Starting phenix.real_space_refine
on Fri May 16 15:00:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt8_37829/05_2025/8wt8_37829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt8_37829/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wt8_37829/05_2025/8wt8_37829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt8_37829/05_2025/8wt8_37829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt8_37829/05_2025/8wt8_37829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt8_37829/05_2025/8wt8_37829.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.20, per 1000 atoms: 0.88
  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: 3.70
  Conformation dependent library (CDL) restraints added in 3.2 seconds
  

  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: 5.82
  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: 5.41

  Time building geometry restraints manager: 4.36 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:             3.170
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.040
  Process input model:                     44.480
  Find NCS groups from input model:        0.560
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.880
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.016   0.004   TRP C 169 
 HIS   0.006   0.002   HIS D 256 
 PHE   0.015   0.002   PHE A 231 
 TYR   0.017   0.002   TYR D  78 
 ARG   0.013   0.002   ARG D 300 

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

*********************** 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  : 1.242 
Fit side-chains
REVERT: A  268 MET cc_start: 0.8145 (mtm) cc_final: 0.7889 (mtp)
  outliers start: 5
  outliers final: 0
  residues processed: 120
  average time/residue: 1.8731
  time to fit residues: 240.4791
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  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0030
   chunk 57 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    1.5998

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.091102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.059836 restraints weight = 75113.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2807 rms_B_bonded: 3.15
r_work: 0.2598 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2600 r_free = 0.2600    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2600 r_free = 0.2600    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  15705  Z= 0.191
  Angle     :  0.616   7.518  22290  Z= 0.344
  Chirality :  0.040   0.236   2581
  Planarity :  0.004   0.037   1996
  Dihedral  : 22.581 168.070   4635
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  7.17 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.23), residues: 1252
  helix:  1.82 (0.17), residues: 814
  sheet: -0.99 (0.36), residues: 138
  loop : -0.96 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  46 
 HIS   0.007   0.001   HIS B 256 
 PHE   0.012   0.002   PHE B 112 
 TYR   0.020   0.002   TYR D 215 
 ARG   0.008   0.001   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05845 (  901)
  hydrogen bonds       : angle       4.13063 ( 2450)
  covalent geometry    : bond        0.00404 (15705)
  covalent geometry    : angle       0.61583 (22290)

*********************** 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
  88 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 1.213 
Fit side-chains
REVERT: D  265 MET cc_start: 0.9206 (mmm) cc_final: 0.8431 (mmm)
  outliers start: 10
  outliers final: 1
  residues processed: 83
  average time/residue: 1.6719
  time to fit residues: 150.3928
Evaluate side-chains
  71 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 64 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 139 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 127 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0670
   chunk 99 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.3722

-------------------------------------------------------------------------------
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 115 GLN
D  54 HIS
D  93 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.091650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.060183 restraints weight = 94433.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 3.50
r_work: 0.2609 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2612 r_free = 0.2612    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15705  Z= 0.165
  Angle     :  0.544   7.555  22290  Z= 0.305
  Chirality :  0.037   0.193   2581
  Planarity :  0.004   0.072   1996
  Dihedral  : 22.619 173.852   4635
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  7.56 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.24), residues: 1252
  helix:  2.37 (0.18), residues: 817
  sheet: -0.65 (0.36), residues: 140
  loop : -0.75 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  46 
 HIS   0.006   0.001   HIS C  54 
 PHE   0.010   0.002   PHE B 112 
 TYR   0.018   0.001   TYR D 307 
 ARG   0.020   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04615 (  901)
  hydrogen bonds       : angle       3.74918 ( 2450)
  covalent geometry    : bond        0.00363 (15705)
  covalent geometry    : angle       0.54369 (22290)

*********************** 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
  87 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 1.469 
Fit side-chains
REVERT: C   54 HIS cc_start: 0.8205 (t70) cc_final: 0.7989 (t70)
REVERT: C  107 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8335 (ttp80)
REVERT: D  265 MET cc_start: 0.9155 (mmm) cc_final: 0.8116 (mmm)
  outliers start: 11
  outliers final: 0
  residues processed: 80
  average time/residue: 1.7708
  time to fit residues: 154.8665
Evaluate side-chains
  70 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 128 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    2.3388

-------------------------------------------------------------------------------
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 = 0.3382 r_free = 0.3382 target = 0.089614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.058276 restraints weight = 91096.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 3.44
r_work: 0.2567 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  15705  Z= 0.228
  Angle     :  0.561   8.149  22290  Z= 0.311
  Chirality :  0.039   0.190   2581
  Planarity :  0.004   0.041   1996
  Dihedral  : 22.715 173.310   4635
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.35 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.24), residues: 1252
  helix:  2.46 (0.18), residues: 818
  sheet: -0.47 (0.35), residues: 143
  loop : -0.72 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  46 
 HIS   0.008   0.001   HIS D 166 
 PHE   0.012   0.002   PHE C 231 
 TYR   0.018   0.002   TYR C 307 
 ARG   0.007   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04926 (  901)
  hydrogen bonds       : angle       3.78223 ( 2450)
  covalent geometry    : bond        0.00512 (15705)
  covalent geometry    : angle       0.56150 (22290)

*********************** 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
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 1.273 
Fit side-chains
REVERT: B   27 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8091 (mtm180)
REVERT: B  238 ARG cc_start: 0.7677 (mtp180) cc_final: 0.6247 (tpt90)
REVERT: C   54 HIS cc_start: 0.8176 (t70) cc_final: 0.7904 (t70)
REVERT: C  107 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8369 (ttp80)
REVERT: D  265 MET cc_start: 0.9208 (mmm) cc_final: 0.8885 (mmt)
  outliers start: 9
  outliers final: 0
  residues processed: 78
  average time/residue: 1.6982
  time to fit residues: 143.4113
Evaluate side-chains
  72 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 63 optimal weight:    9.9990
   chunk 18 optimal weight:    0.7980
   chunk 100 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 118 optimal weight:    6.9990
   overall best weight:    1.5184

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.091105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.059472 restraints weight = 98363.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 3.56
r_work: 0.2592 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15705  Z= 0.165
  Angle     :  0.525   8.525  22290  Z= 0.291
  Chirality :  0.036   0.185   2581
  Planarity :  0.004   0.039   1996
  Dihedral  : 22.687 174.550   4635
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.74 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.24), residues: 1252
  helix:  2.58 (0.18), residues: 819
  sheet: -0.32 (0.35), residues: 139
  loop : -0.69 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  46 
 HIS   0.004   0.001   HIS C  54 
 PHE   0.009   0.002   PHE B 112 
 TYR   0.013   0.001   TYR B 307 
 ARG   0.010   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04349 (  901)
  hydrogen bonds       : angle       3.66648 ( 2450)
  covalent geometry    : bond        0.00366 (15705)
  covalent geometry    : angle       0.52539 (22290)

*********************** 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
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 1.207 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9077 (mt0) cc_final: 0.8870 (mt0)
REVERT: B  238 ARG cc_start: 0.7740 (mtp180) cc_final: 0.6350 (tpt90)
REVERT: C   54 HIS cc_start: 0.8155 (t70) cc_final: 0.7862 (t70)
REVERT: C  107 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8335 (ttp80)
REVERT: D  246 ARG cc_start: 0.7760 (tpp-160) cc_final: 0.7510 (tpp80)
REVERT: D  265 MET cc_start: 0.9165 (mmm) cc_final: 0.8933 (mmt)
  outliers start: 8
  outliers final: 1
  residues processed: 75
  average time/residue: 1.5297
  time to fit residues: 125.0928
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  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 94 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 137 optimal weight:    7.9990
   chunk 135 optimal weight:    7.9990
   chunk 139 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 109 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A  99 ASN
A 304 GLN
D  93 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.088372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.057105 restraints weight = 93043.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.2758 rms_B_bonded: 3.47
r_work: 0.2543 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2543
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2544
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  15705  Z= 0.299
  Angle     :  0.587   8.494  22290  Z= 0.322
  Chirality :  0.041   0.193   2581
  Planarity :  0.005   0.041   1996
  Dihedral  : 22.724 173.251   4635
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  9.04 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.24), residues: 1252
  helix:  2.50 (0.18), residues: 819
  sheet: -0.25 (0.35), residues: 143
  loop : -0.84 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  46 
 HIS   0.007   0.001   HIS D 166 
 PHE   0.013   0.002   PHE C 231 
 TYR   0.014   0.002   TYR B 307 
 ARG   0.012   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05164 (  901)
  hydrogen bonds       : angle       3.83819 ( 2450)
  covalent geometry    : bond        0.00673 (15705)
  covalent geometry    : angle       0.58660 (22290)

*********************** 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
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 1.238 
Fit side-chains
REVERT: B   27 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8107 (mtm180)
REVERT: B   93 GLN cc_start: 0.8987 (mt0) cc_final: 0.8678 (mt0)
REVERT: B  191 MET cc_start: 0.9021 (mtt) cc_final: 0.8738 (mtm)
REVERT: B  238 ARG cc_start: 0.7940 (mtp180) cc_final: 0.6579 (tpt90)
REVERT: C   54 HIS cc_start: 0.8247 (t70) cc_final: 0.8019 (t70)
REVERT: C  107 ARG cc_start: 0.8663 (ttm-80) cc_final: 0.8406 (ttp80)
  outliers start: 11
  outliers final: 2
  residues processed: 75
  average time/residue: 1.5984
  time to fit residues: 130.2469
Evaluate side-chains
  74 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 115 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.092441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.061108 restraints weight = 89182.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 3.37
r_work: 0.2634 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15705  Z= 0.133
  Angle     :  0.511   8.922  22290  Z= 0.282
  Chirality :  0.035   0.180   2581
  Planarity :  0.004   0.043   1996
  Dihedral  : 22.635 175.110   4635
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.14 %
    Favored  : 89.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.24), residues: 1252
  helix:  2.68 (0.18), residues: 819
  sheet: -0.10 (0.35), residues: 137
  loop : -0.75 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  46 
 HIS   0.003   0.001   HIS D 166 
 PHE   0.009   0.001   PHE C 280 
 TYR   0.020   0.001   TYR C 307 
 ARG   0.015   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  901)
  hydrogen bonds       : angle       3.60980 ( 2450)
  covalent geometry    : bond        0.00289 (15705)
  covalent geometry    : angle       0.51071 (22290)

*********************** 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
  86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 1.218 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9075 (mt0) cc_final: 0.8808 (mt0)
REVERT: B   27 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7992 (mtm180)
REVERT: B   93 GLN cc_start: 0.8885 (mt0) cc_final: 0.8684 (mt0)
REVERT: B  191 MET cc_start: 0.8886 (mtt) cc_final: 0.8583 (mtm)
REVERT: B  238 ARG cc_start: 0.7775 (mtp180) cc_final: 0.6352 (tpt90)
REVERT: C   54 HIS cc_start: 0.8206 (t70) cc_final: 0.7910 (t70)
REVERT: C  107 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8281 (ttp80)
REVERT: D  265 MET cc_start: 0.9100 (mmm) cc_final: 0.8665 (mmm)
  outliers start: 9
  outliers final: 2
  residues processed: 81
  average time/residue: 1.5663
  time to fit residues: 137.7654
Evaluate side-chains
  75 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 130 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 125 optimal weight:    8.9990
   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  93 GLN
A  99 ASN
C  40 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 = 0.3393 r_free = 0.3393 target = 0.090505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.058782 restraints weight = 105838.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 3.58
r_work: 0.2582 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2575
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2575 r_free = 0.2575    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2575 r_free = 0.2575    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2575
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  15705  Z= 0.212
  Angle     :  0.544   8.865  22290  Z= 0.297
  Chirality :  0.037   0.183   2581
  Planarity :  0.004   0.046   1996
  Dihedral  : 22.626 174.598   4635
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  9.43 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.24), residues: 1252
  helix:  2.66 (0.18), residues: 819
  sheet: -0.12 (0.35), residues: 137
  loop : -0.81 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  46 
 HIS   0.006   0.001   HIS D 166 
 PHE   0.010   0.002   PHE C 231 
 TYR   0.022   0.002   TYR C 307 
 ARG   0.013   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04510 (  901)
  hydrogen bonds       : angle       3.67306 ( 2450)
  covalent geometry    : bond        0.00477 (15705)
  covalent geometry    : angle       0.54406 (22290)

*********************** 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
  85 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 1.253 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9091 (mt0) cc_final: 0.8877 (mt0)
REVERT: B   27 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8008 (mtm180)
REVERT: B  238 ARG cc_start: 0.7886 (mtp180) cc_final: 0.6515 (tpt90)
REVERT: C   54 HIS cc_start: 0.8232 (t70) cc_final: 0.7977 (t70)
REVERT: C   66 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7551 (ppp)
REVERT: C  107 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8349 (ttp80)
REVERT: D  265 MET cc_start: 0.9192 (mmm) cc_final: 0.8193 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 77
  average time/residue: 1.4866
  time to fit residues: 124.9351
Evaluate side-chains
  77 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain C residue   66 MET
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 124 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 128 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 121 optimal weight:    1.9990
   overall best weight:    1.1186

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.092302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.060731 restraints weight = 100681.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 3.55
r_work: 0.2622 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2621
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15705  Z= 0.142
  Angle     :  0.513   9.050  22290  Z= 0.281
  Chirality :  0.034   0.178   2581
  Planarity :  0.004   0.047   1996
  Dihedral  : 22.584 175.573   4635
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 10.22 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.24), residues: 1252
  helix:  2.73 (0.18), residues: 819
  sheet:  0.09 (0.36), residues: 136
  loop : -0.80 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  46 
 HIS   0.003   0.001   HIS B  50 
 PHE   0.009   0.001   PHE C 280 
 TYR   0.021   0.001   TYR C 307 
 ARG   0.015   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  901)
  hydrogen bonds       : angle       3.55410 ( 2450)
  covalent geometry    : bond        0.00314 (15705)
  covalent geometry    : angle       0.51349 (22290)

*********************** 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
  84 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 1.221 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9083 (mt0) cc_final: 0.8836 (mt0)
REVERT: B   27 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7971 (mtm180)
REVERT: C   54 HIS cc_start: 0.8203 (t70) cc_final: 0.7941 (t70)
REVERT: C  107 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8296 (ttp80)
  outliers start: 8
  outliers final: 3
  residues processed: 78
  average time/residue: 1.5191
  time to fit residues: 129.5110
Evaluate side-chains
  76 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain C residue  268 MET
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 121 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.092909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.061474 restraints weight = 93945.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 3.46
r_work: 0.2637 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.3105

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= 0.132
  Angle     :  0.506   9.336  22290  Z= 0.277
  Chirality :  0.034   0.176   2581
  Planarity :  0.004   0.052   1996
  Dihedral  : 22.546 176.095   4635
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 10.22 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.24), residues: 1252
  helix:  2.77 (0.18), residues: 819
  sheet:  0.23 (0.36), residues: 136
  loop : -0.75 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  46 
 HIS   0.003   0.001   HIS D 145 
 PHE   0.012   0.001   PHE A 280 
 TYR   0.020   0.001   TYR C 307 
 ARG   0.014   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  901)
  hydrogen bonds       : angle       3.49821 ( 2450)
  covalent geometry    : bond        0.00287 (15705)
  covalent geometry    : angle       0.50604 (22290)

********************** 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
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 1.240 
Fit side-chains
REVERT: A  227 GLN cc_start: 0.9075 (mt0) cc_final: 0.8831 (mt0)
REVERT: B   27 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7937 (mtm180)
REVERT: B  238 ARG cc_start: 0.8000 (mtp180) cc_final: 0.7469 (mtp180)
REVERT: C   54 HIS cc_start: 0.8200 (t70) cc_final: 0.7963 (t70)
REVERT: C   66 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7491 (ppp)
REVERT: D  265 MET cc_start: 0.9146 (mmm) cc_final: 0.8248 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 76
  average time/residue: 1.6969
  time to fit residues: 141.1245
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  : 1.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain C residue   66 MET
Chi-restraints excluded: chain C residue  268 MET
Chi-restraints excluded: chain D residue   97 LEU
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 118 optimal weight:    7.9990
   chunk 74 optimal weight:    0.8980
   chunk 124 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0040
   overall best weight:    1.1798

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.092636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.061187 restraints weight = 98321.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 3.50
r_work: 0.2630 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15705  Z= 0.146
  Angle     :  0.510   9.253  22290  Z= 0.279
  Chirality :  0.034   0.176   2581
  Planarity :  0.004   0.051   1996
  Dihedral  : 22.522 176.191   4635
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.31 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.24), residues: 1252
  helix:  2.77 (0.18), residues: 819
  sheet:  0.23 (0.36), residues: 136
  loop : -0.76 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  46 
 HIS   0.003   0.001   HIS D 256 
 PHE   0.010   0.001   PHE B 112 
 TYR   0.022   0.001   TYR C 307 
 ARG   0.015   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  901)
  hydrogen bonds       : angle       3.50074 ( 2450)
  covalent geometry    : bond        0.00326 (15705)
  covalent geometry    : angle       0.51013 (22290)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8428.65 seconds
wall clock time: 146 minutes 17.42 seconds (8777.42 seconds total)