Starting phenix.real_space_refine
on Sat Oct 11 11:33:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn5_40613/10_2025/8sn5_40613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn5_40613/10_2025/8sn5_40613.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn5_40613/10_2025/8sn5_40613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn5_40613/10_2025/8sn5_40613.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn5_40613/10_2025/8sn5_40613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn5_40613/10_2025/8sn5_40613.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8269      2.51       5
     N    2713      2.21       5
     O    3289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14600
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      32.772  74.839  47.610  1.00 92.05           S
  ATOM  12446  SG  CYS K  51      33.544  71.534  45.841  1.00 78.30           S
  ATOM  12470  SG  CYS K  54      32.537  74.397  43.794  1.00100.28           S
  ATOM  12187  SG  CYS K  16      22.380  68.849  53.466  1.00109.61           S
  ATOM  12205  SG  CYS K  19      20.326  66.237  55.227  1.00105.23           S
  ATOM  12335  SG  CYS K  36      23.285  67.916  57.089  1.00 94.72           S
  ATOM  12357  SG  CYS K  39      24.037  65.484  54.484  1.00 92.21           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 3.76, per 1000 atoms: 0.26
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (108.896, 134.128, 127.488, 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      2     29.99
     S      33     16.00
     P     294     15.00
     O    3289      8.00
     N    2713      7.00
     C    8269      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 502.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
      Number of angles added : 9


  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 13 sheets defined
      63.6% alpha, 5.3% beta
      135 base pairs and 233 stacking pairs defined.
    Time for finding SS restraints: 2.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.502A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.794A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.921A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 4.203A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.476A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.813A  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 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.725A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.708A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    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 76
      removed outlier: 3.803A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.571A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.543A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.571A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.619A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.596A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 90
      removed outlier: 3.702A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.773A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 145
      removed outlier: 4.256A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 39
      No H-bonds generated for 'chain 'M' and resid 37 through 39'
    Processing helix  chain 'M' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.679A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.738A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.809A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.826A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.004A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.679A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28
      removed outlier: 4.096A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16
      removed outlier: 3.623A  pdb=" N   VAL M   5 " --> pdb=" O   ILE M  13 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   LEU M  15 " --> pdb=" O   ILE M   3 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE M   3 " --> pdb=" O   LEU M  15 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   LEU M  67 " --> pdb=" O   GLN M   2 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   PHE M   4 " --> pdb=" O   LEU M  67 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU M  69 " --> pdb=" O   PHE M   4 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LYS M   6 " --> pdb=" O   LEU M  69 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   LEU M  71 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG M  42 " --> pdb=" O   VAL M  70 " (cutoff:3.500A)

    501 hydrogen bonds defined for protein.
    1464 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      233 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3384
        1.34 -     1.45: 4369
        1.45 -     1.57: 7084
        1.57 -     1.69: 586
        1.69 -     1.81: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CA  ILE B  29 "
       pdb=" CB  ILE B  29 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.015 1.36e-02 5.41e+03 1.26e+00
  bond pdb=" CB  LYS M  48 "
       pdb=" CG  LYS M  48 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.17e+00
  bond pdb=" C   VAL K  24 "
       pdb=" N   GLU K  25 "
    ideal  model  delta    sigma   weight residual
    1.331  1.353 -0.022 2.07e-02 2.33e+03 1.15e+00
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.29e-01
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 21557
        1.54 -     3.07: 551
        3.07 -     4.61: 41
        4.61 -     6.14: 16
        6.14 -     7.68: 6
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" N   TRP L 141 "
        pdb=" CA  TRP L 141 "
        pdb=" CB  TRP L 141 "
      ideal   model   delta    sigma   weight residual
     110.12  115.65   -5.53 1.47e+00 4.63e-01 1.41e+01
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  127.89   -6.35 1.91e+00 2.74e-01 1.10e+01
  angle pdb=" CB  LYS M  48 "
        pdb=" CG  LYS M  48 "
        pdb=" CD  LYS M  48 "
      ideal   model   delta    sigma   weight residual
     111.30  118.73   -7.43 2.30e+00 1.89e-01 1.04e+01
  angle pdb=" C   GLU L 140 "
        pdb=" N   TRP L 141 "
        pdb=" CA  TRP L 141 "
      ideal   model   delta    sigma   weight residual
     120.28  115.98    4.30 1.34e+00 5.57e-01 1.03e+01
  angle pdb=" CA  TRP L 141 "
        pdb=" CB  TRP L 141 "
        pdb=" CG  TRP L 141 "
      ideal   model   delta    sigma   weight residual
     113.60  118.60   -5.00 1.90e+00 2.77e-01 6.93e+00
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 7298
       35.68 -    71.35: 1294
       71.35 -   107.03: 17
      107.03 -   142.70: 0
      142.70 -   178.38: 2
  Dihedral angle restraints: 8611
    sinusoidal: 5471
      harmonic: 3140
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.38 -178.38     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   76.32  143.68     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" CA  ARG L 131 "
           pdb=" C   ARG L 131 "
           pdb=" N   ASP L 132 "
           pdb=" CA  ASP L 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.15  -17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1794
       0.031 -    0.061: 526
       0.061 -    0.092: 118
       0.092 -    0.123: 66
       0.123 -    0.153: 12
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.88e-01
  chirality pdb=" CA  GLN A 125 "
            pdb=" N   GLN A 125 "
            pdb=" C   GLN A 125 "
            pdb=" CB  GLN A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.78e-01
  chirality pdb=" CA  GLU K  25 "
            pdb=" N   GLU K  25 "
            pdb=" C   GLU K  25 "
            pdb=" CB  GLU K  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.52e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L 141 "    0.030 2.00e-02 2.50e+03   2.98e-02 2.23e+01
        pdb=" CG  TRP L 141 "   -0.081 2.00e-02 2.50e+03
        pdb=" CD1 TRP L 141 "    0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP L 141 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP L 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP L 141 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP L 141 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L 141 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP L 141 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.022 2.00e-02 2.50e+03   9.23e-03 2.34e+00
        pdb=" N9   DA I -35 "    0.018 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -54 "    0.020 2.00e-02 2.50e+03   9.03e-03 2.24e+00
        pdb=" N9   DA I -54 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8   DA I -54 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I -54 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I -54 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -54 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -54 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -54 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I -54 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3   DA I -54 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -54 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 413
        2.68 -     3.24: 13032
        3.24 -     3.79: 26278
        3.79 -     4.35: 32109
        4.35 -     4.90: 47543
  Nonbonded interactions: 119375
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.131 2.496
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG  SER L  91 "
            pdb=" OE1 GLN L  92 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OD1 ASP L 130 "
            pdb=" NZ  LYS L 133 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" OE2 GLU A  94 "
            pdb=" NE2 GLN G 104 "
     model   vdw
     2.243 3.120
  ... (remaining 119370 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.17 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.930
  Find NCS groups from input model:        0.130
  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:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
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      :  0.003   0.059  15482  Z= 0.152
  Angle     :  0.574   7.753  22186  Z= 0.329
  Chirality :  0.035   0.153   2516
  Planarity :  0.004   0.037   1794
  Dihedral  : 25.638 178.379   6577
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.22 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.27), residues: 1057
  helix:  2.63 (0.21), residues: 646
  sheet:  0.85 (0.75), residues: 47
  loop : -0.56 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 131 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.006   0.001   PHE D  70 
 TRP   0.081   0.005   TRP L 141 
 HIS   0.005   0.001   HIS D 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (15472)
  covalent geometry    : angle       0.56875 (22171)
  hydrogen bonds       : bond        0.10388 (  848)
  hydrogen bonds       : angle       3.98729 ( 2154)
  metal coordination   : bond        0.02151 (    8)
  metal coordination   : angle       3.91026 (    9)
  link_TRANS           : bond        0.00088 (    2)
  link_TRANS           : angle       0.68680 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.330 
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: A   60 LEU cc_start: 0.9152 (mt) cc_final: 0.8940 (mt)
REVERT: C   39 TYR cc_start: 0.8837 (m-80) cc_final: 0.8516 (m-80)
REVERT: D  108 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8001 (mtmt)
REVERT: H   35 GLU cc_start: 0.8641 (mp0) cc_final: 0.8421 (mp0)
REVERT: H   89 ILE cc_start: 0.9224 (mt) cc_final: 0.9005 (mt)
REVERT: K   13 GLU cc_start: 0.8434 (tp30) cc_final: 0.8139 (tm-30)
REVERT: L   60 TYR cc_start: 0.7143 (t80) cc_final: 0.6810 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1549
  time to fit residues: 60.0718
Evaluate side-chains
  226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  38 ASN
K  81 GLN
K  83 HIS
L  46 GLN
M   2 GLN
M  25 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.117179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.080063 restraints weight = 53905.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.081522 restraints weight = 37482.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.081232 restraints weight = 35512.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.081777 restraints weight = 21869.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.082215 restraints weight = 19251.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  15482  Z= 0.254
  Angle     :  0.670  12.322  22186  Z= 0.372
  Chirality :  0.039   0.154   2516
  Planarity :  0.005   0.050   1794
  Dihedral  : 29.044 178.709   4413
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.64 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.26), residues: 1057
  helix:  2.32 (0.21), residues: 651
  sheet:  0.42 (0.68), residues: 50
  loop : -0.72 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.021   0.002   TYR D  83 
 PHE   0.016   0.002   PHE L  62 
 TRP   0.069   0.004   TRP L 141 
 HIS   0.008   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 (15472)
  covalent geometry    : angle       0.65575 (22171)
  hydrogen bonds       : bond        0.05493 (  848)
  hydrogen bonds       : angle       3.76042 ( 2154)
  metal coordination   : bond        0.02354 (    8)
  metal coordination   : angle       6.95616 (    9)
  link_TRANS           : bond        0.00156 (    2)
  link_TRANS           : angle       0.49328 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 246
  time to evaluate  : 0.316 
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: A   57 SER cc_start: 0.9158 (t) cc_final: 0.8006 (t)
REVERT: A   59 GLU cc_start: 0.8941 (pm20) cc_final: 0.8264 (pm20)
REVERT: A   60 LEU cc_start: 0.9204 (mt) cc_final: 0.8986 (mt)
REVERT: A  125 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7185 (pm20)
REVERT: C  110 ASN cc_start: 0.8576 (p0) cc_final: 0.8362 (p0)
REVERT: D  108 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8066 (mtpt)
REVERT: F   88 TYR cc_start: 0.8899 (m-80) cc_final: 0.8622 (m-80)
REVERT: H   35 GLU cc_start: 0.8980 (mp0) cc_final: 0.8607 (mp0)
REVERT: K   20 MET cc_start: 0.7644 (mmp) cc_final: 0.7403 (mmp)
REVERT: K   21 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7023 (mm-30)
REVERT: K   65 HIS cc_start: 0.7912 (m-70) cc_final: 0.7677 (m-70)
REVERT: K   68 ARG cc_start: 0.7074 (mtm110) cc_final: 0.6292 (mtm110)
REVERT: L   60 TYR cc_start: 0.7573 (t80) cc_final: 0.7248 (t80)
REVERT: L   88 ILE cc_start: 0.8704 (mp) cc_final: 0.8479 (mp)
REVERT: M   24 GLU cc_start: 0.5995 (tp30) cc_final: 0.5551 (mp0)
  outliers start: 19
  outliers final: 14
  residues processed: 249
  average time/residue: 0.1450
  time to fit residues: 50.5254
Evaluate side-chains
  230 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 215
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   10 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   45 TYR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0050
   chunk 39 optimal weight:    0.8980
   chunk 101 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 102 optimal weight:    9.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
H  47 GLN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 ASN
L  46 GLN
L  55 HIS
M  25 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.119075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.080300 restraints weight = 47711.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.079944 restraints weight = 28390.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.080396 restraints weight = 28978.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.080906 restraints weight = 20365.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.081428 restraints weight = 17956.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15482  Z= 0.156
  Angle     :  0.584   9.820  22186  Z= 0.332
  Chirality :  0.035   0.150   2516
  Planarity :  0.004   0.046   1794
  Dihedral  : 28.981 179.593   4413
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.58 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.27), residues: 1057
  helix:  2.53 (0.21), residues: 651
  sheet:  0.75 (0.65), residues: 48
  loop : -0.71 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.013   0.002   TYR L  74 
 PHE   0.014   0.001   PHE L  62 
 TRP   0.013   0.002   TRP L 141 
 HIS   0.004   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (15472)
  covalent geometry    : angle       0.57384 (22171)
  hydrogen bonds       : bond        0.04375 (  848)
  hydrogen bonds       : angle       3.35282 ( 2154)
  metal coordination   : bond        0.01666 (    8)
  metal coordination   : angle       5.43266 (    9)
  link_TRANS           : bond        0.00029 (    2)
  link_TRANS           : angle       0.36197 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 241
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9119 (t) cc_final: 0.7770 (t)
REVERT: A   59 GLU cc_start: 0.8830 (pm20) cc_final: 0.8310 (pm20)
REVERT: A  123 ASP cc_start: 0.8729 (m-30) cc_final: 0.8458 (m-30)
REVERT: A  125 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7025 (pm20)
REVERT: C   13 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7869 (tppt)
REVERT: D  108 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8011 (mtpt)
REVERT: F   88 TYR cc_start: 0.8957 (m-80) cc_final: 0.8570 (m-10)
REVERT: G  118 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7795 (tmtt)
REVERT: H   35 GLU cc_start: 0.8971 (mp0) cc_final: 0.8607 (mp0)
REVERT: H   40 TYR cc_start: 0.9230 (m-80) cc_final: 0.8792 (m-80)
REVERT: K   68 ARG cc_start: 0.7036 (mtm110) cc_final: 0.6701 (mtm110)
REVERT: L    8 LYS cc_start: 0.9279 (mtmt) cc_final: 0.9032 (mtmt)
REVERT: L   60 TYR cc_start: 0.7555 (t80) cc_final: 0.7235 (t80)
REVERT: L   88 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8342 (mp)
REVERT: L  134 TYR cc_start: 0.7061 (t80) cc_final: 0.6708 (t80)
  outliers start: 14
  outliers final: 9
  residues processed: 246
  average time/residue: 0.1389
  time to fit residues: 48.0011
Evaluate side-chains
  234 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 223
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 102 optimal weight:    0.2980
   chunk 60 optimal weight:    0.1980
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 128 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
G  38 ASN
K  41 GLN
L  55 HIS
L 143 GLN
M  25 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.120106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.086338 restraints weight = 62306.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.088546 restraints weight = 65512.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.089275 restraints weight = 33239.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.089925 restraints weight = 24736.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.090522 restraints weight = 21276.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15482  Z= 0.152
  Angle     :  0.584  12.536  22186  Z= 0.327
  Chirality :  0.035   0.162   2516
  Planarity :  0.004   0.047   1794
  Dihedral  : 29.010 179.241   4413
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.29 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.27), residues: 1057
  helix:  2.46 (0.21), residues: 660
  sheet:  0.86 (0.67), residues: 48
  loop : -0.77 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.015   0.001   TYR E  99 
 PHE   0.015   0.001   PHE L  62 
 TRP   0.013   0.002   TRP K  61 
 HIS   0.012   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (15472)
  covalent geometry    : angle       0.57329 (22171)
  hydrogen bonds       : bond        0.04185 (  848)
  hydrogen bonds       : angle       3.25499 ( 2154)
  metal coordination   : bond        0.01626 (    8)
  metal coordination   : angle       5.44329 (    9)
  link_TRANS           : bond        0.00039 (    2)
  link_TRANS           : angle       0.28035 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 241
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9074 (t) cc_final: 0.7736 (t)
REVERT: A   59 GLU cc_start: 0.8808 (pm20) cc_final: 0.8080 (pm20)
REVERT: A  123 ASP cc_start: 0.8884 (m-30) cc_final: 0.8603 (m-30)
REVERT: A  125 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7204 (pm20)
REVERT: B   63 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8031 (mt-10)
REVERT: B   67 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7899 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7648 (mtp-110) cc_final: 0.7203 (mtm110)
REVERT: D  108 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7912 (mtmt)
REVERT: F   88 TYR cc_start: 0.8796 (m-80) cc_final: 0.8472 (m-10)
REVERT: H   35 GLU cc_start: 0.8784 (mp0) cc_final: 0.8537 (mp0)
REVERT: H   40 TYR cc_start: 0.9221 (m-80) cc_final: 0.8827 (m-80)
REVERT: L   31 PHE cc_start: 0.7752 (m-10) cc_final: 0.7445 (m-80)
REVERT: L   88 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8205 (mp)
REVERT: M   52 ASP cc_start: 0.6314 (m-30) cc_final: 0.5458 (m-30)
  outliers start: 21
  outliers final: 13
  residues processed: 247
  average time/residue: 0.1533
  time to fit residues: 52.6181
Evaluate side-chains
  236 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 221
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 87 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 126 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  38 ASN
K  41 GLN
** L  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  55 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.117726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.082529 restraints weight = 52464.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.085209 restraints weight = 51312.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.084818 restraints weight = 35338.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.084470 restraints weight = 27699.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.085002 restraints weight = 23248.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  15482  Z= 0.204
  Angle     :  0.635  11.999  22186  Z= 0.352
  Chirality :  0.037   0.196   2516
  Planarity :  0.004   0.048   1794
  Dihedral  : 29.101 179.062   4413
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.02 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.26), residues: 1057
  helix:  2.36 (0.21), residues: 658
  sheet:  0.54 (0.66), residues: 48
  loop : -0.88 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  71 
 TYR   0.018   0.002   TYR L 134 
 PHE   0.013   0.001   PHE L  62 
 TRP   0.015   0.002   TRP L  33 
 HIS   0.011   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 (15472)
  covalent geometry    : angle       0.62467 (22171)
  hydrogen bonds       : bond        0.04799 (  848)
  hydrogen bonds       : angle       3.47190 ( 2154)
  metal coordination   : bond        0.02080 (    8)
  metal coordination   : angle       5.82114 (    9)
  link_TRANS           : bond        0.00154 (    2)
  link_TRANS           : angle       0.35703 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 227
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9034 (t) cc_final: 0.7673 (t)
REVERT: A   59 GLU cc_start: 0.8828 (pm20) cc_final: 0.7902 (pm20)
REVERT: A  125 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7223 (pm20)
REVERT: B   63 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8122 (mt-10)
REVERT: D   33 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.7144 (mtm110)
REVERT: D  108 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8012 (mtpt)
REVERT: F   88 TYR cc_start: 0.9055 (m-10) cc_final: 0.8623 (m-10)
REVERT: G   24 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8285 (mm-40)
REVERT: H   35 GLU cc_start: 0.8775 (mp0) cc_final: 0.8490 (mp0)
REVERT: H   40 TYR cc_start: 0.9270 (m-80) cc_final: 0.8946 (m-80)
REVERT: K   41 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8670 (tp40)
REVERT: K   84 TYR cc_start: 0.7701 (m-80) cc_final: 0.6700 (m-80)
REVERT: L   31 PHE cc_start: 0.7825 (m-10) cc_final: 0.7578 (m-80)
REVERT: L   88 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8298 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 236
  average time/residue: 0.1430
  time to fit residues: 47.7314
Evaluate side-chains
  237 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 216
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 63 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 122 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 110 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0050
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  38 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 ASN
L  46 GLN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.120250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.082954 restraints weight = 51840.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.084278 restraints weight = 34005.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.083947 restraints weight = 33306.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.084620 restraints weight = 20131.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.084995 restraints weight = 17559.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15482  Z= 0.148
  Angle     :  0.611  12.529  22186  Z= 0.339
  Chirality :  0.035   0.180   2516
  Planarity :  0.004   0.043   1794
  Dihedral  : 28.994 179.611   4413
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.89 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.27), residues: 1057
  helix:  2.47 (0.21), residues: 659
  sheet:  0.34 (0.67), residues: 49
  loop : -0.87 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  71 
 TYR   0.027   0.001   TYR L 134 
 PHE   0.010   0.001   PHE L  62 
 TRP   0.028   0.003   TRP L 141 
 HIS   0.009   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (15472)
  covalent geometry    : angle       0.60157 (22171)
  hydrogen bonds       : bond        0.04126 (  848)
  hydrogen bonds       : angle       3.22003 ( 2154)
  metal coordination   : bond        0.01677 (    8)
  metal coordination   : angle       5.22584 (    9)
  link_TRANS           : bond        0.00038 (    2)
  link_TRANS           : angle       0.23494 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 228
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9091 (t) cc_final: 0.8877 (t)
REVERT: A  123 ASP cc_start: 0.8859 (m-30) cc_final: 0.8614 (m-30)
REVERT: A  125 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7016 (pm20)
REVERT: B   63 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8022 (mt-10)
REVERT: B   67 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7928 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7476 (mtp-110)
REVERT: D  108 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7995 (mtpt)
REVERT: E   61 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9117 (mm)
REVERT: F   88 TYR cc_start: 0.9066 (m-10) cc_final: 0.8864 (m-10)
REVERT: H   35 GLU cc_start: 0.8930 (mp0) cc_final: 0.8563 (mp0)
REVERT: H   40 TYR cc_start: 0.9255 (m-80) cc_final: 0.8868 (m-80)
REVERT: K   68 ARG cc_start: 0.6879 (mtm110) cc_final: 0.6285 (mtm110)
REVERT: K   84 TYR cc_start: 0.7778 (m-80) cc_final: 0.6834 (m-80)
REVERT: L   31 PHE cc_start: 0.7955 (m-10) cc_final: 0.7573 (m-80)
REVERT: L   88 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8328 (mp)
REVERT: M    1 MET cc_start: 0.5816 (tmm) cc_final: 0.5224 (tpt)
  outliers start: 19
  outliers final: 14
  residues processed: 236
  average time/residue: 0.1440
  time to fit residues: 47.6342
Evaluate side-chains
  238 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 221
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
K  69 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.118822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.084020 restraints weight = 54420.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.083675 restraints weight = 53066.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.084291 restraints weight = 42404.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.086207 restraints weight = 26236.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.086146 restraints weight = 22742.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3042
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3042
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  15482  Z= 0.178
  Angle     :  0.628  13.083  22186  Z= 0.347
  Chirality :  0.036   0.180   2516
  Planarity :  0.004   0.044   1794
  Dihedral  : 29.048 179.036   4413
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.67 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.27), residues: 1057
  helix:  2.43 (0.21), residues: 659
  sheet:  0.30 (0.68), residues: 48
  loop : -0.89 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  31 
 TYR   0.022   0.002   TYR L 134 
 PHE   0.014   0.001   PHE L  62 
 TRP   0.042   0.003   TRP L 141 
 HIS   0.010   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (15472)
  covalent geometry    : angle       0.61809 (22171)
  hydrogen bonds       : bond        0.04502 (  848)
  hydrogen bonds       : angle       3.36502 ( 2154)
  metal coordination   : bond        0.01856 (    8)
  metal coordination   : angle       5.54202 (    9)
  link_TRANS           : bond        0.00099 (    2)
  link_TRANS           : angle       0.28338 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 228
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.8940 (m-30) cc_final: 0.8658 (m-30)
REVERT: A  125 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7185 (pm20)
REVERT: B   63 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: D   33 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7502 (mtp-110)
REVERT: D  108 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8018 (mtpt)
REVERT: E   61 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9132 (mm)
REVERT: F   84 MET cc_start: 0.8886 (mmm) cc_final: 0.8601 (mmm)
REVERT: F   88 TYR cc_start: 0.9143 (m-10) cc_final: 0.8865 (m-10)
REVERT: G   24 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8213 (mm-40)
REVERT: H   35 GLU cc_start: 0.8786 (mp0) cc_final: 0.8497 (mp0)
REVERT: H   40 TYR cc_start: 0.9246 (m-80) cc_final: 0.9036 (m-80)
REVERT: K   21 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7088 (mm-30)
REVERT: K   68 ARG cc_start: 0.6881 (mtm110) cc_final: 0.6296 (mtm110)
REVERT: K   84 TYR cc_start: 0.7688 (m-80) cc_final: 0.6760 (m-80)
REVERT: L   31 PHE cc_start: 0.7915 (m-10) cc_final: 0.7591 (m-80)
REVERT: L   60 TYR cc_start: 0.7415 (t80) cc_final: 0.7182 (t80)
REVERT: L   88 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8242 (mp)
REVERT: M    1 MET cc_start: 0.5306 (tmm) cc_final: 0.4791 (tpt)
  outliers start: 22
  outliers final: 17
  residues processed: 236
  average time/residue: 0.1410
  time to fit residues: 46.8180
Evaluate side-chains
  241 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 221
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0060
   chunk 120 optimal weight:    3.9990
   chunk 116 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 127 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
M  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.120008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.084128 restraints weight = 58652.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.087101 restraints weight = 42830.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.086109 restraints weight = 32945.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.086661 restraints weight = 20672.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.087143 restraints weight = 18153.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15482  Z= 0.156
  Angle     :  0.634  13.734  22186  Z= 0.347
  Chirality :  0.036   0.186   2516
  Planarity :  0.004   0.043   1794
  Dihedral  : 28.998 179.280   4413
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.43 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.27), residues: 1057
  helix:  2.42 (0.21), residues: 659
  sheet:  0.25 (0.69), residues: 48
  loop : -0.92 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  31 
 TYR   0.020   0.002   TYR E  99 
 PHE   0.014   0.001   PHE L  62 
 TRP   0.076   0.004   TRP L 141 
 HIS   0.009   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (15472)
  covalent geometry    : angle       0.62435 (22171)
  hydrogen bonds       : bond        0.04210 (  848)
  hydrogen bonds       : angle       3.26807 ( 2154)
  metal coordination   : bond        0.01636 (    8)
  metal coordination   : angle       5.54978 (    9)
  link_TRANS           : bond        0.00043 (    2)
  link_TRANS           : angle       0.25087 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 227
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8802 (pm20) cc_final: 0.8455 (pm20)
REVERT: A  123 ASP cc_start: 0.8967 (m-30) cc_final: 0.8724 (m-30)
REVERT: A  125 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6993 (pm20)
REVERT: B   63 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: B   67 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7898 (ttp-170)
REVERT: D  108 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7984 (mtpt)
REVERT: E   61 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9070 (mm)
REVERT: F   84 MET cc_start: 0.8908 (mmm) cc_final: 0.8624 (mmm)
REVERT: F   88 TYR cc_start: 0.9029 (m-10) cc_final: 0.8740 (m-10)
REVERT: H   35 GLU cc_start: 0.8956 (mp0) cc_final: 0.8595 (mp0)
REVERT: H   40 TYR cc_start: 0.9248 (m-80) cc_final: 0.8892 (m-80)
REVERT: K   41 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.8834 (tp40)
REVERT: K   68 ARG cc_start: 0.6955 (mtm110) cc_final: 0.6476 (mtm110)
REVERT: K   84 TYR cc_start: 0.7759 (m-80) cc_final: 0.6816 (m-80)
REVERT: L   31 PHE cc_start: 0.8195 (m-10) cc_final: 0.7741 (m-80)
REVERT: L   56 PHE cc_start: 0.7948 (m-80) cc_final: 0.7729 (m-80)
REVERT: L   74 TYR cc_start: 0.6990 (t80) cc_final: 0.6631 (t80)
REVERT: L   88 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8342 (mp)
REVERT: L  147 MET cc_start: 0.7871 (mmp) cc_final: 0.7044 (ptp)
REVERT: M    1 MET cc_start: 0.5228 (tmm) cc_final: 0.4747 (tpt)
  outliers start: 27
  outliers final: 20
  residues processed: 238
  average time/residue: 0.1337
  time to fit residues: 45.2469
Evaluate side-chains
  249 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 225
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   15 ARG
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    0.5980
   chunk 72 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
K  41 GLN
** L  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 143 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.119778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.083190 restraints weight = 45528.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.083599 restraints weight = 39644.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.083951 restraints weight = 42017.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.084388 restraints weight = 26764.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.085613 restraints weight = 23515.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15482  Z= 0.160
  Angle     :  0.640  13.653  22186  Z= 0.351
  Chirality :  0.036   0.251   2516
  Planarity :  0.004   0.063   1794
  Dihedral  : 29.025 178.856   4413
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.75 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.27), residues: 1057
  helix:  2.43 (0.21), residues: 653
  sheet:  0.25 (0.69), residues: 48
  loop : -0.87 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.028   0.002   TYR L  74 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.089   0.005   TRP L 141 
 HIS   0.009   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (15472)
  covalent geometry    : angle       0.63174 (22171)
  hydrogen bonds       : bond        0.04330 (  848)
  hydrogen bonds       : angle       3.33310 ( 2154)
  metal coordination   : bond        0.01706 (    8)
  metal coordination   : angle       5.09608 (    9)
  link_TRANS           : bond        0.00055 (    2)
  link_TRANS           : angle       0.24071 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 226
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8744 (pm20) cc_final: 0.8327 (pm20)
REVERT: A  123 ASP cc_start: 0.8931 (m-30) cc_final: 0.8670 (m-30)
REVERT: A  125 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7186 (pm20)
REVERT: B   63 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8080 (mt-10)
REVERT: D   59 MET cc_start: 0.8464 (tpp) cc_final: 0.7832 (tpp)
REVERT: D  108 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8075 (mtmt)
REVERT: E   61 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9097 (mm)
REVERT: F   84 MET cc_start: 0.8883 (mmm) cc_final: 0.8608 (mmm)
REVERT: F   88 TYR cc_start: 0.9149 (m-10) cc_final: 0.8905 (m-10)
REVERT: H   35 GLU cc_start: 0.8817 (mp0) cc_final: 0.8518 (mp0)
REVERT: H   40 TYR cc_start: 0.9201 (m-80) cc_final: 0.8868 (m-80)
REVERT: K   20 MET cc_start: 0.7615 (mmp) cc_final: 0.7246 (mmp)
REVERT: K   41 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8818 (tp40)
REVERT: K   68 ARG cc_start: 0.6676 (mtm110) cc_final: 0.6006 (mtm110)
REVERT: K   84 TYR cc_start: 0.7630 (m-80) cc_final: 0.6707 (m-80)
REVERT: L   31 PHE cc_start: 0.7848 (m-10) cc_final: 0.7491 (m-80)
REVERT: L   88 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8200 (mp)
REVERT: M    1 MET cc_start: 0.4900 (tmm) cc_final: 0.4422 (tpt)
  outliers start: 28
  outliers final: 23
  residues processed: 236
  average time/residue: 0.1324
  time to fit residues: 44.6806
Evaluate side-chains
  244 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 217
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   15 ARG
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 18 optimal weight:    0.2980
   chunk 81 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 111 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0270
   chunk 114 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.6442

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 143 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.120217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.087870 restraints weight = 61960.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.089218 restraints weight = 71262.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.090656 restraints weight = 33210.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.091877 restraints weight = 23722.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.092166 restraints weight = 21234.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15482  Z= 0.157
  Angle     :  0.646  14.731  22186  Z= 0.353
  Chirality :  0.036   0.227   2516
  Planarity :  0.004   0.066   1794
  Dihedral  : 29.024 178.863   4413
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.29 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.27), residues: 1057
  helix:  2.43 (0.21), residues: 659
  sheet:  0.30 (0.69), residues: 48
  loop : -0.92 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG L 139 
 TYR   0.022   0.001   TYR E  99 
 PHE   0.014   0.001   PHE L  62 
 TRP   0.101   0.006   TRP L 141 
 HIS   0.009   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (15472)
  covalent geometry    : angle       0.63754 (22171)
  hydrogen bonds       : bond        0.04272 (  848)
  hydrogen bonds       : angle       3.30879 ( 2154)
  metal coordination   : bond        0.01617 (    8)
  metal coordination   : angle       5.38408 (    9)
  link_TRANS           : bond        0.00043 (    2)
  link_TRANS           : angle       0.22477 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 226
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8743 (pm20) cc_final: 0.8266 (pm20)
REVERT: A  123 ASP cc_start: 0.8866 (m-30) cc_final: 0.8594 (m-30)
REVERT: A  125 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7203 (pm20)
REVERT: B   63 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8062 (mt-10)
REVERT: B   67 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7904 (ttp-170)
REVERT: D   59 MET cc_start: 0.8495 (tpp) cc_final: 0.7880 (tpp)
REVERT: D  108 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7973 (mtmt)
REVERT: E   61 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9069 (mm)
REVERT: F   84 MET cc_start: 0.8763 (mmm) cc_final: 0.8484 (mmm)
REVERT: F   88 TYR cc_start: 0.9004 (m-10) cc_final: 0.8736 (m-10)
REVERT: H   35 GLU cc_start: 0.8790 (mp0) cc_final: 0.8546 (mp0)
REVERT: H   40 TYR cc_start: 0.9205 (m-80) cc_final: 0.8873 (m-80)
REVERT: K   20 MET cc_start: 0.7542 (mmp) cc_final: 0.7184 (mmp)
REVERT: K   41 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8862 (tp40)
REVERT: K   68 ARG cc_start: 0.6630 (mtm110) cc_final: 0.5911 (mtm110)
REVERT: K   84 TYR cc_start: 0.7637 (m-80) cc_final: 0.6731 (m-80)
REVERT: L   31 PHE cc_start: 0.7859 (m-10) cc_final: 0.7509 (m-80)
REVERT: L   56 PHE cc_start: 0.7916 (m-80) cc_final: 0.7687 (m-80)
REVERT: L   88 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8166 (mp)
REVERT: M    1 MET cc_start: 0.4980 (tmm) cc_final: 0.4520 (tpt)
  outliers start: 24
  outliers final: 21
  residues processed: 236
  average time/residue: 0.1324
  time to fit residues: 44.7759
Evaluate side-chains
  247 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 223
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   15 ARG
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 128 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 71 optimal weight:    0.3980
   chunk 113 optimal weight:    0.0170
   chunk 24 optimal weight:    0.5980
   chunk 87 optimal weight:    6.9990
   chunk 123 optimal weight:    2.9990
   chunk 127 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0000
   overall best weight:    0.3822

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
K  41 GLN
** L  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.122194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.088582 restraints weight = 54014.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.087316 restraints weight = 57581.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.088495 restraints weight = 45030.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.090437 restraints weight = 27449.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.090417 restraints weight = 24459.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15482  Z= 0.149
  Angle     :  0.650  14.648  22186  Z= 0.355
  Chirality :  0.036   0.221   2516
  Planarity :  0.004   0.061   1794
  Dihedral  : 28.975 178.737   4413
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.84 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.27), residues: 1057
  helix:  2.49 (0.21), residues: 653
  sheet:  0.26 (0.69), residues: 48
  loop : -0.86 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.022   0.002   TYR E  99 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.082   0.005   TRP L 141 
 HIS   0.008   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (15472)
  covalent geometry    : angle       0.64174 (22171)
  hydrogen bonds       : bond        0.04119 (  848)
  hydrogen bonds       : angle       3.26394 ( 2154)
  metal coordination   : bond        0.01423 (    8)
  metal coordination   : angle       5.23060 (    9)
  link_TRANS           : bond        0.00015 (    2)
  link_TRANS           : angle       0.19825 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2386.30 seconds
wall clock time: 41 minutes 55.12 seconds (2515.12 seconds total)