Starting phenix.real_space_refine
on Thu Aug  6 07:41:59 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn9_40617/08_2026/8sn9_40617.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn9_40617/08_2026/8sn9_40617.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn9_40617/08_2026/8sn9_40617.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn9_40617/08_2026/8sn9_40617.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8sn9_40617/08_2026/8sn9_40617.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8sn9_40617/08_2026/8sn9_40617.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn9_40617/08_2026/8sn9_40617.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn9_40617/08_2026/8sn9_40617.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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    8264      2.51       5
     N    2710      2.21       5
     O    3288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14591
  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: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 682
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 3
    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      53.370  71.554  45.709  1.00 90.47           S
  ATOM  12446  SG  CYS K  51      52.485  67.970  44.923  1.00 88.01           S
  ATOM  12470  SG  CYS K  54      52.408  70.634  42.129  1.00 89.07           S
  ATOM  12187  SG  CYS K  16      43.387  65.421  52.089  1.00 95.41           S
  ATOM  12205  SG  CYS K  19      43.026  62.019  53.804  1.00 88.88           S
  ATOM  12335  SG  CYS K  36      44.943  64.767  55.368  1.00 85.82           S
  ATOM  12357  SG  CYS K  39      46.383  62.853  52.270  1.00 90.71           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: 2.64, per 1000 atoms: 0.18
  Number of scatterers: 14591
  At special positions: 0
  Unit cell: (130.144, 130.144, 124.832, 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    3288      8.00
     N    2710      7.00
     C    8264      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: 1.00
  Conformation dependent library (CDL) restraints added in 412.3 milliseconds
  
  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  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
      Number of angles added : 9


  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 13 sheets defined
      61.6% alpha, 5.5% beta
      136 base pairs and 252 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.817A  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: 3.578A  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: 3.946A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.650A  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: 3.931A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.717A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.619A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.849A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.670A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.752A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.743A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.866A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.553A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.577A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    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: 3.893A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (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 36
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    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
      removed outlier: 3.782A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.811A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.550A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 68
      removed outlier: 3.806A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.294A  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 91
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 4.081A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.591A  pdb=" N   ASP L 111 " --> pdb=" O   ALA L 107 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.652A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.925A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 34
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.585A  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
    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: 7.806A  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: 6.783A  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: 7.563A  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: 7.747A  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 26 through 28
    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

    492 hydrogen bonds defined for protein.
    1453 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      252 stacking parallelities
  Total time for adding SS restraints: 2.67

  Time building geometry restraints manager: 1.31 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: 3546
        1.34 -     1.46: 4319
        1.46 -     1.58: 6962
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15462
  Sorted by residual:
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.35e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.15e+01
  bond pdb=" C3'  DG I -40 "
       pdb=" C2'  DG I -40 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.00e+01
  bond pdb=" C3'  DT J -17 "
       pdb=" C2'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.35e+00
  ... (remaining 15457 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 20912
        1.53 -     3.07: 1173
        3.07 -     4.60: 53
        4.60 -     6.13: 16
        6.13 -     7.67: 2
  Bond angle restraints: 22156
  Sorted by residual:
  angle pdb=" O4'  DT I -26 "
        pdb=" C4'  DT I -26 "
        pdb=" C3'  DT I -26 "
      ideal   model   delta    sigma   weight residual
     106.00  102.64    3.36 6.00e-01 2.78e+00 3.14e+01
  angle pdb=" O4'  DG I  47 "
        pdb=" C4'  DG I  47 "
        pdb=" C3'  DG I  47 "
      ideal   model   delta    sigma   weight residual
     106.00  103.23    2.77 6.00e-01 2.78e+00 2.12e+01
  angle pdb=" N3   DT J   9 "
        pdb=" C4   DT J   9 "
        pdb=" O4   DT J   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.62   -2.72 6.00e-01 2.78e+00 2.06e+01
  angle pdb=" O4'  DC J -71 "
        pdb=" C4'  DC J -71 "
        pdb=" C3'  DC J -71 "
      ideal   model   delta    sigma   weight residual
     106.00  103.33    2.67 6.00e-01 2.78e+00 1.99e+01
  angle pdb=" N3   DT I   1 "
        pdb=" C4   DT I   1 "
        pdb=" O4   DT I   1 "
      ideal   model   delta    sigma   weight residual
     119.90  122.48   -2.58 6.00e-01 2.78e+00 1.85e+01
  ... (remaining 22151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    36.00: 7251
       36.00 -    71.99: 1335
       71.99 -   107.99: 14
      107.99 -   143.99: 0
      143.99 -   179.99: 2
  Dihedral angle restraints: 8602
    sinusoidal: 5466
      harmonic: 3136
  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
     220.00   40.01  179.99     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   70.83  149.17     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CG  ARG D  92 "
           pdb=" CD  ARG D  92 "
           pdb=" NE  ARG D  92 "
           pdb=" CZ  ARG D  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.58   44.42     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 8599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1474
       0.032 -    0.064: 671
       0.064 -    0.096: 255
       0.096 -    0.128: 105
       0.128 -    0.161: 9
  Chirality restraints: 2514
  Sorted by residual:
  chirality pdb=" C3'  DT J -17 "
            pdb=" C4'  DT J -17 "
            pdb=" O3'  DT J -17 "
            pdb=" C2'  DT J -17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.57   -0.16 2.00e-01 2.50e+01 6.45e-01
  chirality pdb=" CB  VAL K  58 "
            pdb=" CA  VAL K  58 "
            pdb=" CG1 VAL K  58 "
            pdb=" CG2 VAL K  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  ASP E  81 "
            pdb=" N   ASP E  81 "
            pdb=" C   ASP E  81 "
            pdb=" CB  ASP E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.19e-01
  ... (remaining 2511 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  88 "   -0.009 2.00e-02 2.50e+03   1.38e-02 3.81e+00
        pdb=" CG  TYR F  88 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  88 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  88 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  88 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F  88 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.025 2.00e-02 2.50e+03   1.06e-02 3.07e+00
        pdb=" N9   DA I -35 "    0.021 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 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.024 2.00e-02 2.50e+03   9.63e-03 2.78e+00
        pdb=" N9   DG I  47 "    0.019 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.007 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 164
        2.63 -     3.20: 12082
        3.20 -     3.77: 25513
        3.77 -     4.33: 32901
        4.33 -     4.90: 48665
  Nonbonded interactions: 119325
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  22 "
            pdb=" OG1 THR L  36 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.106 2.496
  nonbonded pdb=" NH2 ARG B  35 "
            pdb=" OP2  DG J   8 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" O   TYR G  39 "
            pdb=" OG  SER H  78 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER D  64 "
            pdb=" O   GLY F 101 "
     model   vdw
     2.226 3.040
  ... (remaining 119320 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=0.25 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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.070
  Find NCS groups from input model:        0.120
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
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      :  0.005   0.034  15472  Z= 0.477
  Angle     :  0.705   7.668  22171  Z= 0.603
  Chirality :  0.044   0.161   2514
  Planarity :  0.003   0.040   1792
  Dihedral  : 25.887 179.987   6570
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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 are not related in a simple way.
  whole:  1.88 (0.26), residues: 1056
  helix:  2.33 (0.21), residues: 640
  sheet:  1.42 (0.81), residues: 48
  loop : -0.80 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG L  15 
 TYR   0.033   0.002   TYR F  88 
 PHE   0.010   0.001   PHE L  69 
 TRP   0.017   0.002   TRP L  93 
 HIS   0.002   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00542 /  0.48 (15462)
  covalent geometry    : angle       0.70190 /  0.60 (22156)
  hydrogen bonds       : bond        0.10647 /  6.91 (  841)
  hydrogen bonds       : angle       3.84937 /  2.72 ( 2147)
  metal coordination   : bond        0.00697 /  0.28 (    8)
  metal coordination   : angle       3.45337 /  1.76 (    9)
  link_TRANS           : bond        0.00058 /  0.03 (    2)
  link_TRANS           : angle       0.24804 /  0.08 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8580 (tppt)
REVERT: D   83 TYR cc_start: 0.8301 (m-80) cc_final: 0.7966 (m-80)
REVERT: D  116 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8815 (tttt)
REVERT: D  120 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8480 (tttp)
REVERT: G   30 VAL cc_start: 0.9252 (t) cc_final: 0.9023 (m)
REVERT: H   35 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8135 (mt-10)
REVERT: K   41 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7631 (mm-40)
REVERT: K   49 LEU cc_start: 0.8683 (tp) cc_final: 0.8430 (tp)
REVERT: K   57 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.6992 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1184
  time to fit residues: 30.6745
Evaluate side-chains
  150 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   overall best weight:    1.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.140820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.086588 restraints weight = 37572.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.087036 restraints weight = 25835.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.086665 restraints weight = 20297.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.086664 restraints weight = 19119.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.086763 restraints weight = 18742.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (10 function evaluations)
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  15472  Z= 0.228
  Angle     :  0.686  10.443  22171  Z= 0.387
  Chirality :  0.045   0.286   2514
  Planarity :  0.004   0.036   1792
  Dihedral  : 29.223 177.582   4410
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  9.88 %
    Favored  : 89.03 %
  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 are not related in a simple way.
  whole:  1.63 (0.26), residues: 1056
  helix:  2.21 (0.20), residues: 642
  sheet:  1.22 (0.79), residues: 48
  loop : -1.05 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  15 
 TYR   0.026   0.002   TYR H  83 
 PHE   0.009   0.001   PHE D  65 
 TRP   0.007   0.001   TRP L 141 
 HIS   0.006   0.001   HIS L  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00493 /  0.23 (15462)
  covalent geometry    : angle       0.67902 /  0.39 (22156)
  hydrogen bonds       : bond        0.06222 /  4.28 (  841)
  hydrogen bonds       : angle       3.59047 /  2.54 ( 2147)
  metal coordination   : bond        0.00941 /  0.42 (    8)
  metal coordination   : angle       5.04314 /  2.60 (    9)
  link_TRANS           : bond        0.00215 /  0.11 (    2)
  link_TRANS           : angle       0.46124 /  0.24 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8736 (tptt)
REVERT: D   51 ASP cc_start: 0.8069 (t0) cc_final: 0.7722 (t0)
REVERT: D   83 TYR cc_start: 0.8650 (m-80) cc_final: 0.7608 (m-10)
REVERT: D  116 LYS cc_start: 0.9202 (ttpp) cc_final: 0.8793 (tttt)
REVERT: D  120 LYS cc_start: 0.9110 (ttpt) cc_final: 0.8549 (tttp)
REVERT: H   51 ASP cc_start: 0.8728 (p0) cc_final: 0.8520 (p0)
REVERT: L   34 GLN cc_start: 0.8926 (tp40) cc_final: 0.8585 (tp40)
REVERT: L   97 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8698 (tp)
  outliers start: 10
  outliers final: 7
  residues processed: 158
  average time/residue: 0.1207
  time to fit residues: 27.4118
Evaluate side-chains
  154 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   97 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 106 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.1980
   chunk 128 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 33 optimal weight:    0.4980
   chunk 105 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
L  34 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.142174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.111226 restraints weight = 37963.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.113096 restraints weight = 83174.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.114570 restraints weight = 28329.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.115573 restraints weight = 18885.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.115948 restraints weight = 13328.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3306
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15472  Z= 0.155
  Angle     :  0.621  11.059  22171  Z= 0.356
  Chirality :  0.043   0.270   2514
  Planarity :  0.004   0.035   1792
  Dihedral  : 29.200 178.324   4410
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.62 %
    Favored  : 87.08 %
  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 are not related in a simple way.
  whole:  1.83 (0.26), residues: 1056
  helix:  2.37 (0.21), residues: 644
  sheet:  1.06 (0.78), residues: 48
  loop : -0.97 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  33 
 TYR   0.025   0.002   TYR H  83 
 PHE   0.010   0.001   PHE D  65 
 TRP   0.008   0.001   TRP L 141 
 HIS   0.002   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.15 (15462)
  covalent geometry    : angle       0.61462 /  0.36 (22156)
  hydrogen bonds       : bond        0.05364 /  3.69 (  841)
  hydrogen bonds       : angle       3.30337 /  2.33 ( 2147)
  metal coordination   : bond        0.00681 /  0.30 (    8)
  metal coordination   : angle       4.48813 /  2.26 (    9)
  link_TRANS           : bond        0.00136 /  0.07 (    2)
  link_TRANS           : angle       0.34426 /  0.17 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8556 (tptt)
REVERT: D   83 TYR cc_start: 0.8618 (m-10) cc_final: 0.8038 (m-10)
REVERT: D  116 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8737 (tttt)
REVERT: D  120 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8396 (tttp)
REVERT: K   41 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7886 (mm-40)
REVERT: L   97 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8276 (tp)
  outliers start: 12
  outliers final: 8
  residues processed: 160
  average time/residue: 0.1201
  time to fit residues: 27.4982
Evaluate side-chains
  162 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   55 HIS
Chi-restraints excluded: chain L residue   60 TYR
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   97 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 48 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 127 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 40 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9980
   chunk 125 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  34 GLN
L  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.142576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.095010 restraints weight = 42778.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.088551 restraints weight = 38949.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.087816 restraints weight = 33694.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.088299 restraints weight = 28588.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.088681 restraints weight = 22660.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  15472  Z= 0.148
  Angle     :  0.609  11.021  22171  Z= 0.348
  Chirality :  0.042   0.276   2514
  Planarity :  0.004   0.034   1792
  Dihedral  : 29.205 177.641   4410
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.05 %
    Favored  : 85.99 %
  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 are not related in a simple way.
  whole:  1.89 (0.26), residues: 1056
  helix:  2.41 (0.21), residues: 644
  sheet:  1.08 (0.76), residues: 46
  loop : -0.91 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  33 
 TYR   0.024   0.002   TYR H  83 
 PHE   0.020   0.001   PHE L  62 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.006   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.15 (15462)
  covalent geometry    : angle       0.60242 /  0.35 (22156)
  hydrogen bonds       : bond        0.05107 /  3.51 (  841)
  hydrogen bonds       : angle       3.19738 /  2.26 ( 2147)
  metal coordination   : bond        0.00664 /  0.30 (    8)
  metal coordination   : angle       4.43756 /  2.25 (    9)
  link_TRANS           : bond        0.00099 /  0.05 (    2)
  link_TRANS           : angle       0.28873 /  0.14 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7632 (mt-10)
REVERT: D   46 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8677 (tptt)
REVERT: D   71 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7588 (tm-30)
REVERT: D   83 TYR cc_start: 0.8651 (m-10) cc_final: 0.8097 (m-10)
REVERT: D  116 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8706 (tttt)
REVERT: D  120 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8533 (tttp)
REVERT: L   34 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8432 (tp40)
REVERT: L   97 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8650 (tp)
REVERT: M   27 LYS cc_start: 0.6947 (tppp) cc_final: 0.6643 (tptm)
  outliers start: 18
  outliers final: 13
  residues processed: 160
  average time/residue: 0.1236
  time to fit residues: 28.7189
Evaluate side-chains
  166 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   60 TYR
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  147 MET
Chi-restraints excluded: chain M residue   56 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 104 optimal weight:    0.5980
   chunk 90 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 119 optimal weight:   30.0000
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.142770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.091232 restraints weight = 50086.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.089765 restraints weight = 34798.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.089541 restraints weight = 25913.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.089417 restraints weight = 18142.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.089485 restraints weight = 17908.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15472  Z= 0.145
  Angle     :  0.605  11.231  22171  Z= 0.345
  Chirality :  0.042   0.274   2514
  Planarity :  0.004   0.034   1792
  Dihedral  : 29.207 177.491   4410
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.36 %
    Favored  : 84.69 %
  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 are not related in a simple way.
  whole:  1.90 (0.26), residues: 1056
  helix:  2.41 (0.21), residues: 648
  sheet:  0.96 (0.76), residues: 46
  loop : -0.90 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG M  42 
 TYR   0.021   0.001   TYR H  83 
 PHE   0.015   0.001   PHE L  62 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.003   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.14 (15462)
  covalent geometry    : angle       0.59949 /  0.34 (22156)
  hydrogen bonds       : bond        0.04963 /  3.41 (  841)
  hydrogen bonds       : angle       3.14662 /  2.22 ( 2147)
  metal coordination   : bond        0.00620 /  0.28 (    8)
  metal coordination   : angle       4.03970 /  2.01 (    9)
  link_TRANS           : bond        0.00164 /  0.08 (    2)
  link_TRANS           : angle       0.83091 /  0.45 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7693 (mt-10)
REVERT: D   46 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8665 (tptt)
REVERT: D   51 ASP cc_start: 0.7582 (t70) cc_final: 0.7220 (t0)
REVERT: D   83 TYR cc_start: 0.8660 (m-10) cc_final: 0.8052 (m-10)
REVERT: D  116 LYS cc_start: 0.9156 (ttpp) cc_final: 0.8760 (tttt)
REVERT: D  120 LYS cc_start: 0.9025 (ttpt) cc_final: 0.8498 (tttp)
REVERT: M   27 LYS cc_start: 0.7033 (tppp) cc_final: 0.6727 (tptm)
  outliers start: 18
  outliers final: 14
  residues processed: 156
  average time/residue: 0.1259
  time to fit residues: 28.2019
Evaluate side-chains
  162 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue   60 TYR
Chi-restraints excluded: chain L residue   89 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0370
   chunk 30 optimal weight:    0.6980
   chunk 110 optimal weight:   30.0000
   chunk 128 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 100 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9980
   chunk 112 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    1.1462

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
** L  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.093709 restraints weight = 49941.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.090087 restraints weight = 41868.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.086827 restraints weight = 33414.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.087380 restraints weight = 31164.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.087878 restraints weight = 24646.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15472  Z= 0.170
  Angle     :  0.626  11.323  22171  Z= 0.352
  Chirality :  0.042   0.282   2514
  Planarity :  0.004   0.033   1792
  Dihedral  : 29.244 177.043   4410
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.20 %
    Favored  : 82.63 %
  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 are not related in a simple way.
  whole:  1.82 (0.26), residues: 1056
  helix:  2.38 (0.20), residues: 647
  sheet:  0.58 (0.75), residues: 48
  loop : -0.95 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  33 
 TYR   0.021   0.002   TYR L  60 
 PHE   0.013   0.001   PHE L  62 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.004   0.001   HIS L  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.17 (15462)
  covalent geometry    : angle       0.62174 /  0.35 (22156)
  hydrogen bonds       : bond        0.05138 /  3.53 (  841)
  hydrogen bonds       : angle       3.19316 /  2.25 ( 2147)
  metal coordination   : bond        0.00612 /  0.27 (    8)
  metal coordination   : angle       3.82682 /  1.91 (    9)
  link_TRANS           : bond        0.00146 /  0.07 (    2)
  link_TRANS           : angle       0.51639 /  0.28 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7747 (mt-10)
REVERT: D   46 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8757 (tptt)
REVERT: D  116 LYS cc_start: 0.9190 (ttpp) cc_final: 0.8773 (tttt)
REVERT: D  120 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8803 (mtpt)
  outliers start: 20
  outliers final: 16
  residues processed: 161
  average time/residue: 0.1280
  time to fit residues: 29.3655
Evaluate side-chains
  167 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue   60 TYR
Chi-restraints excluded: chain M residue   56 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 40 optimal weight:    0.2980
   chunk 79 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0870
   chunk 104 optimal weight:    1.9990
   chunk 128 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 94 optimal weight:    9.9990
   chunk 96 optimal weight:    9.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
M  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.143188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.096014 restraints weight = 42822.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.091245 restraints weight = 38963.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.091397 restraints weight = 33010.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.091470 restraints weight = 25875.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.091646 restraints weight = 23309.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  15472  Z= 0.138
  Angle     :  0.610  12.874  22171  Z= 0.344
  Chirality :  0.041   0.270   2514
  Planarity :  0.004   0.034   1792
  Dihedral  : 29.211 177.323   4410
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 15.85 %
    Favored  : 82.52 %
  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 are not related in a simple way.
  whole:  1.88 (0.26), residues: 1056
  helix:  2.44 (0.21), residues: 648
  sheet:  0.35 (0.77), residues: 48
  loop : -0.93 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  33 
 TYR   0.021   0.001   TYR L  60 
 PHE   0.013   0.001   PHE M   4 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.003   0.001   HIS L  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.14 (15462)
  covalent geometry    : angle       0.60537 /  0.34 (22156)
  hydrogen bonds       : bond        0.04873 /  3.34 (  841)
  hydrogen bonds       : angle       3.10159 /  2.19 ( 2147)
  metal coordination   : bond        0.00551 /  0.25 (    8)
  metal coordination   : angle       3.57209 /  1.77 (    9)
  link_TRANS           : bond        0.00075 /  0.04 (    2)
  link_TRANS           : angle       0.58212 /  0.31 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7756 (mt-10)
REVERT: D   46 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8659 (tptt)
REVERT: D   71 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: D   83 TYR cc_start: 0.8675 (m-10) cc_final: 0.8059 (m-10)
REVERT: D  116 LYS cc_start: 0.9124 (ttpp) cc_final: 0.8708 (tttt)
REVERT: D  120 LYS cc_start: 0.8958 (ttpt) cc_final: 0.8727 (mtpt)
  outliers start: 15
  outliers final: 13
  residues processed: 164
  average time/residue: 0.1219
  time to fit residues: 28.7562
Evaluate side-chains
  165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue   60 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 110 optimal weight:   30.0000
   chunk 51 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 80 optimal weight:   10.0000
   chunk 104 optimal weight:    0.6980
   chunk 121 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0870
   overall best weight:    0.6960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.143149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.105301 restraints weight = 29899.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110204 restraints weight = 62496.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.108889 restraints weight = 28191.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.109588 restraints weight = 22985.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.109744 restraints weight = 19497.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15472  Z= 0.143
  Angle     :  0.615  13.005  22171  Z= 0.345
  Chirality :  0.042   0.274   2514
  Planarity :  0.004   0.035   1792
  Dihedral  : 29.227 176.915   4410
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.07 %
    Favored  : 82.19 %
  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 are not related in a simple way.
  whole:  1.86 (0.26), residues: 1056
  helix:  2.40 (0.20), residues: 650
  sheet:  0.27 (0.79), residues: 48
  loop : -0.89 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  33 
 TYR   0.021   0.001   TYR L  60 
 PHE   0.014   0.001   PHE M   4 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.004   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.14 (15462)
  covalent geometry    : angle       0.61145 /  0.34 (22156)
  hydrogen bonds       : bond        0.04850 /  3.32 (  841)
  hydrogen bonds       : angle       3.12544 /  2.20 ( 2147)
  metal coordination   : bond        0.00538 /  0.24 (    8)
  metal coordination   : angle       3.38432 /  1.68 (    9)
  link_TRANS           : bond        0.00095 /  0.05 (    2)
  link_TRANS           : angle       0.54660 /  0.29 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7728 (mt-10)
REVERT: D   46 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8634 (tptt)
REVERT: D   71 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7677 (tm-30)
REVERT: D   83 TYR cc_start: 0.8636 (m-10) cc_final: 0.8278 (m-10)
REVERT: D  116 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8776 (tttt)
REVERT: D  120 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8690 (mtpt)
REVERT: H  105 GLU cc_start: 0.6112 (tt0) cc_final: 0.5877 (tt0)
REVERT: H  121 TYR cc_start: 0.9048 (t80) cc_final: 0.8753 (t80)
REVERT: L  147 MET cc_start: 0.4469 (mtt) cc_final: 0.4152 (mtt)
  outliers start: 16
  outliers final: 16
  residues processed: 163
  average time/residue: 0.1323
  time to fit residues: 30.7989
Evaluate side-chains
  167 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue   60 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 85 optimal weight:   20.0000
   chunk 113 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0770
   chunk 54 optimal weight:    0.5980
   chunk 86 optimal weight:   20.0000
   chunk 102 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.143763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.111798 restraints weight = 36088.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.113723 restraints weight = 82881.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.114187 restraints weight = 31297.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118801 restraints weight = 22002.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.118085 restraints weight = 11452.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  15472  Z= 0.135
  Angle     :  0.608  12.729  22171  Z= 0.341
  Chirality :  0.041   0.269   2514
  Planarity :  0.004   0.036   1792
  Dihedral  : 29.216 176.912   4410
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.61 %
    Favored  : 81.87 %
  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 are not related in a simple way.
  whole:  1.89 (0.26), residues: 1056
  helix:  2.42 (0.20), residues: 650
  sheet:  0.33 (0.83), residues: 48
  loop : -0.88 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  33 
 TYR   0.021   0.001   TYR L  60 
 PHE   0.013   0.001   PHE M   4 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.14 (15462)
  covalent geometry    : angle       0.60461 /  0.34 (22156)
  hydrogen bonds       : bond        0.04737 /  3.24 (  841)
  hydrogen bonds       : angle       3.07888 /  2.17 ( 2147)
  metal coordination   : bond        0.00518 /  0.23 (    8)
  metal coordination   : angle       3.20884 /  1.60 (    9)
  link_TRANS           : bond        0.00081 /  0.04 (    2)
  link_TRANS           : angle       0.57684 /  0.31 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7639 (mt-10)
REVERT: D   46 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8423 (tptt)
REVERT: D   71 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: D   83 TYR cc_start: 0.8622 (m-10) cc_final: 0.8288 (m-10)
REVERT: D  116 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8726 (tttt)
REVERT: D  120 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8630 (mtpt)
REVERT: E   59 GLU cc_start: 0.8749 (pm20) cc_final: 0.8330 (pm20)
REVERT: H  121 TYR cc_start: 0.8909 (t80) cc_final: 0.8644 (t80)
  outliers start: 14
  outliers final: 13
  residues processed: 165
  average time/residue: 0.1120
  time to fit residues: 26.6617
Evaluate side-chains
  169 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue  119 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 F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue   60 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 64 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 121 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 92 optimal weight:    9.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.142593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.111638 restraints weight = 37939.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.113438 restraints weight = 87194.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.115002 restraints weight = 30251.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.115723 restraints weight = 19951.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117038 restraints weight = 14171.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15472  Z= 0.160
  Angle     :  0.631  14.615  22171  Z= 0.350
  Chirality :  0.042   0.279   2514
  Planarity :  0.004   0.033   1792
  Dihedral  : 29.278 176.186   4410
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 16.72 %
    Favored  : 81.87 %
  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 are not related in a simple way.
  whole:  1.77 (0.26), residues: 1056
  helix:  2.30 (0.20), residues: 662
  sheet:  0.13 (0.81), residues: 48
  loop : -0.96 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  99 
 TYR   0.021   0.002   TYR L  60 
 PHE   0.011   0.001   PHE M   4 
 TRP   0.013   0.001   TRP K  61 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.16 (15462)
  covalent geometry    : angle       0.62839 /  0.35 (22156)
  hydrogen bonds       : bond        0.05020 /  3.44 (  841)
  hydrogen bonds       : angle       3.17911 /  2.24 ( 2147)
  metal coordination   : bond        0.00556 /  0.24 (    8)
  metal coordination   : angle       3.15412 /  1.57 (    9)
  link_TRANS           : bond        0.00099 /  0.05 (    2)
  link_TRANS           : angle       0.50381 /  0.27 (    6)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7647 (mt-10)
REVERT: D   46 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8655 (tppt)
REVERT: D   62 MET cc_start: 0.9422 (mmt) cc_final: 0.8936 (mmt)
REVERT: D   71 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: D   83 TYR cc_start: 0.8670 (m-10) cc_final: 0.8265 (m-10)
REVERT: D  116 LYS cc_start: 0.9086 (ttpp) cc_final: 0.8724 (tttt)
REVERT: D  120 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8643 (mtpt)
REVERT: E   59 GLU cc_start: 0.8725 (pm20) cc_final: 0.8340 (pm20)
REVERT: H   33 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7616 (mtp-110)
  outliers start: 13
  outliers final: 12
  residues processed: 158
  average time/residue: 0.1214
  time to fit residues: 27.6044
Evaluate side-chains
  164 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue  119 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 F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue   60 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 126 optimal weight:    0.0980
   chunk 23 optimal weight:    0.7980
   chunk 96 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 128 optimal weight:    0.8980
   chunk 125 optimal weight:   50.0000
   chunk 108 optimal weight:    8.9990
   chunk 93 optimal weight:    9.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.143300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.111357 restraints weight = 37163.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.113398 restraints weight = 83768.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.114584 restraints weight = 31005.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.115344 restraints weight = 21751.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.116870 restraints weight = 15597.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15472  Z= 0.140
  Angle     :  0.636  19.795  22171  Z= 0.348
  Chirality :  0.042   0.289   2514
  Planarity :  0.004   0.037   1792
  Dihedral  : 29.252 176.590   4410
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.83 %
    Favored  : 81.65 %
  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 are not related in a simple way.
  whole:  1.82 (0.26), residues: 1056
  helix:  2.33 (0.20), residues: 662
  sheet:  0.10 (0.81), residues: 48
  loop : -0.92 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG M  42 
 TYR   0.021   0.002   TYR H 121 
 PHE   0.012   0.001   PHE M   4 
 TRP   0.012   0.001   TRP K  61 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.14 (15462)
  covalent geometry    : angle       0.63058 /  0.35 (22156)
  hydrogen bonds       : bond        0.04832 /  3.31 (  841)
  hydrogen bonds       : angle       3.13887 /  2.21 ( 2147)
  metal coordination   : bond        0.00647 /  0.28 (    8)
  metal coordination   : angle       4.05442 /  2.08 (    9)
  link_TRANS           : bond        0.00109 /  0.05 (    2)
  link_TRANS           : angle       0.54909 /  0.30 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2219.13 seconds
wall clock time: 38 minutes 56.14 seconds (2336.14 seconds total)