      removed outlier: 4.028A  pdb=" N   ASP K 780 " --> pdb=" O   GLY K 776 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 794 through 798
    Processing helix  chain 'K' and resid 804 through 822
      removed outlier: 3.731A  pdb=" N   PHE K 822 " --> pdb=" O   LYS K 818 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 219 through 223
      removed outlier: 3.845A  pdb=" N   SER L 223 " --> pdb=" O   PHE L 220 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 1 through 5
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 4.088A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 113
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.546A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.607A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.682A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.545A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 79
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.747A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 113
      removed outlier: 3.599A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.550A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 75
      removed outlier: 3.697A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   HIS F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.863A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 88
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.519A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 4.309A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 120
      removed outlier: 3.603A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA H 107 " --> pdb=" O   LEU H 103 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 82 through 86
      removed outlier: 6.483A  pdb=" N   GLU K  89 " --> pdb=" O   LEU K  85 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 139 through 141
    Processing sheet with id=AA3, first strand: chain 'K' and resid 592 through 593
      removed outlier: 8.208A  pdb=" N   GLN K 593 " --> pdb=" O   VAL K 408 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL K 410 " --> pdb=" O   GLN K 593 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL K 385 " --> pdb=" O   THR K 409 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   LEU K 411 " --> pdb=" O   VAL K 385 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE K 387 " --> pdb=" O   LEU K 411 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 423 through 424
    Processing sheet with id=AA5, first strand: chain 'K' and resid 438 through 440
    Processing sheet with id=AA6, first strand: chain 'K' and resid 467 through 468
      removed outlier: 5.345A  pdb=" N   ALA K 695 " --> pdb=" O   HIS K 683 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   VAL K 696 " --> pdb=" O   VAL K 712 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL K 712 " --> pdb=" O   VAL K 696 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LYS K 751 " --> pdb=" O   GLN K 665 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 617 through 620
      removed outlier: 6.794A  pdb=" N   GLN K 599 " --> pdb=" O   GLN K 638 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   ASN K 640 " --> pdb=" O   GLN K 599 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE K 601 " --> pdb=" O   ASN K 640 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 654 through 657
    Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.061A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.678A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AB4, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.780A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AB6, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.766A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'G' and resid 77 through 78

    614 hydrogen bonds defined for protein.
    1755 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      363 hydrogen bonds
      722 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 5.63

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2381
        1.31 -     1.44: 6614
        1.44 -     1.57: 9642
        1.57 -     1.69: 586
        1.69 -     1.82: 81
  Bond restraints: 19304
  Sorted by residual:
  bond pdb=" O5B FAD K 901 "
       pdb=" PA  FAD K 901 "
    ideal  model  delta    sigma   weight residual
    1.634  1.386  0.248 2.00e-02 2.50e+03 1.54e+02
  bond pdb=" O3P FAD K 901 "
       pdb=" P   FAD K 901 "
    ideal  model  delta    sigma   weight residual
    1.660  1.469  0.191 2.00e-02 2.50e+03 9.08e+01
  bond pdb=" O3P FAD K 901 "
       pdb=" PA  FAD K 901 "
    ideal  model  delta    sigma   weight residual
    1.633  1.454  0.179 2.00e-02 2.50e+03 8.02e+01
  bond pdb=" O5' FAD K 901 "
       pdb=" P   FAD K 901 "
    ideal  model  delta    sigma   weight residual
    1.637  1.464  0.173 2.00e-02 2.50e+03 7.49e+01
  bond pdb=" C1'  DG J  71 "
       pdb=" N9   DG J  71 "
    ideal  model  delta    sigma   weight residual
    1.468  1.353  0.115 1.40e-02 5.10e+03 6.81e+01
  ... (remaining 19299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.44: 27012
        3.44 -     6.88: 314
        6.88 -    10.32: 18
       10.32 -    13.76: 3
       13.76 -    17.20: 2
  Bond angle restraints: 27349
  Sorted by residual:
  angle pdb=" C   LYS K  75 "
        pdb=" CA  LYS K  75 "
        pdb=" CB  LYS K  75 "
      ideal   model   delta    sigma   weight residual
     117.23  108.24    8.99 1.36e+00 5.41e-01 4.37e+01
  angle pdb=" O1P FAD K 901 "
        pdb=" P   FAD K 901 "
        pdb=" O2P FAD K 901 "
      ideal   model   delta    sigma   weight residual
     122.50  105.30   17.20 3.00e+00 1.11e-01 3.29e+01
  angle pdb=" C   ASP L 214 "
        pdb=" N   PRO L 215 "
        pdb=" CA  PRO L 215 "
      ideal   model   delta    sigma   weight residual
     119.47  125.88   -6.41 1.16e+00 7.43e-01 3.05e+01
  angle pdb=" CA  ILE K 332 "
        pdb=" C   ILE K 332 "
        pdb=" N   PRO K 333 "
      ideal   model   delta    sigma   weight residual
     120.83  117.59    3.24 5.90e-01 2.87e+00 3.02e+01
  angle pdb=" CA  LYS K  75 "
        pdb=" C   LYS K  75 "
        pdb=" N   ASN K  76 "
      ideal   model   delta    sigma   weight residual
     119.98  115.34    4.64 8.50e-01 1.38e+00 2.98e+01
  ... (remaining 27344 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 9161
       35.90 -    71.80: 1631
       71.80 -   107.71: 31
      107.71 -   143.61: 1
      143.61 -   179.51: 1
  Dihedral angle restraints: 10825
    sinusoidal: 6349
      harmonic: 4476
  Sorted by residual:
  dihedral pdb=" CD  ARG A  40 "
           pdb=" NE  ARG A  40 "
           pdb=" CZ  ARG A  40 "
           pdb=" NH1 ARG A  40 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.61   85.61     1      1.00e+01 1.00e-02 8.87e+01
  dihedral pdb=" CD  ARG G  11 "
           pdb=" NE  ARG G  11 "
           pdb=" CZ  ARG G  11 "
           pdb=" NH1 ARG G  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -66.86   66.86     1      1.00e+01 1.00e-02 5.83e+01
  dihedral pdb=" CD  ARG H  30 "
           pdb=" NE  ARG H  30 "
           pdb=" CZ  ARG H  30 "
           pdb=" NH1 ARG H  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -57.41   57.41     1      1.00e+01 1.00e-02 4.43e+01
  ... (remaining 10822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 2234
       0.063 -    0.125: 684
       0.125 -    0.188: 121
       0.188 -    0.250: 17
       0.250 -    0.313: 3
  Chirality restraints: 3059
  Sorted by residual:
  chirality pdb=" C3' FAD K 901 "
            pdb=" C2' FAD K 901 "
            pdb=" C4' FAD K 901 "
            pdb=" O3' FAD K 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.24   -0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" CA  THR K 143 "
            pdb=" N   THR K 143 "
            pdb=" C   THR K 143 "
            pdb=" CB  THR K 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CG  LEU G  34 "
            pdb=" CB  LEU G  34 "
            pdb=" CD1 LEU G  34 "
            pdb=" CD2 LEU G  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 3056 not shown)

  Planarity restraints: 2447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FAD K 901 "    0.396 2.00e-02 2.50e+03   2.24e-01 2.38e+03
        pdb=" C10 FAD K 901 "    0.139 2.00e-02 2.50e+03
        pdb=" C2  FAD K 901 "   -0.215 2.00e-02 2.50e+03
        pdb=" C4  FAD K 901 "   -0.037 2.00e-02 2.50e+03
        pdb=" C4X FAD K 901 "    0.149 2.00e-02 2.50e+03
        pdb=" C5X FAD K 901 "    0.219 2.00e-02 2.50e+03
        pdb=" C6  FAD K 901 "    0.124 2.00e-02 2.50e+03
        pdb=" C7  FAD K 901 "   -0.076 2.00e-02 2.50e+03
        pdb=" C7M FAD K 901 "   -0.199 2.00e-02 2.50e+03
        pdb=" C8  FAD K 901 "   -0.172 2.00e-02 2.50e+03
        pdb=" C8M FAD K 901 "   -0.382 2.00e-02 2.50e+03
        pdb=" C9  FAD K 901 "   -0.055 2.00e-02 2.50e+03
        pdb=" C9A FAD K 901 "    0.149 2.00e-02 2.50e+03
        pdb=" N1  FAD K 901 "   -0.045 2.00e-02 2.50e+03
        pdb=" N10 FAD K 901 "    0.261 2.00e-02 2.50e+03
        pdb=" N3  FAD K 901 "   -0.223 2.00e-02 2.50e+03
        pdb=" N5  FAD K 901 "    0.370 2.00e-02 2.50e+03
        pdb=" O2  FAD K 901 "   -0.371 2.00e-02 2.50e+03
        pdb=" O4  FAD K 901 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  40 "   -1.098 9.50e-02 1.11e+02   4.92e-01 1.46e+02
        pdb=" NE  ARG A  40 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  40 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  40 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  40 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  11 "    1.006 9.50e-02 1.11e+02   4.51e-01 1.23e+02
        pdb=" NE  ARG G  11 "   -0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  11 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  11 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  11 "    0.023 2.00e-02 2.50e+03
  ... (remaining 2444 not shown)

  Histogram of nonbonded interaction distances:
        1.04 -     1.81: 12
        1.81 -     2.58: 204
        2.58 -     3.35: 23208
        3.35 -     4.13: 55301
        4.13 -     4.90: 85202
  Nonbonded interactions: 163927
  Sorted by model distance:
  nonbonded pdb=" CB  GLN M  19 "
            pdb=" O5'  DC J -20 "
     model   vdw
     1.036 3.440
  nonbonded pdb=" OE1 GLN M  19 "
            pdb=" OP2  DC J -20 "
     model   vdw
     1.301 3.040
  nonbonded pdb=" CG  GLN M  19 "
            pdb=" O5'  DC J -20 "
     model   vdw
     1.349 3.440
  nonbonded pdb=" CD  GLN M  19 "
            pdb=" OP2  DC J -20 "
     model   vdw
     1.474 3.270
  nonbonded pdb=" O   HIS E  39 "
            pdb=" O   ARG E  40 "
     model   vdw
     1.497 3.040
  ... (remaining 163922 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 37 through 134)
  selection = (chain 'E' and resid 37 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 17 through 120)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 25 through 121)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     23.820
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4457
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      :  0.010   0.347  19316  Z= 0.700
  Angle     :  1.135  17.201  27362  Z= 0.852
  Chirality :  0.061   0.313   3059
  Planarity :  0.023   0.492   2447
  Dihedral  : 25.683 179.511   7941
  Min Nonbonded Distance : 1.036

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  4.87 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  :  4.68 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    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 are not related in a simple way.
  whole: -2.97 (0.18), residues: 1518
  helix: -2.25 (0.14), residues: 782
  sheet:  0.51 (0.69), residues: 61
  loop : -1.69 (0.21), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG K  72 
 TYR   0.018   0.003   TYR K 767 
 PHE   0.033   0.003   PHE C  25 
 TRP   0.014   0.002   TRP K 117 
 HIS   0.014   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00927 /  0.69 (19304)
  covalent geometry    : angle       1.13042 /  0.85 (27349)
  hydrogen bonds       : bond        0.12828 /  8.66 (  977)
  hydrogen bonds       : angle       7.23156 /  5.11 ( 2477)
  metal coordination   : bond        0.14838 / 10.46 (   12)
  metal coordination   : angle       4.91515 /  2.82 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 215
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  119 SER cc_start: 0.1979 (OUTLIER) cc_final: 0.1684 (t)
REVERT: K  230 MET cc_start: 0.5294 (mtm) cc_final: 0.4220 (ttt)
REVERT: K  265 MET cc_start: -0.0069 (ttm) cc_final: -0.0413 (tpp)
REVERT: K  267 ARG cc_start: 0.4737 (OUTLIER) cc_final: 0.4253 (mpp-170)
REVERT: K  458 MET cc_start: -0.1116 (mtm) cc_final: -0.1583 (mtt)
REVERT: M    4 MET cc_start: -0.5283 (tpp) cc_final: -0.5685 (tpt)
REVERT: M   18 LYS cc_start: 0.0005 (OUTLIER) cc_final: -0.0271 (pttt)
REVERT: D   38 VAL cc_start: 0.9645 (t) cc_final: 0.9413 (m)
REVERT: E   65 LEU cc_start: 0.8813 (mt) cc_final: 0.8370 (mt)
REVERT: F   25 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8047 (t0)
REVERT: F   62 LEU cc_start: 0.9357 (mt) cc_final: 0.8954 (tt)
REVERT: G  112 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8164 (mm-40)
  outliers start: 74
  outliers final: 14
  residues processed: 282
  average time/residue: 0.2117
  time to fit residues: 81.2074
Evaluate side-chains
  116 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:   50.0000
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    3.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  76 ASN
K  93 ASN
K  98 HIS
K 400 GLN
K 440 ASN
K 803 GLN
L 218 HIS
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
F  93 GLN
H  46 HIS
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 106 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.100933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.067055 restraints weight = 226069.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.066671 restraints weight = 168088.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.062733 restraints weight = 140837.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.060409 restraints weight = 86659.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.060338 restraints weight = 63775.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  19316  Z= 0.197
  Angle     :  0.816  10.809  27362  Z= 0.444
  Chirality :  0.051   0.266   3059
  Planarity :  0.007   0.117   2447
  Dihedral  : 29.947 179.520   4917
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.43 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.45 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    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 are not related in a simple way.
  whole: -0.68 (0.20), residues: 1518
  helix: -0.08 (0.17), residues: 796
  sheet:  1.16 (0.66), residues: 61
  loop : -0.97 (0.23), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG A  83 
 TYR   0.019   0.002   TYR D  37 
 PHE   0.027   0.002   PHE C  25 
 TRP   0.007   0.001   TRP K 762 
 HIS   0.008   0.002   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.20 (19304)
  covalent geometry    : angle       0.81236 /  0.44 (27349)
  hydrogen bonds       : bond        0.07309 /  4.90 (  977)
  hydrogen bonds       : angle       4.52454 /  3.25 ( 2477)
  metal coordination   : bond        0.01618 /  1.24 (   12)
  metal coordination   : angle       3.58534 /  1.88 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  230 MET cc_start: 0.4362 (mtm) cc_final: 0.3972 (ttt)
REVERT: K  458 MET cc_start: 0.6748 (mtm) cc_final: 0.6346 (mtt)
REVERT: M    4 MET cc_start: -0.2865 (tpp) cc_final: -0.3875 (tpt)
REVERT: D   34 TYR cc_start: 0.8557 (m-10) cc_final: 0.8271 (m-10)
REVERT: D   99 LEU cc_start: 0.9352 (mm) cc_final: 0.8999 (tp)
REVERT: F   62 LEU cc_start: 0.9710 (mt) cc_final: 0.9482 (tt)
REVERT: H   59 MET cc_start: 0.9526 (tpt) cc_final: 0.9061 (tpp)
REVERT: H   77 LEU cc_start: 0.9374 (tt) cc_final: 0.9164 (pp)
  outliers start: 2
  outliers final: 1
  residues processed: 133
  average time/residue: 0.1988
  time to fit residues: 37.3262
Evaluate side-chains
  83 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 147 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 83 optimal weight:   10.0000
   chunk 133 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 68 optimal weight:   50.0000
   overall best weight:    5.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** 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 = 0.3680 r_free = 0.3680 target = 0.097142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.060872 restraints weight = 229354.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.055728 restraints weight = 185714.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.053856 restraints weight = 95933.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.053879 restraints weight = 67330.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.053870 restraints weight = 67420.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  19316  Z= 0.228
  Angle     :  0.752  11.783  27362  Z= 0.416
  Chirality :  0.047   0.226   3059
  Planarity :  0.005   0.067   2447
  Dihedral  : 30.022 178.334   4917
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.75 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.14 %
    Favored  : 96.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    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 are not related in a simple way.
  whole:  0.28 (0.21), residues: 1518
  helix:  0.84 (0.18), residues: 795
  sheet:  1.35 (0.60), residues: 71
  loop : -0.71 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  83 
 TYR   0.023   0.002   TYR B  88 
 PHE   0.016   0.002   PHE K  91 
 TRP   0.009   0.001   TRP K 762 
 HIS   0.007   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00428 /  0.23 (19304)
  covalent geometry    : angle       0.74766 /  0.42 (27349)
  hydrogen bonds       : bond        0.10129 /  6.63 (  977)
  hydrogen bonds       : angle       4.17682 /  3.01 ( 2477)
  metal coordination   : bond        0.01460 /  1.12 (   12)
  metal coordination   : angle       3.87104 /  2.17 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  230 MET cc_start: 0.4311 (mtm) cc_final: 0.3867 (ttt)
REVERT: D   34 TYR cc_start: 0.8598 (m-10) cc_final: 0.8149 (m-10)
REVERT: D   99 LEU cc_start: 0.9248 (mm) cc_final: 0.8929 (tp)
REVERT: H   59 MET cc_start: 0.9547 (tpt) cc_final: 0.9067 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.2075
  time to fit residues: 31.2884
Evaluate side-chains
  79 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 153 optimal weight:   30.0000
   chunk 96 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 164 optimal weight:   30.0000
   chunk 24 optimal weight:    0.2980
   chunk 98 optimal weight:    4.9990
   chunk 116 optimal weight:    4.9990
   chunk 159 optimal weight:   30.0000
   chunk 66 optimal weight:   30.0000
   chunk 170 optimal weight:   30.0000
   chunk 64 optimal weight:    6.9990
   overall best weight:    3.8588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 803 GLN
M   5 GLN
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
H  81 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.096793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.057177 restraints weight = 230187.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.052352 restraints weight = 179736.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.051438 restraints weight = 110513.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.050982 restraints weight = 90245.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.051103 restraints weight = 87413.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  19316  Z= 0.176
  Angle     :  0.690  10.120  27362  Z= 0.383
  Chirality :  0.046   0.245   3059
  Planarity :  0.005   0.055   2447
  Dihedral  : 30.035 179.811   4917
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.45 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    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 are not related in a simple way.
  whole:  0.59 (0.22), residues: 1518
  helix:  1.12 (0.18), residues: 800
  sheet:  1.00 (0.61), residues: 81
  loop : -0.56 (0.25), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  83 
 TYR   0.016   0.002   TYR E  99 
 PHE   0.014   0.001   PHE A 104 
 TRP   0.037   0.002   TRP K 559 
 HIS   0.008   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.18 (19304)
  covalent geometry    : angle       0.68764 /  0.38 (27349)
  hydrogen bonds       : bond        0.07052 /  4.66 (  977)
  hydrogen bonds       : angle       3.97201 /  2.87 ( 2477)
  metal coordination   : bond        0.00809 /  0.62 (   12)
  metal coordination   : angle       2.68126 /  1.53 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  171 MET cc_start: 0.4820 (ttp) cc_final: 0.4373 (ptm)
REVERT: K  230 MET cc_start: 0.4509 (mtm) cc_final: 0.4007 (ttt)
REVERT: K  483 MET cc_start: 0.2362 (mtm) cc_final: 0.2150 (mtp)
REVERT: M    4 MET cc_start: -0.4119 (tpt) cc_final: -0.4390 (tpt)
REVERT: A  120 MET cc_start: 0.8458 (mmp) cc_final: 0.8114 (mmm)
REVERT: D   34 TYR cc_start: 0.8685 (m-10) cc_final: 0.8440 (m-10)
REVERT: D   99 LEU cc_start: 0.9128 (mm) cc_final: 0.8844 (tp)
REVERT: H   59 MET cc_start: 0.9646 (tpt) cc_final: 0.8978 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 103
  average time/residue: 0.1883
  time to fit residues: 27.9391
Evaluate side-chains
  73 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 73 optimal weight:   50.0000
   chunk 16 optimal weight:   50.0000
   chunk 123 optimal weight:    8.9990
   chunk 105 optimal weight:    5.9990
   chunk 147 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 79 optimal weight:    8.9990
   chunk 124 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   chunk 129 optimal weight:    5.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** 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 = 0.3647 r_free = 0.3647 target = 0.095431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.051010 restraints weight = 229516.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.052064 restraints weight = 172527.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.049335 restraints weight = 131591.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.048198 restraints weight = 131324.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.048218 restraints weight = 116664.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  19316  Z= 0.185
  Angle     :  0.691  10.399  27362  Z= 0.383
  Chirality :  0.045   0.245   3059
  Planarity :  0.005   0.053   2447
  Dihedral  : 30.025 179.698   4917
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.23 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.38 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    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 are not related in a simple way.
  whole:  0.63 (0.21), residues: 1518
  helix:  1.14 (0.18), residues: 802
  sheet:  0.96 (0.61), residues: 81
  loop : -0.54 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  76 
 TYR   0.037   0.002   TYR K 273 
 PHE   0.015   0.001   PHE H  67 
 TRP   0.015   0.001   TRP K 559 
 HIS   0.009   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.19 (19304)
  covalent geometry    : angle       0.68952 /  0.38 (27349)
  hydrogen bonds       : bond        0.08366 /  5.47 (  977)
  hydrogen bonds       : angle       3.92315 /  2.82 ( 2477)
  metal coordination   : bond        0.00547 /  0.42 (   12)
  metal coordination   : angle       2.23178 /  1.34 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  171 MET cc_start: 0.4856 (ttp) cc_final: 0.4399 (ptm)
REVERT: K  230 MET cc_start: 0.4558 (mtm) cc_final: 0.4094 (ttt)
REVERT: A  120 MET cc_start: 0.8539 (mmp) cc_final: 0.8049 (mmm)
REVERT: D   34 TYR cc_start: 0.8992 (m-10) cc_final: 0.8739 (m-10)
REVERT: D   96 ARG cc_start: 0.9493 (mtp180) cc_final: 0.9164 (mtm110)
REVERT: D   99 LEU cc_start: 0.9068 (mm) cc_final: 0.8831 (tp)
REVERT: H   59 MET cc_start: 0.9667 (tpt) cc_final: 0.8971 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1812
  time to fit residues: 25.3408
Evaluate side-chains
  69 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 56 optimal weight:   50.0000
   chunk 38 optimal weight:    8.9990
   chunk 157 optimal weight:   30.0000
   chunk 59 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 76 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0070
   chunk 88 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    5.6006

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
M   5 GLN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.093504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.053825 restraints weight = 234838.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.047392 restraints weight = 189551.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.045955 restraints weight = 111956.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.045508 restraints weight = 82456.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.045508 restraints weight = 82548.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  19316  Z= 0.215
  Angle     :  0.719  14.261  27362  Z= 0.393
  Chirality :  0.045   0.229   3059
  Planarity :  0.005   0.079   2447
  Dihedral  : 30.155 179.196   4917
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.16 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.76 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    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 are not related in a simple way.
  whole:  0.78 (0.22), residues: 1518
  helix:  1.25 (0.18), residues: 803
  sheet:  0.93 (0.60), residues: 81
  loop : -0.43 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  69 
 TYR   0.031   0.002   TYR K 273 
 PHE   0.021   0.001   PHE G  25 
 TRP   0.015   0.001   TRP K 559 
 HIS   0.008   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.22 (19304)
  covalent geometry    : angle       0.71715 /  0.39 (27349)
  hydrogen bonds       : bond        0.10022 /  6.51 (  977)
  hydrogen bonds       : angle       4.01101 /  2.90 ( 2477)
  metal coordination   : bond        0.00748 /  0.58 (   12)
  metal coordination   : angle       2.15421 /  1.23 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  171 MET cc_start: 0.4737 (ttp) cc_final: 0.4215 (mtm)
REVERT: K  230 MET cc_start: 0.4656 (mtm) cc_final: 0.4198 (ttt)
REVERT: K  483 MET cc_start: 0.2790 (mtm) cc_final: 0.2331 (mtm)
REVERT: A  120 MET cc_start: 0.8831 (mmp) cc_final: 0.8450 (mmm)
REVERT: D   56 MET cc_start: 0.9554 (mmm) cc_final: 0.9312 (mmm)
REVERT: D   96 ARG cc_start: 0.9492 (mtp180) cc_final: 0.9045 (mtm110)
REVERT: D   99 LEU cc_start: 0.9118 (mm) cc_final: 0.8878 (tp)
REVERT: H   59 MET cc_start: 0.9680 (tpt) cc_final: 0.9024 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 89
  average time/residue: 0.1734
  time to fit residues: 22.5785
Evaluate side-chains
  66 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 147 optimal weight:    5.9990
   chunk 56 optimal weight:   50.0000
   chunk 30 optimal weight:    9.9990
   chunk 166 optimal weight:   30.0000
   chunk 9 optimal weight:   50.0000
   chunk 138 optimal weight:    1.9990
   chunk 29 optimal weight:   20.0000
   chunk 47 optimal weight:   50.0000
   chunk 127 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    5.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.093233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.053652 restraints weight = 235606.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.049650 restraints weight = 194414.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.047527 restraints weight = 152930.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.047587 restraints weight = 121390.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.051763 restraints weight = 120141.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.5177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  19316  Z= 0.201
  Angle     :  0.694  10.242  27362  Z= 0.385
  Chirality :  0.045   0.253   3059
  Planarity :  0.005   0.053   2447
  Dihedral  : 30.284 178.016   4917
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.16 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    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 are not related in a simple way.
  whole:  0.78 (0.22), residues: 1518
  helix:  1.21 (0.18), residues: 802
  sheet:  0.85 (0.60), residues: 81
  loop : -0.34 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  88 
 TYR   0.035   0.002   TYR E  54 
 PHE   0.016   0.001   PHE H  67 
 TRP   0.008   0.001   TRP K 762 
 HIS   0.009   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.20 (19304)
  covalent geometry    : angle       0.69335 /  0.39 (27349)
  hydrogen bonds       : bond        0.08835 /  5.76 (  977)
  hydrogen bonds       : angle       4.01251 /  2.89 ( 2477)
  metal coordination   : bond        0.00424 /  0.32 (   12)
  metal coordination   : angle       1.56495 /  0.99 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.570 
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: K  171 MET cc_start: 0.4721 (ttp) cc_final: 0.4178 (mtm)
REVERT: K  230 MET cc_start: 0.4860 (mtm) cc_final: 0.4385 (ttt)
REVERT: K  483 MET cc_start: 0.3009 (mtm) cc_final: 0.2619 (mtm)
REVERT: D   96 ARG cc_start: 0.9528 (mtp180) cc_final: 0.9092 (mtm110)
REVERT: H   56 MET cc_start: 0.9385 (tpp) cc_final: 0.9183 (tpp)
REVERT: H   59 MET cc_start: 0.9643 (tpt) cc_final: 0.9041 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1791
  time to fit residues: 22.2065
Evaluate side-chains
  60 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 31 optimal weight:   50.0000
   chunk 71 optimal weight:   30.0000
   chunk 77 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 124 optimal weight:    0.9990
   chunk 173 optimal weight:   40.0000
   chunk 126 optimal weight:    2.9990
   chunk 141 optimal weight:    7.9990
   chunk 149 optimal weight:   20.0000
   chunk 62 optimal weight:   20.0000
   chunk 35 optimal weight:   30.0000
   overall best weight:    5.7992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.092089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.051166 restraints weight = 235939.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.049826 restraints weight = 194671.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.047501 restraints weight = 177405.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.047500 restraints weight = 164256.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.047500 restraints weight = 164250.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.5581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  19316  Z= 0.219
  Angle     :  0.723  10.690  27362  Z= 0.395
  Chirality :  0.046   0.220   3059
  Planarity :  0.005   0.056   2447
  Dihedral  : 30.417 177.244   4917
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.16 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    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 are not related in a simple way.
  whole:  0.84 (0.22), residues: 1518
  helix:  1.17 (0.18), residues: 807
  sheet:  0.81 (0.60), residues: 81
  loop : -0.18 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  53 
 TYR   0.028   0.002   TYR E  54 
 PHE   0.030   0.001   PHE C  25 
 TRP   0.009   0.001   TRP K 762 
 HIS   0.010   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.22 (19304)
  covalent geometry    : angle       0.72228 /  0.39 (27349)
  hydrogen bonds       : bond        0.10250 /  6.65 (  977)
  hydrogen bonds       : angle       4.09432 /  2.96 ( 2477)
  metal coordination   : bond        0.00612 /  0.47 (   12)
  metal coordination   : angle       1.80370 /  1.02 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  171 MET cc_start: 0.4735 (ttp) cc_final: 0.4153 (mtm)
REVERT: K  230 MET cc_start: 0.4767 (mtm) cc_final: 0.4315 (ttt)
REVERT: K  483 MET cc_start: 0.2340 (mtm) cc_final: 0.1619 (ttm)
REVERT: A  120 MET cc_start: 0.8829 (mmp) cc_final: 0.8505 (mmm)
REVERT: D   96 ARG cc_start: 0.9379 (mtp180) cc_final: 0.8998 (mtm110)
REVERT: H   59 MET cc_start: 0.9695 (tpt) cc_final: 0.9029 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1833
  time to fit residues: 21.8304
Evaluate side-chains
  57 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 66 optimal weight:   40.0000
   chunk 138 optimal weight:    2.9990
   chunk 9 optimal weight:   50.0000
   chunk 132 optimal weight:    8.9990
   chunk 63 optimal weight:    9.9990
   chunk 7 optimal weight:   30.0000
   chunk 131 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0470
   chunk 154 optimal weight:   30.0000
   overall best weight:    1.2882

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.094730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.060832 restraints weight = 227998.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.056713 restraints weight = 186453.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.054685 restraints weight = 145583.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.055113 restraints weight = 98115.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.055157 restraints weight = 81917.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.5555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.064  19316  Z= 0.133
  Angle     :  0.673  11.841  27362  Z= 0.367
  Chirality :  0.045   0.257   3059
  Planarity :  0.004   0.070   2447
  Dihedral  : 30.291 176.504   4917
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.96 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 are not related in a simple way.
  whole:  1.01 (0.22), residues: 1518
  helix:  1.39 (0.18), residues: 809
  sheet:  0.77 (0.60), residues: 81
  loop : -0.22 (0.26), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  88 
 TYR   0.018   0.001   TYR E  99 
 PHE   0.014   0.001   PHE C  25 
 TRP   0.008   0.001   TRP K 762 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.13 (19304)
  covalent geometry    : angle       0.67305 /  0.37 (27349)
  hydrogen bonds       : bond        0.05028 /  3.33 (  977)
  hydrogen bonds       : angle       3.87015 /  2.82 ( 2477)
  metal coordination   : bond        0.00274 /  0.21 (   12)
  metal coordination   : angle       1.22476 /  0.77 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  171 MET cc_start: 0.4991 (ttp) cc_final: 0.4446 (mtm)
REVERT: K  230 MET cc_start: 0.4702 (mtm) cc_final: 0.4276 (ttt)
REVERT: K  483 MET cc_start: 0.2761 (mtm) cc_final: 0.2009 (ttm)
REVERT: A  120 MET cc_start: 0.9063 (mmp) cc_final: 0.8608 (mmm)
REVERT: H   59 MET cc_start: 0.9680 (tpt) cc_final: 0.8990 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1792
  time to fit residues: 22.4903
Evaluate side-chains
  65 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 175 optimal weight:   30.0000
   chunk 57 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 120 optimal weight:    1.9990
   chunk 62 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 161 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 109 optimal weight:    0.0060
   chunk 85 optimal weight:    5.9990
   chunk 5 optimal weight:   30.0000
   overall best weight:    4.8004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.051721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.023304 restraints weight = 194025.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.023872 restraints weight = 131709.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.024173 restraints weight = 101912.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.024353 restraints weight = 85955.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.024528 restraints weight = 77306.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.2513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.5842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  19316  Z= 0.188
  Angle     :  0.679  10.140  27362  Z= 0.373
  Chirality :  0.044   0.321   3059
  Planarity :  0.005   0.066   2447
  Dihedral  : 30.307 176.782   4917
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.10 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 are not related in a simple way.
  whole:  0.99 (0.22), residues: 1518
  helix:  1.34 (0.18), residues: 808
  sheet:  0.72 (0.60), residues: 81
  loop : -0.15 (0.26), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  35 
 TYR   0.027   0.002   TYR E  54 
 PHE   0.016   0.001   PHE C  25 
 TRP   0.008   0.001   TRP K 762 
 HIS   0.009   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.19 (19304)
  covalent geometry    : angle       0.67863 /  0.37 (27349)
  hydrogen bonds       : bond        0.09192 /  5.96 (  977)
  hydrogen bonds       : angle       3.97594 /  2.89 ( 2477)
  metal coordination   : bond        0.00430 /  0.33 (   12)
  metal coordination   : angle       1.36564 /  0.80 (   13)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  171 MET cc_start: 0.4945 (ttp) cc_final: 0.4362 (mtm)
REVERT: K  230 MET cc_start: 0.4785 (mtm) cc_final: 0.4335 (ttt)
REVERT: K  483 MET cc_start: 0.2019 (mtm) cc_final: 0.1322 (ttm)
REVERT: A  120 MET cc_start: 0.8954 (mmp) cc_final: 0.8553 (mmm)
REVERT: D   96 ARG cc_start: 0.9523 (mtp180) cc_final: 0.9059 (mtm110)
REVERT: H   59 MET cc_start: 0.9657 (tpt) cc_final: 0.8973 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1776
  time to fit residues: 20.5074
Evaluate side-chains
  59 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 157 optimal weight:   30.0000
   chunk 45 optimal weight:   50.0000
   chunk 117 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 132 optimal weight:    0.9980
   chunk 30 optimal weight:   30.0000
   chunk 63 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9990
   chunk 150 optimal weight:   30.0000
   chunk 69 optimal weight:    6.9990
   overall best weight:    4.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 184 HIS
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** H  46 HIS ** 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 = 0.3310 r_free = 0.3310 target = 0.051767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.023778 restraints weight = 191467.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.024293 restraints weight = 131252.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.024632 restraints weight = 102284.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.024822 restraints weight = 86810.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.024997 restraints weight = 78449.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.2507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.6085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  19316  Z= 0.171
  Angle     :  0.669  10.915  27362  Z= 0.368
  Chirality :  0.044   0.229   3059
  Planarity :  0.005   0.064   2447
  Dihedral  : 30.419 176.992   4917
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.36 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.59 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 are not related in a simple way.
  whole:  0.99 (0.22), residues: 1518
  helix:  1.32 (0.18), residues: 811
  sheet:  0.74 (0.60), residues: 81
  loop : -0.13 (0.26), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K 722 
 TYR   0.025   0.002   TYR C  50 
 PHE   0.017   0.001   PHE C  25 
 TRP   0.008   0.001   TRP K 762 
 HIS   0.008   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.17 (19304)
  covalent geometry    : angle       0.66876 /  0.37 (27349)
  hydrogen bonds       : bond        0.07251 /  4.71 (  977)
  hydrogen bonds       : angle       4.00719 /  2.92 ( 2477)
  metal coordination   : bond        0.00315 /  0.24 (   12)
  metal coordination   : angle       1.10544 /  0.65 (   13)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6081.33 seconds
wall clock time: 104 minutes 37.08 seconds (6277.08 seconds total)