Starting phenix.real_space_refine
on Fri Jun 13 03:43:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt9_37830/06_2025/8wt9_37830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt9_37830/06_2025/8wt9_37830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wt9_37830/06_2025/8wt9_37830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt9_37830/06_2025/8wt9_37830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt9_37830/06_2025/8wt9_37830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt9_37830/06_2025/8wt9_37830.cif"
  }
  resolution = 2.7
  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=   0.028
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      2      5.21       5
     S      48      5.16       5
     C    8557      2.51       5
     N    2771      2.21       5
     O    3363      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14982
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 2530
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 319, 2515
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 12, 'TRANS': 306}
      Conformer: "B"
        Number of residues, atoms: 319, 2515
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 12, 'TRANS': 306}
          bond proxies already assigned to first conformer: 2547
    Chain: "B"
      Number of atoms: 2449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2449
          Classifications: {'peptide': 311}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 2517
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 318, 2506
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
      Conformer: "B"
        Number of residues, atoms: 318, 2506
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          bond proxies already assigned to first conformer: 2543
    Chain: "D"
      Number of atoms: 2456
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 310, 2447
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 310, 2447
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 2485
    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': 14, 'rna3p': 44}
    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': 7, 'rna3p_pur': 27, 'rna3p_pyr': 28}
          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 breaks: 1
    Chain: "I"
      Number of atoms: 555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 555
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "J"
      Number of atoms: 643
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 29, 602
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
      Conformer: "B"
        Number of residues, atoms: 29, 602
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 630
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "J"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  AGLN A 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 139 " occ=0.50
    residue:
      pdb=" N  ASER A 241 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A 241 " occ=0.50
    residue:
      pdb=" N  AARG C 237 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C 237 " 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=" P  A DT J  28 " occ=0.50
      ... (38 atoms not shown)
      pdb=" C6 B DT J  28 " occ=0.50
    residue:
      pdb=" P  A DA J  29 " occ=0.50
      ... (40 atoms not shown)
      pdb=" C4 B DA J  29 " occ=0.50
  Time building chain proxies: 13.24, per 1000 atoms: 0.88
  Number of scatterers: 14982
  At special positions: 0
  Unit cell: (122.84, 123.947, 116.2, 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      2     11.99
     O    3363      8.00
     N    2771      7.00
     C    8557      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: 3.88
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      67.2% alpha, 10.7% beta
      87 base pairs and 148 stacking pairs defined.
    Time for finding SS restraints: 7.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 50
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 84 through 95
      removed outlier: 3.627A  pdb=" N   GLY A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 117
    Processing helix  chain 'A' and resid 125 through 155
      removed outlier: 4.162A  pdb=" N   GLU A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   THR A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 188
      removed outlier: 3.656A  pdb=" N   ASP A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 199
    Processing helix  chain 'A' and resid 205 through 217
    Processing helix  chain 'A' and resid 224 through 232
      removed outlier: 3.671A  pdb=" N   PHE A 228 " --> pdb=" O   HIS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 263
      removed outlier: 3.756A  pdb=" N   LEU A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 274 through 287
      removed outlier: 3.532A  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: 3.588A  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 63 through 65
      No H-bonds generated for 'chain 'B' and resid 63 through 65'
    Processing helix  chain 'B' and resid 66 through 77
    Processing helix  chain 'B' and resid 84 through 95
      removed outlier: 3.532A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 117
    Processing helix  chain 'B' and resid 125 through 154
      removed outlier: 3.810A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 188
      removed outlier: 3.624A  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
    Processing helix  chain 'B' and resid 224 through 232
      removed outlier: 3.729A  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
    Processing helix  chain 'B' and resid 274 through 287
      removed outlier: 3.714A  pdb=" N   ASN B 287 " --> pdb=" O   ARG B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 313
    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
      removed outlier: 3.544A  pdb=" N   GLY C  88 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY C  96 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 117
    Processing helix  chain 'C' and resid 125 through 153
      removed outlier: 3.912A  pdb=" N   GLU C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 188
      removed outlier: 3.626A  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
    Processing helix  chain 'C' and resid 224 through 232
      removed outlier: 3.649A  pdb=" N   PHE C 228 " --> pdb=" O   HIS C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 262
      removed outlier: 3.596A  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 287
    Processing helix  chain 'C' and resid 290 through 313
    Processing helix  chain 'C' and resid 317 through 321
    Processing helix  chain 'D' and resid 36 through 49
    Processing helix  chain 'D' and resid 66 through 77
    Processing helix  chain 'D' and resid 84 through 95
    Processing helix  chain 'D' and resid 101 through 117
      removed outlier: 3.511A  pdb=" N   ALA D 110 " --> pdb=" O   ALA D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 125 through 152
    Processing helix  chain 'D' and resid 159 through 188
      removed outlier: 3.653A  pdb=" N   ASP D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 200
    Processing helix  chain 'D' and resid 205 through 216
    Processing helix  chain 'D' and resid 224 through 232
      removed outlier: 3.831A  pdb=" N   PHE D 228 " --> pdb=" O   HIS D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 262
      removed outlier: 3.519A  pdb=" N   ALA D 262 " --> pdb=" O   SER D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 263 through 274
    Processing helix  chain 'D' and resid 274 through 286
    Processing helix  chain 'D' and resid 290 through 313
    Processing helix  chain 'D' and resid 317 through 322
      removed outlier: 3.633A  pdb=" N   ASN D 322 " --> pdb=" O   SER D 319 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34
      removed outlier: 6.540A  pdb=" N   HIS A   6 " --> pdb=" O   HIS A  56 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   CYS A  58 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ILE A   8 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 8.517A  pdb=" N   GLU A  60 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   ILE A  10 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 241
      removed outlier: 3.685A  pdb=" N   ARG A 250 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   TYR A 239 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   ALA A 248 " --> pdb=" O   TYR A 239 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N  ASER A 241 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   ARG A 246 " --> pdb=" O  ASER A 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 34
      removed outlier: 4.434A  pdb=" N   GLU B  60 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR B  12 " --> pdb=" O   GLU B  60 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 237
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34
      removed outlier: 6.782A  pdb=" N   HIS C   6 " --> pdb=" O   HIS C  56 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   CYS C  58 " --> pdb=" O   HIS C   6 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE C   8 " --> pdb=" O   CYS C  58 " (cutoff:3.500A)
      removed outlier: 8.496A  pdb=" N   GLU C  60 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   ILE C  10 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 241
      removed outlier: 3.915A  pdb=" N   ARG C 250 " --> pdb=" O  AARG C 237 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   TYR C 239 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ALA C 248 " --> pdb=" O   TYR C 239 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   SER C 241 " --> pdb=" O   ARG C 246 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   ARG C 246 " --> pdb=" O   SER C 241 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 34
      removed outlier: 6.664A  pdb=" N   HIS D   6 " --> pdb=" O   HIS D  56 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   CYS D  58 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ILE D   8 " --> pdb=" O   CYS D  58 " (cutoff:3.500A)
      removed outlier: 8.576A  pdb=" N   GLU D  60 " --> pdb=" O   ILE D   8 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   ILE D  10 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 236 through 237

    680 hydrogen bonds defined for protein.
    2003 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      222 hydrogen bonds
      438 hydrogen bond angles
      0 basepair planarities
      87 basepair parallelities
      150 stacking parallelities
  Total time for adding SS restraints: 6.00

  Time building geometry restraints manager: 4.59 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: 3485
        1.34 -     1.46: 5386
        1.46 -     1.58: 6336
        1.58 -     1.69: 475
        1.69 -     1.81: 84
  Bond restraints: 15766
  Sorted by residual:
  bond pdb=" P     A F 110 "
       pdb=" OP2   A F 110 "
    ideal  model  delta    sigma   weight residual
    1.485  1.560 -0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" P     A F 110 "
       pdb=" OP1   A F 110 "
    ideal  model  delta    sigma   weight residual
    1.485  1.559 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" P     A F 110 "
       pdb=" O5'   A F 110 "
    ideal  model  delta    sigma   weight residual
    1.593  1.633 -0.040 1.50e-02 4.44e+03 7.07e+00
  bond pdb=" C   THR D 235 "
       pdb=" N   PRO D 236 "
    ideal  model  delta    sigma   weight residual
    1.329  1.358 -0.029 1.20e-02 6.94e+03 5.98e+00
  bond pdb=" C   ILE A 201 "
       pdb=" N   PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.357 -0.024 1.01e-02 9.80e+03 5.58e+00
  ... (remaining 15761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 19710
        2.10 -     4.19: 2427
        4.19 -     6.29: 216
        6.29 -     8.38: 14
        8.38 -    10.48: 2
  Bond angle restraints: 22369
  Sorted by residual:
  angle pdb=" O3'  DC G  15 "
        pdb=" P    DC G  16 "
        pdb=" O5'  DC G  16 "
      ideal   model   delta    sigma   weight residual
     104.00   94.68    9.32 1.50e+00 4.44e-01 3.86e+01
  angle pdb=" O3'   U F 159 "
        pdb=" P     U F 160 "
        pdb=" O5'   U F 160 "
      ideal   model   delta    sigma   weight residual
     104.00   95.77    8.23 1.50e+00 4.44e-01 3.01e+01
  angle pdb=" O3'  DC G  23 "
        pdb=" P    DC G  24 "
        pdb=" O5'  DC G  24 "
      ideal   model   delta    sigma   weight residual
     104.00   96.79    7.21 1.50e+00 4.44e-01 2.31e+01
  angle pdb=" CG  MET D 108 "
        pdb=" SD  MET D 108 "
        pdb=" CE  MET D 108 "
      ideal   model   delta    sigma   weight residual
     100.90  111.38  -10.48 2.20e+00 2.07e-01 2.27e+01
  angle pdb=" O3'   U F 168 "
        pdb=" P     G F 169 "
        pdb=" O5'   G F 169 "
      ideal   model   delta    sigma   weight residual
     104.00  111.04   -7.04 1.50e+00 4.44e-01 2.20e+01
  ... (remaining 22364 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.07: 8729
       34.07 -    68.13: 676
       68.13 -   102.20: 52
      102.20 -   136.26: 0
      136.26 -   170.33: 1
  Dihedral angle restraints: 9458
    sinusoidal: 5803
      harmonic: 3655
  Sorted by residual:
  dihedral pdb=" C5'   C E  95 "
           pdb=" C4'   C E  95 "
           pdb=" C3'   C E  95 "
           pdb=" O3'   C E  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   86.35   60.65     1      8.00e+00 1.56e-02 7.65e+01
  dihedral pdb=" O4'   C E  95 "
           pdb=" C4'   C E  95 "
           pdb=" C3'   C E  95 "
           pdb=" C2'   C E  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -32.53   56.53     1      8.00e+00 1.56e-02 6.73e+01
  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   61.67  170.33     1      1.70e+01 3.46e-03 6.60e+01
  ... (remaining 9455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 2386
       0.148 -    0.297: 199
       0.297 -    0.445: 0
       0.445 -    0.594: 1
       0.594 -    0.742: 5
  Chirality restraints: 2591
  Sorted by residual:
  chirality pdb=" P     A F 110 "
            pdb=" OP1   A F 110 "
            pdb=" OP2   A F 110 "
            pdb=" O5'   A F 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.15   -0.74 2.00e-01 2.50e+01 1.38e+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   -2.99   -0.65 2.00e-01 2.50e+01 1.05e+01
  chirality pdb=" P    DG I   5 "
            pdb=" OP1  DG I   5 "
            pdb=" OP2  DG I   5 "
            pdb=" O5'  DG I   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.96   -0.62 2.00e-01 2.50e+01 9.57e+00
  ... (remaining 2588 not shown)

  Planarity restraints: 2007
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F 157 "   -0.037 2.00e-02 2.50e+03   1.49e-02 6.10e+00
        pdb=" N9    A F 157 "    0.022 2.00e-02 2.50e+03
        pdb=" C8    A F 157 "    0.008 2.00e-02 2.50e+03
        pdb=" N7    A F 157 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A F 157 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    A F 157 "   -0.010 2.00e-02 2.50e+03
        pdb=" N6    A F 157 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1    A F 157 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A F 157 "    0.007 2.00e-02 2.50e+03
        pdb=" N3    A F 157 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    A F 157 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA J  35 "   -0.031 2.00e-02 2.50e+03   1.31e-02 4.72e+00
        pdb=" N9   DA J  35 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DA J  35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA J  35 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DA J  35 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA J  35 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6   DA J  35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA J  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA J  35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA J  35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA J  35 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F 168 "   -0.024 2.00e-02 2.50e+03   1.35e-02 4.11e+00
        pdb=" N1    U F 168 "    0.031 2.00e-02 2.50e+03
        pdb=" C2    U F 168 "    0.003 2.00e-02 2.50e+03
        pdb=" O2    U F 168 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U F 168 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    U F 168 "   -0.005 2.00e-02 2.50e+03
        pdb=" O4    U F 168 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    U F 168 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    U F 168 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2004 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 9
        2.27 -     2.92: 5260
        2.92 -     3.58: 22496
        3.58 -     4.24: 40738
        4.24 -     4.90: 62012
  Nonbonded interactions: 130515
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 241 "
            pdb=" P    DC H  18 "
     model   vdw
     1.607 3.400
  nonbonded pdb=" OG BSER A 241 "
            pdb=" P  B DA J  29 "
     model   vdw
     1.608 3.400
  nonbonded pdb="MG    MG B 401 "
            pdb=" O   HOH B 502 "
     model   vdw
     2.065 2.170
  nonbonded pdb="MG    MG B 401 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.072 2.170
  nonbonded pdb=" OE1 GLU B  60 "
            pdb="MG    MG B 401 "
     model   vdw
     2.086 2.170
  ... (remaining 130510 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 236 or (resid 238 throu \ 
gh 239 and (name N or name CA or name C or name O or name CB )) or resid 248 thr \ 
ough 322))
  selection = (chain 'B' and (resid 5 through 138 or resid 140 through 236 or resid 238 throug \ 
h 322))
  selection = (chain 'C' and (resid 5 through 138 or resid 140 through 236 or (resid 238 throu \ 
gh 239 and (name N or name CA or name C or name O or name CB )) or resid 248 thr \ 
ough 322))
  selection = (chain 'D' and (resid 5 through 138 or resid 140 through 236 or (resid 238 throu \ 
gh 248 and (name N or name CA or name C or name O or name CB )) or resid 249 thr \ 
ough 322))
}

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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     45.820
  Find NCS groups from input model:        0.590
  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:14.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
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   0.075  15766  Z= 0.477
  Angle     :  1.362  10.479  22369  Z= 0.878
  Chirality :  0.080   0.742   2591
  Planarity :  0.003   0.029   2007
  Dihedral  : 20.155 170.329   7094
  Min Nonbonded Distance : 1.607

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  2.44 %
    Favored  : 96.58 %
  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: -1.58 (0.19), residues: 1258
  helix: -0.66 (0.15), residues: 794
  sheet: -1.40 (0.34), residues: 153
  loop : -1.36 (0.29), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.006   TRP B 169 
 HIS   0.006   0.002   HIS D 256 
 PHE   0.017   0.003   PHE D 231 
 TYR   0.017   0.002   TYR B  78 
 ARG   0.015   0.002   ARG C 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20347 (  902)
  hydrogen bonds       : angle       6.71794 ( 2441)
  covalent geometry    : bond        0.00793 (15766)
  covalent geometry    : angle       1.36173 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 1.619 
Fit side-chains
REVERT: A   66 MET cc_start: 0.8236 (ppp) cc_final: 0.7997 (pp-130)
REVERT: B  273 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8471 (mttm)
REVERT: C  298 MET cc_start: 0.8201 (tpt) cc_final: 0.7879 (tpt)
REVERT: D  287 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8324 (t0)
  outliers start: 10
  outliers final: 0
  residues processed: 112
  average time/residue: 1.9802
  time to fit residues: 238.5686
Evaluate side-chains
  77 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 LYS
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:    4.9990
   chunk 108 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 129 optimal weight:   10.0000
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN
C  93 GLN
C 287 ASN
D  99 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.088459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.055404 restraints weight = 80075.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2653 rms_B_bonded: 3.16
r_work: 0.2421 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2435 r_free = 0.2435    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2435 r_free = 0.2435    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  15766  Z= 0.247
  Angle     :  0.635   7.175  22369  Z= 0.354
  Chirality :  0.042   0.219   2591
  Planarity :  0.005   0.049   2007
  Dihedral  : 22.140 162.271   4647
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.06 %
    Favored  : 93.26 %
  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:  1.27 (0.23), residues: 1258
  helix:  1.86 (0.17), residues: 799
  sheet: -0.94 (0.35), residues: 165
  loop : -0.84 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP D 276 
 HIS   0.005   0.001   HIS B  50 
 PHE   0.014   0.002   PHE C 231 
 TYR   0.019   0.002   TYR A  74 
 ARG   0.009   0.001   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06176 (  902)
  hydrogen bonds       : angle       4.12143 ( 2441)
  covalent geometry    : bond        0.00558 (15766)
  covalent geometry    : angle       0.63542 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 1.227 
Fit side-chains
REVERT: B  273 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8824 (mtpt)
REVERT: C  139 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7257 (tm-30)
REVERT: D  191 MET cc_start: 0.9025 (mmm) cc_final: 0.8725 (mtp)
REVERT: D  287 ASN cc_start: 0.9002 (t0) cc_final: 0.8729 (m110)
  outliers start: 6
  outliers final: 2
  residues processed: 77
  average time/residue: 1.6013
  time to fit residues: 134.2368
Evaluate side-chains
  67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  273 LYS
Chi-restraints excluded: chain C residue  139 GLN
Chi-restraints excluded: chain D residue   38 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 85 optimal weight:    0.2980
   chunk 47 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.092590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.059532 restraints weight = 83675.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.2702 rms_B_bonded: 3.29
r_work: 0.2474 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2474
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2524
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2524 r_free = 0.2524    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2524 r_free = 0.2524    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2524
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15766  Z= 0.131
  Angle     :  0.525   6.743  22369  Z= 0.295
  Chirality :  0.037   0.189   2591
  Planarity :  0.004   0.043   2007
  Dihedral  : 22.153 165.092   4645
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.45 %
    Favored  : 92.67 %
  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:  2.13 (0.24), residues: 1258
  helix:  2.52 (0.18), residues: 805
  sheet: -0.51 (0.38), residues: 161
  loop : -0.64 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 276 
 HIS   0.006   0.001   HIS B 256 
 PHE   0.010   0.001   PHE B 280 
 TYR   0.020   0.002   TYR A  74 
 ARG   0.007   0.000   ARG A 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04299 (  902)
  hydrogen bonds       : angle       3.65691 ( 2441)
  covalent geometry    : bond        0.00274 (15766)
  covalent geometry    : angle       0.52512 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 1.366 
Fit side-chains
REVERT: D   54 HIS cc_start: 0.8669 (m90) cc_final: 0.8443 (m90)
REVERT: D  191 MET cc_start: 0.8959 (mmm) cc_final: 0.8632 (mtp)
REVERT: D  275 GLU cc_start: 0.8265 (pm20) cc_final: 0.8026 (pm20)
REVERT: D  287 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8787 (m110)
  outliers start: 8
  outliers final: 0
  residues processed: 84
  average time/residue: 1.5135
  time to fit residues: 139.3722
Evaluate side-chains
  68 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 140 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0470
   chunk 103 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0170
   chunk 4 optimal weight:    6.9990
   chunk 118 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 132 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
D 304 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.092643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.060113 restraints weight = 93164.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.2721 rms_B_bonded: 3.34
r_work: 0.2488 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2488
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2496 r_free = 0.2496    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2496 r_free = 0.2496    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15766  Z= 0.125
  Angle     :  0.494   6.143  22369  Z= 0.277
  Chirality :  0.035   0.193   2591
  Planarity :  0.004   0.045   2007
  Dihedral  : 22.093 168.507   4641
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.94 %
    Favored  : 92.38 %
  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:  2.51 (0.24), residues: 1258
  helix:  2.81 (0.18), residues: 805
  sheet: -0.26 (0.40), residues: 147
  loop : -0.52 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  46 
 HIS   0.003   0.001   HIS B 256 
 PHE   0.011   0.001   PHE D 112 
 TYR   0.013   0.001   TYR C 307 
 ARG   0.006   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  902)
  hydrogen bonds       : angle       3.49357 ( 2441)
  covalent geometry    : bond        0.00268 (15766)
  covalent geometry    : angle       0.49434 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 1.405 
Fit side-chains
REVERT: A  265 MET cc_start: 0.9111 (mmm) cc_final: 0.8855 (mmp)
REVERT: A  299 MET cc_start: 0.9124 (mtp) cc_final: 0.8921 (mtp)
REVERT: C  322 ASN cc_start: 0.7594 (m-40) cc_final: 0.7385 (m-40)
REVERT: D   54 HIS cc_start: 0.8671 (m90) cc_final: 0.8455 (m90)
REVERT: D  191 MET cc_start: 0.8912 (mmm) cc_final: 0.8638 (mtp)
REVERT: D  287 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8802 (m110)
  outliers start: 6
  outliers final: 1
  residues processed: 81
  average time/residue: 1.3353
  time to fit residues: 119.9785
Evaluate side-chains
  71 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 141 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 50 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.088303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.055712 restraints weight = 96539.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2599 rms_B_bonded: 3.37
r_work: 0.2359 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2411
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2411 r_free = 0.2411    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2411 r_free = 0.2411    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2411
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055  15766  Z= 0.314
  Angle     :  0.593   6.009  22369  Z= 0.325
  Chirality :  0.042   0.208   2591
  Planarity :  0.005   0.048   2007
  Dihedral  : 22.262 162.247   4641
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.62 %
    Favored  : 91.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.24), residues: 1258
  helix:  2.58 (0.18), residues: 804
  sheet: -0.73 (0.37), residues: 165
  loop : -0.52 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  46 
 HIS   0.005   0.001   HIS B 145 
 PHE   0.018   0.002   PHE C 112 
 TYR   0.024   0.002   TYR A  74 
 ARG   0.004   0.001   ARG B 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05398 (  902)
  hydrogen bonds       : angle       3.71571 ( 2441)
  covalent geometry    : bond        0.00721 (15766)
  covalent geometry    : angle       0.59289 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 1.593 
Fit side-chains
REVERT: C  322 ASN cc_start: 0.7794 (m-40) cc_final: 0.7576 (m-40)
REVERT: D  191 MET cc_start: 0.8954 (mmm) cc_final: 0.8699 (mtp)
REVERT: D  275 GLU cc_start: 0.8213 (pm20) cc_final: 0.7998 (pm20)
REVERT: D  287 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8783 (m110)
  outliers start: 7
  outliers final: 2
  residues processed: 66
  average time/residue: 1.4683
  time to fit residues: 107.8814
Evaluate side-chains
  66 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 119 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.091139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.058633 restraints weight = 88382.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.2689 rms_B_bonded: 3.27
r_work: 0.2457 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2464 r_free = 0.2464    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2464 r_free = 0.2464    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15766  Z= 0.131
  Angle     :  0.502   6.077  22369  Z= 0.280
  Chirality :  0.035   0.188   2591
  Planarity :  0.004   0.047   2007
  Dihedral  : 22.191 164.211   4641
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.02 %
    Favored  : 91.20 %
  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:  2.50 (0.24), residues: 1258
  helix:  2.78 (0.18), residues: 805
  sheet: -0.26 (0.40), residues: 147
  loop : -0.47 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  46 
 HIS   0.003   0.001   HIS D 256 
 PHE   0.010   0.001   PHE A 280 
 TYR   0.017   0.001   TYR A  74 
 ARG   0.006   0.000   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  902)
  hydrogen bonds       : angle       3.50293 ( 2441)
  covalent geometry    : bond        0.00286 (15766)
  covalent geometry    : angle       0.50222 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 1.206 
Fit side-chains
REVERT: C  322 ASN cc_start: 0.7755 (m-40) cc_final: 0.7554 (m-40)
REVERT: D  191 MET cc_start: 0.8914 (mmm) cc_final: 0.8661 (mtp)
REVERT: D  275 GLU cc_start: 0.8238 (pm20) cc_final: 0.8021 (pm20)
REVERT: D  287 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8857 (m110)
  outliers start: 7
  outliers final: 2
  residues processed: 74
  average time/residue: 1.4872
  time to fit residues: 120.8665
Evaluate side-chains
  72 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 137 optimal weight:    8.9990
   chunk 126 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9980
   chunk 140 optimal weight:    4.9990
   chunk 135 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 114 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.087501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.054769 restraints weight = 80738.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.2653 rms_B_bonded: 3.18
r_work: 0.2421 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2432 r_free = 0.2432    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2432 r_free = 0.2432    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  15766  Z= 0.303
  Angle     :  0.575   5.939  22369  Z= 0.315
  Chirality :  0.041   0.202   2591
  Planarity :  0.004   0.051   2007
  Dihedral  : 22.266 162.838   4641
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.11 %
    Favored  : 91.20 %
  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:  2.29 (0.24), residues: 1258
  helix:  2.62 (0.18), residues: 805
  sheet: -0.63 (0.38), residues: 163
  loop : -0.37 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  46 
 HIS   0.005   0.001   HIS B 145 
 PHE   0.017   0.002   PHE C 112 
 TYR   0.018   0.002   TYR A 264 
 ARG   0.004   0.001   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05198 (  902)
  hydrogen bonds       : angle       3.64717 ( 2441)
  covalent geometry    : bond        0.00692 (15766)
  covalent geometry    : angle       0.57498 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 1.356 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8939 (mmm) cc_final: 0.8733 (mtp)
  outliers start: 6
  outliers final: 2
  residues processed: 65
  average time/residue: 1.3861
  time to fit residues: 100.0418
Evaluate side-chains
  64 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 109 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 89 optimal weight:    0.7980
   chunk 132 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
C 322 ASN
D 287 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.089594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.056937 restraints weight = 85621.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.2654 rms_B_bonded: 3.21
r_work: 0.2421 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2473 r_free = 0.2473    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2473 r_free = 0.2473    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15766  Z= 0.162
  Angle     :  0.509   6.032  22369  Z= 0.282
  Chirality :  0.036   0.190   2591
  Planarity :  0.004   0.049   2007
  Dihedral  : 22.232 163.637   4641
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  7.72 %
    Favored  : 91.89 %
  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:  2.49 (0.24), residues: 1258
  helix:  2.76 (0.18), residues: 806
  sheet: -0.29 (0.40), residues: 147
  loop : -0.43 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  46 
 HIS   0.004   0.001   HIS D 256 
 PHE   0.010   0.002   PHE D 112 
 TYR   0.014   0.001   TYR A 307 
 ARG   0.005   0.000   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04374 (  902)
  hydrogen bonds       : angle       3.54597 ( 2441)
  covalent geometry    : bond        0.00363 (15766)
  covalent geometry    : angle       0.50937 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 1.444 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8930 (mmm) cc_final: 0.8700 (mtp)
  outliers start: 3
  outliers final: 2
  residues processed: 66
  average time/residue: 1.3934
  time to fit residues: 101.9513
Evaluate side-chains
  66 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 73 optimal weight:    0.1980
   chunk 120 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 114 optimal weight:    3.9990
   chunk 118 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.092630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.060148 restraints weight = 88809.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 3.28
r_work: 0.2494 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2508 r_free = 0.2508    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2508 r_free = 0.2508    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15766  Z= 0.120
  Angle     :  0.482   6.877  22369  Z= 0.267
  Chirality :  0.034   0.205   2591
  Planarity :  0.004   0.049   2007
  Dihedral  : 22.136 167.957   4641
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  7.92 %
    Favored  : 91.79 %
  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:  2.75 (0.24), residues: 1258
  helix:  2.95 (0.18), residues: 805
  sheet: -0.22 (0.40), residues: 149
  loop : -0.25 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  46 
 HIS   0.003   0.001   HIS D 256 
 PHE   0.010   0.001   PHE D 112 
 TYR   0.022   0.002   TYR A  74 
 ARG   0.005   0.000   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  902)
  hydrogen bonds       : angle       3.40278 ( 2441)
  covalent geometry    : bond        0.00258 (15766)
  covalent geometry    : angle       0.48164 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 1.304 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8909 (mmm) cc_final: 0.8652 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 73
  average time/residue: 1.4711
  time to fit residues: 118.9801
Evaluate side-chains
  67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 12 optimal weight:    0.4980
   chunk 79 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 26 optimal weight:    0.4980
   chunk 107 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 24 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.093642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.061271 restraints weight = 83942.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2748 rms_B_bonded: 3.22
r_work: 0.2520 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2520
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15766  Z= 0.117
  Angle     :  0.468   5.925  22369  Z= 0.259
  Chirality :  0.034   0.205   2591
  Planarity :  0.004   0.049   2007
  Dihedral  : 22.091 169.230   4641
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  8.11 %
    Favored  : 91.50 %
  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:  2.94 (0.24), residues: 1258
  helix:  3.07 (0.18), residues: 807
  sheet: -0.04 (0.41), residues: 149
  loop : -0.20 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  46 
 HIS   0.002   0.001   HIS D 256 
 PHE   0.010   0.001   PHE D 112 
 TYR   0.014   0.001   TYR A  74 
 ARG   0.005   0.000   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03625 (  902)
  hydrogen bonds       : angle       3.34976 ( 2441)
  covalent geometry    : bond        0.00250 (15766)
  covalent geometry    : angle       0.46759 (22369)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 2.150 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8917 (mmm) cc_final: 0.8699 (mtp)
  outliers start: 3
  outliers final: 1
  residues processed: 79
  average time/residue: 1.4924
  time to fit residues: 132.1877
Evaluate side-chains
  70 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 123 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0470
   chunk 71 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
D 287 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.093900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.061565 restraints weight = 82388.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 3.21
r_work: 0.2524 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2524
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2580 r_free = 0.2580    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2580 r_free = 0.2580    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  15766  Z= 0.115
  Angle     :  0.477   7.992  22369  Z= 0.260
  Chirality :  0.034   0.211   2591
  Planarity :  0.004   0.049   2007
  Dihedral  : 22.075 168.765   4641
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  8.60 %
    Favored  : 91.20 %
  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:  2.97 (0.24), residues: 1258
  helix:  3.09 (0.18), residues: 807
  sheet: -0.03 (0.40), residues: 149
  loop : -0.18 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  46 
 HIS   0.002   0.000   HIS B 256 
 PHE   0.011   0.001   PHE D 112 
 TYR   0.012   0.001   TYR C 307 
 ARG   0.005   0.000   ARG D 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  902)
  hydrogen bonds       : angle       3.32940 ( 2441)
  covalent geometry    : bond        0.00248 (15766)
  covalent geometry    : angle       0.47660 (22369)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9209.66 seconds
wall clock time: 160 minutes 41.19 seconds (9641.19 seconds total)