Starting phenix.real_space_refine
on Fri Jul  3 00:29:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gch_51230/07_2026/9gch_51230.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gch_51230/07_2026/9gch_51230.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gch_51230/07_2026/9gch_51230.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gch_51230/07_2026/9gch_51230.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gch_51230/07_2026/9gch_51230.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gch_51230/07_2026/9gch_51230.map"
  }
  resolution = 1.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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      70      5.49       5
     Mg      1      5.21       5
     S      48      5.16       5
     C    6828      2.51       5
     N    1971      2.21       5
     O    2313      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11231
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1848
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1848
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241}
    Chain: "C"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1848
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241}
    Chain: "D"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1848
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241}
    Chain: "F"
      Number of atoms: 2355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2355
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 1415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 1415
          Classifications: {'RNA': 67}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 23, 'rna3p_pyr': 27}
          Link IDs: {'rna2p': 16, 'rna3p': 50}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
    Chain: "T"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "T"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 2.27, per 1000 atoms: 0.20
  Number of scatterers: 11231
  At special positions: 0
  Unit cell: (103.644, 97.3417, 135.858, 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      70     15.00
     Mg      1     11.99
     O    2313      8.00
     N    1971      7.00
     C    6828      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 399.6 milliseconds
  

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2340

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 10 sheets defined
      54.1% alpha, 11.9% beta
      18 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 33
    Processing helix  chain 'A' and resid 46 through 55
      removed outlier: 3.560A  pdb=" N   GLN A  50 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 83
    Processing helix  chain 'A' and resid 110 through 122
    Processing helix  chain 'A' and resid 122 through 138
      removed outlier: 3.790A  pdb=" N   GLY A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 159
    Processing helix  chain 'A' and resid 165 through 187
      removed outlier: 4.547A  pdb=" N   LEU A 180 " --> pdb=" O   VAL A 176 " (cutoff:3.500A)
      Proline residue:  A 181  - end of helix
    Processing helix  chain 'A' and resid 203 through 208
    Processing helix  chain 'A' and resid 210 through 220
    Processing helix  chain 'A' and resid 229 through 243
    Processing helix  chain 'B' and resid 20 through 33
    Processing helix  chain 'B' and resid 46 through 55
      removed outlier: 3.526A  pdb=" N   GLN B  50 " --> pdb=" O   GLY B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 83
    Processing helix  chain 'B' and resid 110 through 122
    Processing helix  chain 'B' and resid 122 through 138
      removed outlier: 3.804A  pdb=" N   GLY B 134 " --> pdb=" O   ARG B 130 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLN B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 161
    Processing helix  chain 'B' and resid 165 through 187
      removed outlier: 4.501A  pdb=" N   LEU B 180 " --> pdb=" O   VAL B 176 " (cutoff:3.500A)
      Proline residue:  B 181  - end of helix
    Processing helix  chain 'B' and resid 203 through 208
    Processing helix  chain 'B' and resid 210 through 221
    Processing helix  chain 'B' and resid 229 through 243
    Processing helix  chain 'C' and resid 20 through 33
    Processing helix  chain 'C' and resid 46 through 55
    Processing helix  chain 'C' and resid 67 through 83
    Processing helix  chain 'C' and resid 110 through 122
    Processing helix  chain 'C' and resid 122 through 138
      removed outlier: 3.807A  pdb=" N   GLY C 134 " --> pdb=" O   ARG C 130 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN C 138 " --> pdb=" O   GLY C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 159
    Processing helix  chain 'C' and resid 165 through 187
      removed outlier: 4.558A  pdb=" N   LEU C 180 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
      Proline residue:  C 181  - end of helix
    Processing helix  chain 'C' and resid 203 through 208
    Processing helix  chain 'C' and resid 210 through 221
      removed outlier: 3.629A  pdb=" N   VAL C 221 " --> pdb=" O   LEU C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 243
      removed outlier: 3.510A  pdb=" N   TYR C 233 " --> pdb=" O   ASP C 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 33
    Processing helix  chain 'D' and resid 46 through 55
      removed outlier: 3.520A  pdb=" N   GLN D  50 " --> pdb=" O   GLY D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 83
    Processing helix  chain 'D' and resid 110 through 122
    Processing helix  chain 'D' and resid 122 through 138
      removed outlier: 3.853A  pdb=" N   GLY D 134 " --> pdb=" O   ARG D 130 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN D 138 " --> pdb=" O   GLY D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 159
    Processing helix  chain 'D' and resid 165 through 187
      removed outlier: 4.456A  pdb=" N   LEU D 180 " --> pdb=" O   VAL D 176 " (cutoff:3.500A)
      Proline residue:  D 181  - end of helix
    Processing helix  chain 'D' and resid 203 through 208
    Processing helix  chain 'D' and resid 210 through 221
    Processing helix  chain 'D' and resid 229 through 243
    Processing helix  chain 'F' and resid 93 through 104
      removed outlier: 4.113A  pdb=" N   GLU F  99 " --> pdb=" O   ARG F  95 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   MET F 100 " --> pdb=" O   GLU F  96 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   TRP F 101 " --> pdb=" O   PHE F  97 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU F 103 " --> pdb=" O   GLU F  99 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU F 104 " --> pdb=" O   MET F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 113 through 123
      removed outlier: 3.945A  pdb=" N   GLU F 122 " --> pdb=" O   LYS F 118 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   CYS F 123 " --> pdb=" O   THR F 119 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 125 through 164
      removed outlier: 3.502A  pdb=" N   ALA F 160 " --> pdb=" O   ALA F 156 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 182 through 202
      removed outlier: 3.556A  pdb=" N   GLN F 200 " --> pdb=" O   ALA F 196 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 211 through 215
    Processing helix  chain 'F' and resid 216 through 237
    Processing helix  chain 'F' and resid 252 through 263
    Processing helix  chain 'F' and resid 264 through 269
      removed outlier: 3.711A  pdb=" N   ASP F 267 " --> pdb=" O   GLU F 264 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 277 through 281
    Processing helix  chain 'F' and resid 283 through 285
      No H-bonds generated for 'chain 'F' and resid 283 through 285'
    Processing helix  chain 'F' and resid 320 through 329
      removed outlier: 3.546A  pdb=" N   LEU F 329 " --> pdb=" O   LYS F 325 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 337 through 341
    Processing helix  chain 'F' and resid 352 through 365
    Processing helix  chain 'F' and resid 368 through 373
    Processing helix  chain 'F' and resid 374 through 376
      No H-bonds generated for 'chain 'F' and resid 374 through 376'
    Processing helix  chain 'F' and resid 377 through 379
      No H-bonds generated for 'chain 'F' and resid 377 through 379'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62
      removed outlier: 6.605A  pdb=" N   ALA A  37 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   ALA A  61 " --> pdb=" O   ALA A  37 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   LEU A  39 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ALA A  88 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   THR A 153 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   ASN A  90 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 6.599A  pdb=" N   ALA B  37 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   ALA B  61 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   LEU B  39 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ALA B  88 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   THR B 153 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   ASN B  90 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102
    Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62
      removed outlier: 6.569A  pdb=" N   ALA C  37 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   ALA C  61 " --> pdb=" O   ALA C  37 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   LEU C  39 " --> pdb=" O   ALA C  61 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ALA C  88 " --> pdb=" O   ILE C 151 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   THR C 153 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   ASN C  90 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
    Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62
      removed outlier: 6.619A  pdb=" N   ALA D  37 " --> pdb=" O   VAL D  59 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ALA D  61 " --> pdb=" O   ALA D  37 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   LEU D  39 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ALA D  88 " --> pdb=" O   ILE D 151 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   THR D 153 " --> pdb=" O   ALA D  88 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   ASN D  90 " --> pdb=" O   THR D 153 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102
    Processing sheet with id=AA9, first strand: chain 'F' and resid 272 through 273
      removed outlier: 6.212A  pdb=" N   LEU F 205 " --> pdb=" O   TYR F 244 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   CYS F 246 " --> pdb=" O   LEU F 205 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   PHE F 207 " --> pdb=" O   CYS F 246 " (cutoff:3.500A)
      removed outlier: 8.585A  pdb=" N   ILE F 309 " --> pdb=" O   PRO F 204 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL F 206 " --> pdb=" O   ILE F 309 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   GLY F 310 " --> pdb=" O   LEU F 290 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ALA F 332 " --> pdb=" O   ILE F 287 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 342 through 344
      removed outlier: 4.474A  pdb=" N   GLY F 383 " --> pdb=" O   GLN F 343 " (cutoff:3.500A)

    531 hydrogen bonds defined for protein.
    1530 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      40 hydrogen bonds
      80 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3069
        1.34 -     1.46: 3182
        1.46 -     1.58: 5073
        1.58 -     1.71: 137
        1.71 -     1.83: 81
  Bond restraints: 11542
  Sorted by residual:
  bond pdb=" P     U T   2 "
       pdb=" OP2   U T   2 "
    ideal  model  delta    sigma   weight residual
    1.485  1.561 -0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" CG  HIS F 242 "
       pdb=" CD2 HIS F 242 "
    ideal  model  delta    sigma   weight residual
    1.354  1.322  0.032 1.10e-02 8.26e+03 8.35e+00
  bond pdb=" CE1 HIS F 242 "
       pdb=" NE2 HIS F 242 "
    ideal  model  delta    sigma   weight residual
    1.321  1.294  0.027 1.00e-02 1.00e+04 7.19e+00
  bond pdb=" C5' GTP T 101 "
       pdb=" O5' GTP T 101 "
    ideal  model  delta    sigma   weight residual
    1.410  1.463 -0.053 2.00e-02 2.50e+03 6.96e+00
  bond pdb=" O5'   U T  52 "
       pdb=" C5'   U T  52 "
    ideal  model  delta    sigma   weight residual
    1.420  1.454 -0.034 1.50e-02 4.44e+03 5.17e+00
  ... (remaining 11537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 15568
        2.21 -     4.42: 351
        4.42 -     6.64: 18
        6.64 -     8.85: 7
        8.85 -    11.06: 4
  Bond angle restraints: 15948
  Sorted by residual:
  angle pdb=" OG1 THR C 110 "
        pdb=" CB  THR C 110 "
        pdb=" CG2 THR C 110 "
      ideal   model   delta    sigma   weight residual
     109.30  101.30    8.00 2.00e+00 2.50e-01 1.60e+01
  angle pdb=" C4' GTP T 101 "
        pdb=" C3' GTP T 101 "
        pdb=" O3' GTP T 101 "
      ideal   model   delta    sigma   weight residual
     109.47   98.41   11.06 3.00e+00 1.11e-01 1.36e+01
  angle pdb=" O1B GTP T 101 "
        pdb=" PB  GTP T 101 "
        pdb=" O2B GTP T 101 "
      ideal   model   delta    sigma   weight residual
     109.50  120.13  -10.63 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" C2' GTP T 101 "
        pdb=" C3' GTP T 101 "
        pdb=" O3' GTP T 101 "
      ideal   model   delta    sigma   weight residual
     109.47  119.88  -10.41 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" OG1 THR A 110 "
        pdb=" CB  THR A 110 "
        pdb=" CG2 THR A 110 "
      ideal   model   delta    sigma   weight residual
     109.30  102.69    6.61 2.00e+00 2.50e-01 1.09e+01
  ... (remaining 15943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.70: 6783
       35.70 -    71.39: 209
       71.39 -   107.09: 38
      107.09 -   142.78: 1
      142.78 -   178.48: 3
  Dihedral angle restraints: 7034
    sinusoidal: 3374
      harmonic: 3660
  Sorted by residual:
  dihedral pdb=" O4'   C T  44 "
           pdb=" C1'   C T  44 "
           pdb=" N1    C T  44 "
           pdb=" C2    C T  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.52  178.48     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" C8  GTP T 101 "
           pdb=" C1' GTP T 101 "
           pdb=" N9  GTP T 101 "
           pdb=" O4' GTP T 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -63.20  167.79     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" C5' GTP T 101 "
           pdb=" O5' GTP T 101 "
           pdb=" PA  GTP T 101 "
           pdb=" O3A GTP T 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -137.17 -153.56     1      2.00e+01 2.50e-03 4.55e+01
  ... (remaining 7031 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1678
       0.104 -    0.207: 219
       0.207 -    0.311: 2
       0.311 -    0.415: 0
       0.415 -    0.518: 2
  Chirality restraints: 1901
  Sorted by residual:
  chirality pdb=" P     A T  19 "
            pdb=" OP1   A T  19 "
            pdb=" OP2   A T  19 "
            pdb=" O5'   A T  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.93   -0.52 2.00e-01 2.50e+01 6.72e+00
  chirality pdb=" P     U T   2 "
            pdb=" OP1   U T   2 "
            pdb=" OP2   U T   2 "
            pdb=" O5'   U T   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.86   -0.45 2.00e-01 2.50e+01 5.17e+00
  chirality pdb=" C3' GTP T 101 "
            pdb=" C2' GTP T 101 "
            pdb=" C4' GTP T 101 "
            pdb=" O3' GTP T 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.71    0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 1898 not shown)

  Planarity restraints: 1826
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 223 "   -0.045 2.00e-02 2.50e+03   3.02e-02 1.60e+01
        pdb=" CG  PHE C 223 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 223 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 223 "    0.038 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 223 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 223 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 223 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 223 "   -0.036 2.00e-02 2.50e+03   2.28e-02 9.08e+00
        pdb=" CG  PHE D 223 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 223 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 223 "    0.029 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 223 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 223 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 223 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 223 "    0.036 2.00e-02 2.50e+03   2.28e-02 9.07e+00
        pdb=" CG  PHE B 223 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 223 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 223 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 223 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 223 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 223 "    0.029 2.00e-02 2.50e+03
  ... (remaining 1823 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 65
        2.60 -     3.17: 9534
        3.17 -     3.75: 19294
        3.75 -     4.32: 27785
        4.32 -     4.90: 42544
  Nonbonded interactions: 99222
  Sorted by model distance:
  nonbonded pdb=" OP1   U T  11 "
            pdb="MG    MG T 102 "
     model   vdw
     2.021 2.170
  nonbonded pdb=" NE2 GLN A 115 "
            pdb=" OD1 ASP A 119 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" OH  TYR F 135 "
            pdb=" OP1   A T  42 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" NH2 ARG F 102 "
            pdb=" O   PRO F 109 "
     model   vdw
     2.403 3.120
  nonbonded pdb=" OE2 GLU A  68 "
            pdb=" NH2 ARG A 130 "
     model   vdw
     2.409 3.120
  ... (remaining 99217 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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=1.00 max=1.00 mean=1.00
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:             18.710
  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:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     10.410
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9189
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   0.076  11543  Z= 0.508
  Angle     :  0.906  11.062  15948  Z= 0.568
  Chirality :  0.067   0.518   1901
  Planarity :  0.007   0.067   1826
  Dihedral  : 17.051 178.479   4694
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.23), residues: 1292
  helix:  1.84 (0.21), residues: 630
  sheet: -0.16 (0.33), residues: 201
  loop :  0.51 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.003   ARG C 130 
 TYR   0.016   0.004   TYR F 262 
 PHE   0.045   0.007   PHE C 223 
 TRP   0.022   0.005   TRP F 183 
 HIS   0.012   0.003   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00791 /  0.50 (11542)
  covalent geometry    : angle       0.90617 /  0.57 (15948)
  hydrogen bonds       : bond        0.19401 / 13.58 (  571)
  hydrogen bonds       : angle       7.20900 /  5.34 ( 1610)
  Misc. bond           : bond        0.06063 /  3.19 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8423 (mptt)
REVERT: D  215 ASN cc_start: 0.6687 (t0) cc_final: 0.6485 (t0)
REVERT: F  149 LYS cc_start: 0.7240 (mttt) cc_final: 0.6947 (tmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.7438
  time to fit residues: 133.5512
Evaluate side-chains
  141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    0.0370
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.4980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.4858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  56 ASN
F 370 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.131133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.096778 restraints weight = 10135.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 0.77
r_work: 0.3081 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 2.09 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9109
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11543  Z= 0.161
  Angle     :  0.574   7.617  15948  Z= 0.307
  Chirality :  0.042   0.142   1901
  Planarity :  0.004   0.037   1826
  Dihedral  : 17.382 178.224   2415
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.35 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.23), residues: 1292
  helix:  2.31 (0.21), residues: 610
  sheet: -0.53 (0.32), residues: 193
  loop :  0.76 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 147 
 TYR   0.010   0.002   TYR F 137 
 PHE   0.017   0.002   PHE C 223 
 TRP   0.011   0.001   TRP F 183 
 HIS   0.006   0.001   HIS F 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.16 (11542)
  covalent geometry    : angle       0.57418 /  0.31 (15948)
  hydrogen bonds       : bond        0.06342 /  4.43 (  571)
  hydrogen bonds       : angle       5.48884 /  4.09 ( 1610)
  Misc. bond           : bond        0.00034 /  0.02 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 142
  time to evaluate  : 0.365 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 142
  average time/residue: 0.6626
  time to fit residues: 99.6147
Evaluate side-chains
  126 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  133 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 125 optimal weight:    0.0870
   chunk 68 optimal weight:    0.0980
   chunk 11 optimal weight:    0.0970
   chunk 106 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0060
   chunk 4 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.1972

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 220 GLN
C  56 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.133706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.099845 restraints weight = 10412.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 0.78
r_work: 0.3135 rms_B_bonded: 1.36 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 2.12 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9061
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11543  Z= 0.113
  Angle     :  0.500   7.349  15948  Z= 0.265
  Chirality :  0.040   0.136   1901
  Planarity :  0.004   0.032   1826
  Dihedral  : 17.287 179.300   2415
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.43 %
    Favored  : 91.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.24), residues: 1292
  helix:  2.44 (0.21), residues: 608
  sheet: -0.72 (0.31), residues: 213
  loop :  0.70 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 130 
 TYR   0.005   0.001   TYR D 233 
 PHE   0.014   0.002   PHE F  97 
 TRP   0.008   0.001   TRP F 183 
 HIS   0.003   0.001   HIS F 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.11 (11542)
  covalent geometry    : angle       0.49974 /  0.27 (15948)
  hydrogen bonds       : bond        0.04718 /  3.29 (  571)
  hydrogen bonds       : angle       5.04486 /  3.75 ( 1610)
  Misc. bond           : bond        0.00112 /  0.06 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 148
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8429 (mptt)
  outliers start: 7
  outliers final: 4
  residues processed: 151
  average time/residue: 0.6807
  time to fit residues: 108.6844
Evaluate side-chains
  136 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  133 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 15 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  56 ASN
** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.130472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.096055 restraints weight = 10315.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 0.78
r_work: 0.3068 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9119
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  11543  Z= 0.178
  Angle     :  0.582   6.744  15948  Z= 0.309
  Chirality :  0.042   0.198   1901
  Planarity :  0.005   0.055   1826
  Dihedral  : 17.258 177.339   2415
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.82 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.23), residues: 1292
  helix:  2.33 (0.21), residues: 609
  sheet: -0.72 (0.32), residues: 193
  loop :  0.59 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 130 
 TYR   0.011   0.002   TYR F 135 
 PHE   0.017   0.002   PHE C 223 
 TRP   0.010   0.001   TRP F 183 
 HIS   0.005   0.001   HIS C 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.18 (11542)
  covalent geometry    : angle       0.58218 /  0.31 (15948)
  hydrogen bonds       : bond        0.05765 /  4.02 (  571)
  hydrogen bonds       : angle       5.25902 /  3.92 ( 1610)
  Misc. bond           : bond        0.00076 /  0.04 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: F  152 MET cc_start: 0.6826 (ppp) cc_final: 0.5673 (pp-130)
REVERT: F  153 LYS cc_start: 0.5393 (ptmm) cc_final: 0.5146 (ptpp)
  outliers start: 10
  outliers final: 6
  residues processed: 132
  average time/residue: 0.6269
  time to fit residues: 87.8447
Evaluate side-chains
  128 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  133 LEU
Chi-restraints excluded: chain F residue  217 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0980
   chunk 65 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 220 GLN
C  56 ASN
** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.130892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.096664 restraints weight = 10287.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 0.77
r_work: 0.3079 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 2.12 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9112
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11543  Z= 0.161
  Angle     :  0.562   6.970  15948  Z= 0.299
  Chirality :  0.042   0.187   1901
  Planarity :  0.005   0.041   1826
  Dihedral  : 17.270 177.478   2415
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.82 %
    Favored  : 91.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.23), residues: 1292
  helix:  2.31 (0.21), residues: 609
  sheet: -0.81 (0.32), residues: 193
  loop :  0.57 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 106 
 TYR   0.012   0.002   TYR F 137 
 PHE   0.017   0.002   PHE B 223 
 TRP   0.009   0.001   TRP F 183 
 HIS   0.003   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.16 (11542)
  covalent geometry    : angle       0.56244 /  0.30 (15948)
  hydrogen bonds       : bond        0.05404 /  3.77 (  571)
  hydrogen bonds       : angle       5.19693 /  3.87 ( 1610)
  Misc. bond           : bond        0.00084 /  0.04 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.417 
Fit side-chains
REVERT: D   44 ASN cc_start: 0.7920 (p0) cc_final: 0.7711 (p0)
REVERT: F  152 MET cc_start: 0.6890 (ppp) cc_final: 0.5779 (pp-130)
REVERT: F  153 LYS cc_start: 0.5331 (ptmm) cc_final: 0.5101 (ptpp)
  outliers start: 12
  outliers final: 6
  residues processed: 141
  average time/residue: 0.6874
  time to fit residues: 102.6979
Evaluate side-chains
  133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  133 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 130 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.128918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.094816 restraints weight = 10288.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 0.78
r_work: 0.3051 rms_B_bonded: 1.33 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9135
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  11543  Z= 0.226
  Angle     :  0.637   6.996  15948  Z= 0.339
  Chirality :  0.045   0.274   1901
  Planarity :  0.006   0.066   1826
  Dihedral  : 17.319 176.451   2415
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.02 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.23), residues: 1292
  helix:  2.14 (0.21), residues: 604
  sheet: -0.79 (0.32), residues: 199
  loop :  0.56 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 130 
 TYR   0.013   0.002   TYR F 135 
 PHE   0.020   0.003   PHE B 223 
 TRP   0.010   0.002   TRP F 183 
 HIS   0.005   0.002   HIS F 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00487 /  0.23 (11542)
  covalent geometry    : angle       0.63652 /  0.34 (15948)
  hydrogen bonds       : bond        0.06201 /  4.32 (  571)
  hydrogen bonds       : angle       5.40887 /  4.04 ( 1610)
  Misc. bond           : bond        0.00089 /  0.05 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.333 
Fit side-chains
REVERT: D   44 ASN cc_start: 0.7948 (p0) cc_final: 0.7705 (p0)
REVERT: F  152 MET cc_start: 0.6822 (ppp) cc_final: 0.5739 (pp-130)
REVERT: F  217 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7748 (tpm-80)
  outliers start: 11
  outliers final: 7
  residues processed: 128
  average time/residue: 0.6560
  time to fit residues: 89.2994
Evaluate side-chains
  135 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  133 LEU
Chi-restraints excluded: chain F residue  217 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 66 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0670
   chunk 20 optimal weight:    0.0770
   chunk 95 optimal weight:    2.9990
   chunk 120 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 127 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0980
   chunk 53 optimal weight:    0.0570
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.1394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.133152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.099665 restraints weight = 10369.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 0.77
r_work: 0.3136 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9061
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11543  Z= 0.109
  Angle     :  0.510   7.331  15948  Z= 0.269
  Chirality :  0.040   0.135   1901
  Planarity :  0.004   0.033   1826
  Dihedral  : 17.249 178.740   2415
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.80 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.24), residues: 1292
  helix:  2.43 (0.21), residues: 609
  sheet: -0.90 (0.32), residues: 213
  loop :  0.69 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 147 
 TYR   0.009   0.001   TYR B 233 
 PHE   0.012   0.002   PHE F 179 
 TRP   0.007   0.001   TRP F 183 
 HIS   0.002   0.001   HIS F 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.11 (11542)
  covalent geometry    : angle       0.50977 /  0.27 (15948)
  hydrogen bonds       : bond        0.04307 /  3.00 (  571)
  hydrogen bonds       : angle       4.97105 /  3.69 ( 1610)
  Misc. bond           : bond        0.00084 /  0.04 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.344 
Fit side-chains
REVERT: D   44 ASN cc_start: 0.7820 (p0) cc_final: 0.7593 (p0)
REVERT: F  152 MET cc_start: 0.6827 (ppp) cc_final: 0.5722 (pp-130)
REVERT: F  153 LYS cc_start: 0.5367 (ptmm) cc_final: 0.5148 (ptpp)
  outliers start: 9
  outliers final: 3
  residues processed: 146
  average time/residue: 0.6577
  time to fit residues: 101.8910
Evaluate side-chains
  134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain D residue   16 THR
Chi-restraints excluded: chain F residue  133 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 133 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 98 optimal weight:    0.4980
   chunk 132 optimal weight:    6.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  56 ASN
C  56 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.129633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.095597 restraints weight = 10207.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 0.77
r_work: 0.3065 rms_B_bonded: 1.33 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 2.09 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9122
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  11543  Z= 0.193
  Angle     :  0.605   8.654  15948  Z= 0.320
  Chirality :  0.043   0.213   1901
  Planarity :  0.005   0.057   1826
  Dihedral  : 17.214 176.963   2415
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.48 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.23), residues: 1292
  helix:  2.31 (0.21), residues: 604
  sheet: -0.77 (0.32), residues: 193
  loop :  0.59 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 130 
 TYR   0.012   0.002   TYR F 135 
 PHE   0.018   0.002   PHE B 223 
 TRP   0.010   0.002   TRP F 183 
 HIS   0.004   0.001   HIS C 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.19 (11542)
  covalent geometry    : angle       0.60480 /  0.32 (15948)
  hydrogen bonds       : bond        0.05733 /  3.99 (  571)
  hydrogen bonds       : angle       5.26234 /  3.93 ( 1610)
  Misc. bond           : bond        0.00062 /  0.03 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.257 
Fit side-chains
REVERT: D   44 ASN cc_start: 0.7921 (p0) cc_final: 0.7644 (p0)
REVERT: F  152 MET cc_start: 0.6744 (ppp) cc_final: 0.6128 (ppp)
REVERT: F  153 LYS cc_start: 0.5258 (ptmm) cc_final: 0.5048 (ptpp)
REVERT: F  217 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7711 (tpm-80)
  outliers start: 7
  outliers final: 4
  residues processed: 130
  average time/residue: 0.6474
  time to fit residues: 89.4316
Evaluate side-chains
  129 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  133 LEU
Chi-restraints excluded: chain F residue  217 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 120 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0370
   chunk 117 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  56 ASN
C  56 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.096386 restraints weight = 10187.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 0.76
r_work: 0.3078 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 2.07 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9110
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11543  Z= 0.164
  Angle     :  0.578   9.173  15948  Z= 0.305
  Chirality :  0.042   0.188   1901
  Planarity :  0.005   0.042   1826
  Dihedral  : 17.227 177.273   2415
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 10.07 %
    Favored  : 89.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.23), residues: 1292
  helix:  2.29 (0.21), residues: 604
  sheet: -0.82 (0.32), residues: 193
  loop :  0.56 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 147 
 TYR   0.011   0.002   TYR F 135 
 PHE   0.017   0.002   PHE B 223 
 TRP   0.009   0.001   TRP F 183 
 HIS   0.004   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 (11542)
  covalent geometry    : angle       0.57835 /  0.31 (15948)
  hydrogen bonds       : bond        0.05374 /  3.75 (  571)
  hydrogen bonds       : angle       5.19982 /  3.87 ( 1610)
  Misc. bond           : bond        0.00067 /  0.04 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 0.248 
Fit side-chains
REVERT: D   44 ASN cc_start: 0.7878 (p0) cc_final: 0.7607 (p0)
REVERT: F  152 MET cc_start: 0.6758 (ppp) cc_final: 0.6126 (ppp)
REVERT: F  153 LYS cc_start: 0.5297 (ptmm) cc_final: 0.5093 (ptpp)
REVERT: F  217 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7722 (tpm-80)
  outliers start: 5
  outliers final: 5
  residues processed: 133
  average time/residue: 0.6636
  time to fit residues: 93.6764
Evaluate side-chains
  128 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  133 LEU
Chi-restraints excluded: chain F residue  217 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 106 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 133 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  56 ASN
C  56 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.130318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.096452 restraints weight = 10237.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 0.76
r_work: 0.3079 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 2.08 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9109
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11543  Z= 0.161
  Angle     :  0.576   8.448  15948  Z= 0.304
  Chirality :  0.042   0.186   1901
  Planarity :  0.005   0.042   1826
  Dihedral  : 17.215 177.416   2415
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.87 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.23), residues: 1292
  helix:  2.30 (0.21), residues: 604
  sheet: -0.81 (0.32), residues: 193
  loop :  0.54 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 147 
 TYR   0.011   0.002   TYR F 135 
 PHE   0.016   0.002   PHE B 223 
 TRP   0.009   0.001   TRP F 183 
 HIS   0.004   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 (11542)
  covalent geometry    : angle       0.57604 /  0.30 (15948)
  hydrogen bonds       : bond        0.05311 /  3.70 (  571)
  hydrogen bonds       : angle       5.18727 /  3.86 ( 1610)
  Misc. bond           : bond        0.00064 /  0.03 (    1)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.346 
Fit side-chains
REVERT: F  152 MET cc_start: 0.6757 (ppp) cc_final: 0.6147 (ppp)
REVERT: F  153 LYS cc_start: 0.5292 (ptmm) cc_final: 0.5089 (ptpp)
REVERT: F  217 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7752 (tpm-80)
  outliers start: 6
  outliers final: 4
  residues processed: 133
  average time/residue: 0.6347
  time to fit residues: 89.8182
Evaluate side-chains
  134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain F residue  119 THR
Chi-restraints excluded: chain F residue  133 LEU
Chi-restraints excluded: chain F residue  217 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 133 optimal weight:    7.9990
   chunk 92 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 101 optimal weight:    0.0370
   chunk 102 optimal weight:    0.5980
   chunk 111 optimal weight:    0.0770
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.4016

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  56 ASN
C  56 ASN
D  44 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.131248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.097400 restraints weight = 10352.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 0.77
r_work: 0.3096 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9094
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11543  Z= 0.136
  Angle     :  0.550   8.019  15948  Z= 0.289
  Chirality :  0.041   0.159   1901
  Planarity :  0.004   0.036   1826
  Dihedral  : 17.181 177.847   2415
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.87 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.23), residues: 1292
  helix:  2.37 (0.21), residues: 604
  sheet: -0.75 (0.32), residues: 203
  loop :  0.54 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 147 
 TYR   0.010   0.001   TYR F 135 
 PHE   0.014   0.002   PHE B 223 
 TRP   0.008   0.001   TRP F 183 
 HIS   0.003   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.14 (11542)
  covalent geometry    : angle       0.54982 /  0.29 (15948)
  hydrogen bonds       : bond        0.04906 /  3.42 (  571)
  hydrogen bonds       : angle       5.08980 /  3.78 ( 1610)
  Misc. bond           : bond        0.00062 /  0.03 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5661.03 seconds
wall clock time: 96 minutes 43.58 seconds (5803.58 seconds total)