Starting phenix.real_space_refine
on Sat Oct 11 12:25:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt8_37829/10_2025/8wt8_37829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt8_37829/10_2025/8wt8_37829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt8_37829/10_2025/8wt8_37829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt8_37829/10_2025/8wt8_37829.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wt8_37829/10_2025/8wt8_37829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt8_37829/10_2025/8wt8_37829.map"
  }
  resolution = 2.9
  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=  -0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     241      5.49       5
     Mg      1      5.21       5
     S      48      5.16       5
     C    8521      2.51       5
     N    2759      2.21       5
     O    3346      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14916
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 2429
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 306, 2420
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 12, 'TRANS': 293}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 306, 2420
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 12, 'TRANS': 293}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2457
    Chain: "B"
      Number of atoms: 2527
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 318, 2507
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
      Conformer: "B"
        Number of residues, atoms: 318, 2507
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          bond proxies already assigned to first conformer: 2534
    Chain: "C"
      Number of atoms: 2420
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 305, 2411
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 12, 'TRANS': 292}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 305, 2411
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 12, 'TRANS': 292}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2448
    Chain: "D"
      Number of atoms: 2513
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 317, 2498
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 12, 'TRANS': 304}
      Conformer: "B"
        Number of residues, atoms: 317, 2498
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 12, 'TRANS': 304}
          bond proxies already assigned to first conformer: 2530
    Chain: "E"
      Number of atoms: 1249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 1249
          Classifications: {'RNA': 59}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 15, 'rna3p': 43}
    Chain: "F"
      Number of atoms: 1442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1442
          Classifications: {'RNA': 68}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 27, 'rna3p_pyr': 27}
          Link IDs: {'rna2p': 13, 'rna3p': 54}
    Chain: "G"
      Number of atoms: 580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 580
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "H"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 557
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "I"
      Number of atoms: 596
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 27, 555
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
      Conformer: "B"
        Number of residues, atoms: 27, 555
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 576
    Chain: "J"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 602
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 9
    residue:
      pdb=" N  AGLN A 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 139 " occ=0.50
    residue:
      pdb=" N  AGLN B 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN B 139 " occ=0.50
    residue:
      pdb=" N  AARG B 261 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 261 " occ=0.50
    residue:
      pdb=" N  AGLN C 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN C 139 " occ=0.50
    residue:
      pdb=" N  AGLN D 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN D 139 " occ=0.50
    residue:
      pdb=" N  ASER D 241 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER D 241 " occ=0.50
    residue:
      pdb=" P  A DT I  20 " occ=0.50
      ... (38 atoms not shown)
      pdb=" C6 B DT I  20 " occ=0.50
    residue:
      pdb=" P  A DA I  21 " occ=0.50
      ... (40 atoms not shown)
      pdb=" C4 B DA I  21 " occ=0.50
    residue:
      pdb="MG  B MG I 101 " occ=0.50
  Time building chain proxies: 5.62, per 1000 atoms: 0.38
  Number of scatterers: 14916
  At special positions: 0
  Unit cell: (119.52, 123.947, 110.667, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P     241     15.00
     Mg      1     11.99
     O    3346      8.00
     N    2759      7.00
     C    8521      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 793.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2344

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 7 sheets defined
      68.6% alpha, 9.9% beta
      89 base pairs and 149 stacking pairs defined.
    Time for finding SS restraints: 2.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 50
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 84 through 95
      removed outlier: 3.668A  pdb=" N   GLY A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 117
    Processing helix  chain 'A' and resid 125 through 152
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 159 through 188
      removed outlier: 3.640A  pdb=" N   ASP A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 200
    Processing helix  chain 'A' and resid 205 through 217
    Processing helix  chain 'A' and resid 224 through 232
      removed outlier: 3.672A  pdb=" N   PHE A 228 " --> pdb=" O   HIS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 262
      removed outlier: 3.576A  pdb=" N   ALA A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 274 through 288
      removed outlier: 3.508A  pdb=" N   ASN A 287 " --> pdb=" O   ARG A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 317 through 321
      removed outlier: 3.521A  pdb=" N   ARG A 320 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 50
    Processing helix  chain 'B' and resid 66 through 76
    Processing helix  chain 'B' and resid 84 through 96
      removed outlier: 3.589A  pdb=" N   GLY B  96 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
    Processing helix  chain 'B' and resid 125 through 154
      removed outlier: 3.861A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   THR B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 188
      removed outlier: 3.639A  pdb=" N   ASP B 188 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 200
    Processing helix  chain 'B' and resid 205 through 217
      removed outlier: 3.654A  pdb=" N   ALA B 210 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 233
      removed outlier: 3.766A  pdb=" N   PHE B 228 " --> pdb=" O   HIS B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 263
    Processing helix  chain 'B' and resid 263 through 274
      removed outlier: 3.501A  pdb=" N   SER B 272 " --> pdb=" O   MET B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 287
      removed outlier: 3.876A  pdb=" N   ASN B 287 " --> pdb=" O   ARG B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 313
      removed outlier: 3.503A  pdb=" N   LEU B 310 " --> pdb=" O   ALA B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 321
    Processing helix  chain 'C' and resid 36 through 50
    Processing helix  chain 'C' and resid 66 through 77
    Processing helix  chain 'C' and resid 84 through 96
    Processing helix  chain 'C' and resid 101 through 117
      removed outlier: 3.557A  pdb=" N   ARG C 107 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ALA C 110 " --> pdb=" O   ALA C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 154
      removed outlier: 3.800A  pdb=" N   GLU C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   THR C 154 " --> pdb=" O   ASN C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 188
      removed outlier: 3.620A  pdb=" N   ASP C 188 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 200
    Processing helix  chain 'C' and resid 205 through 217
      removed outlier: 3.542A  pdb=" N   ALA C 210 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 232
      removed outlier: 3.746A  pdb=" N   PHE C 228 " --> pdb=" O   HIS C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 262
      removed outlier: 3.501A  pdb=" N   ALA C 262 " --> pdb=" O   SER C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
    Processing helix  chain 'C' and resid 274 through 288
    Processing helix  chain 'C' and resid 290 through 313
    Processing helix  chain 'C' and resid 317 through 321
      removed outlier: 3.617A  pdb=" N   ARG C 320 " --> pdb=" O   ASP C 317 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 50
    Processing helix  chain 'D' and resid 66 through 77
    Processing helix  chain 'D' and resid 84 through 96
      removed outlier: 3.589A  pdb=" N   GLY D  88 " --> pdb=" O   ASN D  84 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY D  96 " --> pdb=" O   ALA D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 117
    Processing helix  chain 'D' and resid 125 through 154
      removed outlier: 3.990A  pdb=" N   GLU D 153 " --> pdb=" O   LEU D 149 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   THR D 154 " --> pdb=" O   ASN D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 188
      removed outlier: 3.689A  pdb=" N   ASP D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 201
      removed outlier: 3.803A  pdb=" N   ILE D 201 " --> pdb=" O   LEU D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 217
      removed outlier: 3.557A  pdb=" N   ALA D 210 " --> pdb=" O   GLU D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 224 through 233
      removed outlier: 3.606A  pdb=" N   PHE D 228 " --> pdb=" O   HIS D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 263
      removed outlier: 3.595A  pdb=" N   LEU D 263 " --> pdb=" O   LEU D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 263 through 274
    Processing helix  chain 'D' and resid 274 through 288
    Processing helix  chain 'D' and resid 290 through 313
    Processing helix  chain 'D' and resid 317 through 321
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34
      removed outlier: 6.576A  pdb=" N   HIS A   6 " --> pdb=" O   HIS A  56 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   CYS A  58 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE A   8 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 8.540A  pdb=" N   GLU A  60 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   ILE A  10 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 34
      removed outlier: 6.766A  pdb=" N   HIS B   6 " --> pdb=" O   HIS B  56 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   CYS B  58 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ILE B   8 " --> pdb=" O   CYS B  58 " (cutoff:3.500A)
      removed outlier: 8.763A  pdb=" N   GLU B  60 " --> pdb=" O   ILE B   8 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  60 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ALA B  55 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   SER B  81 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ILE B  57 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   ILE B  83 " --> pdb=" O   ILE B  57 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ILE B  59 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237
      removed outlier: 3.853A  pdb=" N   ARG B 250 " --> pdb=" O   ARG B 237 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 241
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34
      removed outlier: 6.290A  pdb=" N   HIS C   6 " --> pdb=" O   HIS C  56 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   CYS C  58 " --> pdb=" O   HIS C   6 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE C   8 " --> pdb=" O   CYS C  58 " (cutoff:3.500A)
      removed outlier: 8.538A  pdb=" N   GLU C  60 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   ILE C  10 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 34
      removed outlier: 4.462A  pdb=" N   GLU D  60 " --> pdb=" O   ILE D  10 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   THR D  12 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA D  55 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   SER D  81 " --> pdb=" O   ALA D  55 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ILE D  57 " --> pdb=" O   SER D  81 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ILE D  83 " --> pdb=" O   ILE D  57 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ILE D  59 " --> pdb=" O   ILE D  83 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 236 through 241
      removed outlier: 3.764A  pdb=" N   ARG D 250 " --> pdb=" O   ARG D 237 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   TYR D 239 " --> pdb=" O   ALA D 248 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   ALA D 248 " --> pdb=" O   TYR D 239 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N  ASER D 241 " --> pdb=" O   ARG D 246 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   ARG D 246 " --> pdb=" O  ASER D 241 " (cutoff:3.500A)

    674 hydrogen bonds defined for protein.
    2000 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      227 hydrogen bonds
      450 hydrogen bond angles
      0 basepair planarities
      89 basepair parallelities
      152 stacking parallelities
  Total time for adding SS restraints: 2.63

  Time building geometry restraints manager: 1.75 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: 3712
        1.34 -     1.46: 5158
        1.46 -     1.58: 6275
        1.58 -     1.69: 476
        1.69 -     1.81: 84
  Bond restraints: 15705
  Sorted by residual:
  bond pdb=" C   ILE D 201 "
       pdb=" N   PRO D 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 8.70e-03 1.32e+04 5.94e+00
  bond pdb=" O5'   A E  68 "
       pdb=" C5'   A E  68 "
    ideal  model  delta    sigma   weight residual
    1.420  1.456 -0.036 1.50e-02 4.44e+03 5.87e+00
  bond pdb=" O5'   G F 133 "
       pdb=" C5'   G F 133 "
    ideal  model  delta    sigma   weight residual
    1.420  1.456 -0.036 1.50e-02 4.44e+03 5.63e+00
  bond pdb=" O5'   G F 169 "
       pdb=" C5'   G F 169 "
    ideal  model  delta    sigma   weight residual
    1.420  1.456 -0.036 1.50e-02 4.44e+03 5.60e+00
  bond pdb=" P    DT G  10 "
       pdb=" OP1  DT G  10 "
    ideal  model  delta    sigma   weight residual
    1.480  1.527 -0.047 2.00e-02 2.50e+03 5.57e+00
  ... (remaining 15700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 17173
        1.47 -     2.94: 4231
        2.94 -     4.42: 749
        4.42 -     5.89: 115
        5.89 -     7.36: 22
  Bond angle restraints: 22290
  Sorted by residual:
  angle pdb=" O3'  DA G  32 "
        pdb=" P    DT G  33 "
        pdb=" O5'  DT G  33 "
      ideal   model   delta    sigma   weight residual
     104.00   96.64    7.36 1.50e+00 4.44e-01 2.41e+01
  angle pdb=" O3'  DT G  31 "
        pdb=" P    DA G  32 "
        pdb=" O5'  DA G  32 "
      ideal   model   delta    sigma   weight residual
     104.00   97.25    6.75 1.50e+00 4.44e-01 2.03e+01
  angle pdb=" CA  ASP C  25 "
        pdb=" CB  ASP C  25 "
        pdb=" CG  ASP C  25 "
      ideal   model   delta    sigma   weight residual
     112.60  117.06   -4.46 1.00e+00 1.00e+00 1.99e+01
  angle pdb=" O3'  DT G  33 "
        pdb=" P    DC G  34 "
        pdb=" O5'  DC G  34 "
      ideal   model   delta    sigma   weight residual
     104.00   97.41    6.59 1.50e+00 4.44e-01 1.93e+01
  angle pdb=" O3'   G F 138 "
        pdb=" P     G F 139 "
        pdb=" O5'   G F 139 "
      ideal   model   delta    sigma   weight residual
     104.00   97.44    6.56 1.50e+00 4.44e-01 1.91e+01
  ... (remaining 22285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.61: 8697
       35.61 -    71.21: 678
       71.21 -   106.82: 49
      106.82 -   142.42: 0
      142.42 -   178.03: 2
  Dihedral angle restraints: 9426
    sinusoidal: 5800
      harmonic: 3626
  Sorted by residual:
  dihedral pdb=" O4'   U F 159 "
           pdb=" C1'   U F 159 "
           pdb=" N1    U F 159 "
           pdb=" C2    U F 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.97  178.03     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" C5'   U F 168 "
           pdb=" C4'   U F 168 "
           pdb=" C3'   U F 168 "
           pdb=" O3'   U F 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   98.77   48.23     1      8.00e+00 1.56e-02 5.01e+01
  dihedral pdb=" O4'   U F 168 "
           pdb=" C4'   U F 168 "
           pdb=" C3'   U F 168 "
           pdb=" C2'   U F 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -14.47   38.47     1      8.00e+00 1.56e-02 3.26e+01
  ... (remaining 9423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 2309
       0.135 -    0.271: 265
       0.271 -    0.406: 1
       0.406 -    0.542: 0
       0.542 -    0.677: 6
  Chirality restraints: 2581
  Sorted by residual:
  chirality pdb=" P    DT G  10 "
            pdb=" OP1  DT G  10 "
            pdb=" OP2  DT G  10 "
            pdb=" O5'  DT G  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.02   -0.68 2.00e-01 2.50e+01 1.15e+01
  chirality pdb=" P    DA H   3 "
            pdb=" OP1  DA H   3 "
            pdb=" OP2  DA H   3 "
            pdb=" O5'  DA H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" P    DG J  12 "
            pdb=" OP1  DG J  12 "
            pdb=" OP2  DG J  12 "
            pdb=" O5'  DG J  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.01e+01
  ... (remaining 2578 not shown)

  Planarity restraints: 1996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F 157 "   -0.024 2.00e-02 2.50e+03   9.85e-03 2.67e+00
        pdb=" N9    A F 157 "    0.015 2.00e-02 2.50e+03
        pdb=" C8    A F 157 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    A F 157 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A F 157 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A F 157 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6    A F 157 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A F 157 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A F 157 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    A F 157 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A F 157 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA G  29 "    0.020 2.00e-02 2.50e+03   8.85e-03 2.15e+00
        pdb=" N9   DA G  29 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DA G  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7   DA G  29 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA G  29 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA G  29 "    0.001 2.00e-02 2.50e+03
        pdb=" N6   DA G  29 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DA G  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA G  29 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DA G  29 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DA G  29 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U E  74 "   -0.021 2.00e-02 2.50e+03   9.59e-03 2.07e+00
        pdb=" N1    U E  74 "    0.013 2.00e-02 2.50e+03
        pdb=" C2    U E  74 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    U E  74 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    U E  74 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    U E  74 "   -0.006 2.00e-02 2.50e+03
        pdb=" O4    U E  74 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    U E  74 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    U E  74 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1993 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 5
        2.27 -     2.93: 5256
        2.93 -     3.58: 22124
        3.58 -     4.24: 40380
        4.24 -     4.90: 61660
  Nonbonded interactions: 129425
  Sorted by model distance:
  nonbonded pdb=" OG BSER D 241 "
            pdb=" P  B DA I  21 "
     model   vdw
     1.611 3.400
  nonbonded pdb=" OE2 GLU A  60 "
            pdb="MG  B MG I 101 "
     model   vdw
     2.078 2.170
  nonbonded pdb=" O3'B DT I  20 "
            pdb="MG  B MG I 101 "
     model   vdw
     2.085 2.170
  nonbonded pdb=" OP1B DA I  21 "
            pdb="MG  B MG I 101 "
     model   vdw
     2.091 2.170
  nonbonded pdb=" OD1 ASP A  11 "
            pdb="MG  B MG I 101 "
     model   vdw
     2.103 2.170
  ... (remaining 129420 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 138 or resid 140 through 260 or resid 262 throug \ 
h 321))
  selection = (chain 'B' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ 
h 260 or resid 262 through 321))
  selection = (chain 'C' and (resid 5 through 138 or resid 140 through 260 or resid 262 throug \ 
h 321))
  selection = (chain 'D' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ 
h 260 or resid 262 through 321))
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     18.700
  Find NCS groups from input model:        0.230
  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:7.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
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      :  0.008   0.047  15705  Z= 0.476
  Angle     :  1.330   7.360  22290  Z= 0.862
  Chirality :  0.079   0.677   2581
  Planarity :  0.003   0.026   1996
  Dihedral  : 20.482 178.027   7082
  Min Nonbonded Distance : 1.611

Molprobity Statistics.
  All-atom Clashscore : 0.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  2.46 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.19), residues: 1252
  helix: -1.14 (0.14), residues: 807
  sheet: -1.67 (0.35), residues: 150
  loop : -1.49 (0.32), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG D 300 
 TYR   0.017   0.002   TYR D  78 
 PHE   0.015   0.002   PHE A 231 
 TRP   0.016   0.004   TRP C 169 
 HIS   0.006   0.002   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00792 (15705)
  covalent geometry    : angle       1.32970 (22290)
  hydrogen bonds       : bond        0.22488 (  901)
  hydrogen bonds       : angle       7.45544 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  268 MET cc_start: 0.8145 (mtm) cc_final: 0.7888 (mtp)
  outliers start: 5
  outliers final: 0
  residues processed: 120
  average time/residue: 1.0017
  time to fit residues: 127.8140
Evaluate side-chains
  78 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
C   6 HIS
C  28 HIS
C  54 HIS
C 115 GLN
D  54 HIS
D  93 GLN
D 287 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.091560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.060046 restraints weight = 90661.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 3.40
r_work: 0.2596 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2600 r_free = 0.2600    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2599 r_free = 0.2599    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  15705  Z= 0.189
  Angle     :  0.621   7.823  22290  Z= 0.344
  Chirality :  0.040   0.216   2581
  Planarity :  0.005   0.038   1996
  Dihedral  : 22.605 167.597   4635
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.37 %
    Favored  : 91.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.23), residues: 1252
  helix:  1.86 (0.18), residues: 814
  sheet: -0.99 (0.36), residues: 138
  loop : -0.96 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 261 
 TYR   0.020   0.002   TYR D 215 
 PHE   0.012   0.002   PHE B 112 
 TRP   0.018   0.003   TRP D  46 
 HIS   0.007   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (15705)
  covalent geometry    : angle       0.62108 (22290)
  hydrogen bonds       : bond        0.05364 (  901)
  hydrogen bonds       : angle       4.06523 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.455 
Fit side-chains
REVERT: B  191 MET cc_start: 0.8927 (mtm) cc_final: 0.8675 (mtt)
REVERT: C  107 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8365 (ttp80)
REVERT: D  265 MET cc_start: 0.9198 (mmm) cc_final: 0.8429 (mmm)
  outliers start: 9
  outliers final: 0
  residues processed: 82
  average time/residue: 0.8629
  time to fit residues: 76.1513
Evaluate side-chains
  69 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 140 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0670
   chunk 61 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   chunk 75 optimal weight:    0.0670
   chunk 52 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 121 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
C 115 GLN
D  54 HIS
D  93 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.093961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.062707 restraints weight = 98604.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 3.57
r_work: 0.2656 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  15705  Z= 0.126
  Angle     :  0.523   7.840  22290  Z= 0.294
  Chirality :  0.035   0.187   2581
  Planarity :  0.004   0.096   1996
  Dihedral  : 22.549 174.534   4635
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.56 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.24), residues: 1252
  helix:  2.41 (0.18), residues: 818
  sheet: -0.59 (0.36), residues: 141
  loop : -0.69 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C  27 
 TYR   0.016   0.001   TYR D 307 
 PHE   0.010   0.001   PHE B 112 
 TRP   0.012   0.002   TRP C  46 
 HIS   0.005   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (15705)
  covalent geometry    : angle       0.52339 (22290)
  hydrogen bonds       : bond        0.04270 (  901)
  hydrogen bonds       : angle       3.68042 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9025 (mt0) cc_final: 0.8784 (mt0)
REVERT: B  304 GLN cc_start: 0.9043 (tt0) cc_final: 0.8645 (mt0)
REVERT: C   54 HIS cc_start: 0.8202 (t70) cc_final: 0.7993 (t70)
REVERT: C  107 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.8188 (ttp80)
REVERT: D  265 MET cc_start: 0.9101 (mmm) cc_final: 0.8548 (mmm)
REVERT: D  304 GLN cc_start: 0.9260 (tt0) cc_final: 0.8832 (mt0)
  outliers start: 9
  outliers final: 1
  residues processed: 88
  average time/residue: 0.7400
  time to fit residues: 71.0935
Evaluate side-chains
  74 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  105 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 108 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 88 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
C 115 GLN
D  54 HIS
D  93 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.093829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.062759 restraints weight = 81414.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 3.31
r_work: 0.2667 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15705  Z= 0.131
  Angle     :  0.515  11.446  22290  Z= 0.285
  Chirality :  0.035   0.185   2581
  Planarity :  0.004   0.039   1996
  Dihedral  : 22.560 175.427   4635
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.45 %
    Favored  : 90.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.24), residues: 1252
  helix:  2.60 (0.18), residues: 819
  sheet: -0.35 (0.36), residues: 143
  loop : -0.55 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  27 
 TYR   0.017   0.001   TYR C 307 
 PHE   0.011   0.001   PHE B 112 
 TRP   0.011   0.001   TRP D  46 
 HIS   0.003   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (15705)
  covalent geometry    : angle       0.51467 (22290)
  hydrogen bonds       : bond        0.03969 (  901)
  hydrogen bonds       : angle       3.60910 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9019 (mt0) cc_final: 0.8790 (mt0)
REVERT: C   54 HIS cc_start: 0.8137 (t70) cc_final: 0.7882 (t70)
  outliers start: 10
  outliers final: 1
  residues processed: 82
  average time/residue: 0.7159
  time to fit residues: 64.1895
Evaluate side-chains
  78 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 126 optimal weight:    6.9990
   chunk 116 optimal weight:    2.9990
   chunk 129 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
D  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.090360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.058936 restraints weight = 89842.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 3.43
r_work: 0.2583 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  15705  Z= 0.216
  Angle     :  0.553   8.109  22290  Z= 0.304
  Chirality :  0.038   0.185   2581
  Planarity :  0.004   0.041   1996
  Dihedral  : 22.658 174.374   4635
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.53 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.37 (0.24), residues: 1252
  helix:  2.64 (0.18), residues: 819
  sheet: -0.26 (0.35), residues: 143
  loop : -0.63 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  27 
 TYR   0.018   0.002   TYR C 307 
 PHE   0.010   0.002   PHE C 231 
 TRP   0.015   0.002   TRP A  46 
 HIS   0.005   0.001   HIS D 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (15705)
  covalent geometry    : angle       0.55318 (22290)
  hydrogen bonds       : bond        0.04731 (  901)
  hydrogen bonds       : angle       3.69499 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.473 
Fit side-chains
REVERT: B   27 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8063 (mtm180)
REVERT: B  238 ARG cc_start: 0.7692 (mtp180) cc_final: 0.6277 (tpt90)
  outliers start: 8
  outliers final: 2
  residues processed: 79
  average time/residue: 0.8272
  time to fit residues: 70.6854
Evaluate side-chains
  73 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0470
   chunk 85 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 129 optimal weight:    6.9990
   chunk 125 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 123 optimal weight:    4.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
D  93 GLN
D 287 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.093921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.062645 restraints weight = 92577.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 3.51
r_work: 0.2666 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15705  Z= 0.120
  Angle     :  0.498   8.273  22290  Z= 0.276
  Chirality :  0.034   0.177   2581
  Planarity :  0.004   0.041   1996
  Dihedral  : 22.557 176.216   4635
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 10.02 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.24), residues: 1252
  helix:  2.80 (0.18), residues: 819
  sheet: -0.07 (0.34), residues: 138
  loop : -0.59 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C  27 
 TYR   0.012   0.001   TYR D 307 
 PHE   0.011   0.001   PHE A 280 
 TRP   0.010   0.001   TRP D  46 
 HIS   0.006   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (15705)
  covalent geometry    : angle       0.49828 (22290)
  hydrogen bonds       : bond        0.03812 (  901)
  hydrogen bonds       : angle       3.51928 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9030 (mt0) cc_final: 0.8796 (mt0)
REVERT: C  107 ARG cc_start: 0.8578 (ptp-110) cc_final: 0.8014 (ptp-110)
REVERT: D  246 ARG cc_start: 0.7760 (tpp-160) cc_final: 0.7527 (tpp80)
  outliers start: 7
  outliers final: 2
  residues processed: 83
  average time/residue: 0.7918
  time to fit residues: 71.5024
Evaluate side-chains
  78 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 129 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 150 ASN
A 304 GLN
D 287 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.091145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.059598 restraints weight = 101313.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 3.60
r_work: 0.2592 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2597
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2597 r_free = 0.2597    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2597 r_free = 0.2597    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15705  Z= 0.199
  Angle     :  0.536   8.334  22290  Z= 0.294
  Chirality :  0.037   0.181   2581
  Planarity :  0.004   0.046   1996
  Dihedral  : 22.532 175.702   4635
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 10.41 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.24), residues: 1252
  helix:  2.79 (0.18), residues: 819
  sheet: -0.03 (0.35), residues: 139
  loop : -0.63 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C  27 
 TYR   0.011   0.001   TYR A 215 
 PHE   0.011   0.002   PHE D 316 
 TRP   0.013   0.002   TRP A  46 
 HIS   0.006   0.001   HIS D 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (15705)
  covalent geometry    : angle       0.53615 (22290)
  hydrogen bonds       : bond        0.04389 (  901)
  hydrogen bonds       : angle       3.62923 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9078 (mt0) cc_final: 0.8834 (mt0)
REVERT: B   51 LYS cc_start: 0.9020 (tppt) cc_final: 0.8818 (tppp)
REVERT: B  238 ARG cc_start: 0.7689 (mtp180) cc_final: 0.6253 (tpt90)
REVERT: C  107 ARG cc_start: 0.8636 (ptp-110) cc_final: 0.8063 (ptp-110)
  outliers start: 6
  outliers final: 2
  residues processed: 79
  average time/residue: 0.8423
  time to fit residues: 72.0290
Evaluate side-chains
  77 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 117 optimal weight:    0.6980
   chunk 136 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 137 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  93 GLN
D 287 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.093192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.061808 restraints weight = 98579.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 3.58
r_work: 0.2644 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2646
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2646
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15705  Z= 0.125
  Angle     :  0.500   8.445  22290  Z= 0.275
  Chirality :  0.034   0.176   2581
  Planarity :  0.004   0.047   1996
  Dihedral  : 22.487 176.431   4635
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 10.51 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.24), residues: 1252
  helix:  2.82 (0.18), residues: 820
  sheet:  0.11 (0.35), residues: 138
  loop : -0.60 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C  27 
 TYR   0.012   0.001   TYR D 307 
 PHE   0.009   0.001   PHE B 112 
 TRP   0.012   0.001   TRP C  46 
 HIS   0.005   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (15705)
  covalent geometry    : angle       0.49972 (22290)
  hydrogen bonds       : bond        0.03823 (  901)
  hydrogen bonds       : angle       3.53639 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9050 (mt0) cc_final: 0.8811 (mt0)
REVERT: B   51 LYS cc_start: 0.9003 (tppt) cc_final: 0.8798 (tppp)
REVERT: B   66 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.7335 (ppp)
REVERT: B  238 ARG cc_start: 0.7636 (mtp180) cc_final: 0.6233 (tpt90)
REVERT: C  107 ARG cc_start: 0.8589 (ptp-110) cc_final: 0.7982 (ptp-110)
REVERT: C  206 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8015 (mm-30)
REVERT: D  246 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7102 (tpp80)
  outliers start: 7
  outliers final: 2
  residues processed: 79
  average time/residue: 0.8018
  time to fit residues: 68.4530
Evaluate side-chains
  80 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 131 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0040
   overall best weight:    1.1596

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 287 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.092773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.061412 restraints weight = 96933.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 3.55
r_work: 0.2633 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2635
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2635 r_free = 0.2635    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2635 r_free = 0.2635    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2635
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15705  Z= 0.145
  Angle     :  0.511   8.803  22290  Z= 0.280
  Chirality :  0.034   0.174   2581
  Planarity :  0.004   0.049   1996
  Dihedral  : 22.462 176.322   4635
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 10.51 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.24), residues: 1252
  helix:  2.83 (0.18), residues: 819
  sheet:  0.18 (0.35), residues: 138
  loop : -0.61 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C  27 
 TYR   0.011   0.001   TYR D 307 
 PHE   0.010   0.001   PHE B 112 
 TRP   0.011   0.001   TRP C  46 
 HIS   0.005   0.001   HIS D 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (15705)
  covalent geometry    : angle       0.51105 (22290)
  hydrogen bonds       : bond        0.03951 (  901)
  hydrogen bonds       : angle       3.52640 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9063 (mt0) cc_final: 0.8828 (mt0)
REVERT: B  238 ARG cc_start: 0.7646 (mtp180) cc_final: 0.6281 (tpt90)
REVERT: C  107 ARG cc_start: 0.8592 (ptp-110) cc_final: 0.7984 (ptp-110)
REVERT: D  246 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7098 (tpp80)
  outliers start: 6
  outliers final: 2
  residues processed: 78
  average time/residue: 0.7910
  time to fit residues: 66.8883
Evaluate side-chains
  75 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 124 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 119 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 121 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
D  93 GLN
D 287 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.093609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.062242 restraints weight = 100314.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 3.61
r_work: 0.2652 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15705  Z= 0.126
  Angle     :  0.495   8.981  22290  Z= 0.271
  Chirality :  0.033   0.173   2581
  Planarity :  0.004   0.050   1996
  Dihedral  : 22.449 176.855   4635
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  0.97 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.20 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.74 (0.24), residues: 1252
  helix:  2.87 (0.18), residues: 819
  sheet:  0.30 (0.34), residues: 138
  loop : -0.57 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG C  27 
 TYR   0.011   0.001   TYR D 307 
 PHE   0.010   0.001   PHE B 112 
 TRP   0.012   0.001   TRP A 276 
 HIS   0.005   0.000   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (15705)
  covalent geometry    : angle       0.49508 (22290)
  hydrogen bonds       : bond        0.03743 (  901)
  hydrogen bonds       : angle       3.46196 ( 2450)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A  153 GLU cc_start: 0.9147 (tp30) cc_final: 0.8895 (tp30)
REVERT: A  227 GLN cc_start: 0.9058 (mt0) cc_final: 0.8822 (mt0)
REVERT: B  238 ARG cc_start: 0.7639 (mtp180) cc_final: 0.6285 (tpt90)
REVERT: C  107 ARG cc_start: 0.8580 (ptp-110) cc_final: 0.7972 (ptp-110)
REVERT: C  206 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8022 (mm-30)
  outliers start: 5
  outliers final: 1
  residues processed: 77
  average time/residue: 0.7378
  time to fit residues: 61.8061
Evaluate side-chains
  77 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain C residue  206 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 139 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 137 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 135 optimal weight:    7.9990
   chunk 95 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.092605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.061230 restraints weight = 96825.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 3.54
r_work: 0.2630 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  15705  Z= 0.151
  Angle     :  0.508   8.848  22290  Z= 0.276
  Chirality :  0.034   0.174   2581
  Planarity :  0.004   0.052   1996
  Dihedral  : 22.458 176.340   4635
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  0.89 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.10 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.24), residues: 1252
  helix:  2.88 (0.18), residues: 820
  sheet:  0.31 (0.34), residues: 138
  loop : -0.58 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG C  27 
 TYR   0.021   0.001   TYR C 307 
 PHE   0.010   0.001   PHE B 112 
 TRP   0.011   0.002   TRP C  46 
 HIS   0.005   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (15705)
  covalent geometry    : angle       0.50786 (22290)
  hydrogen bonds       : bond        0.03979 (  901)
  hydrogen bonds       : angle       3.46793 ( 2450)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4407.38 seconds
wall clock time: 75 minutes 59.91 seconds (4559.91 seconds total)