Starting phenix.real_space_refine
on Wed Aug  5 18:19:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gch_51230/08_2026/9gch_51230.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gch_51230/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gch_51230/08_2026/9gch_51230.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gch_51230/08_2026/9gch_51230.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gch_51230/08_2026/9gch_51230.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gch_51230/08_2026/9gch_51230.cif"
  }
  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-2.2rc3-6140/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: 2.69, per 1000 atoms: 0.24
  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: 0.97
  Conformation dependent library (CDL) restraints added in 483.5 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: 1.25
  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: 1.92

  Time building geometry restraints manager: 1.28 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=" P     U T   2 "
       pdb=" O5'   U T   2 "
    ideal  model  delta    sigma   weight residual
    1.593  1.622 -0.029 1.00e-02 1.00e+04 8.61e+00
  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=" P     A T  19 "
       pdb=" O5'   A T  19 "
    ideal  model  delta    sigma   weight residual
    1.593  1.622 -0.029 1.00e-02 1.00e+04 8.23e+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
  ... (remaining 11537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 15579
        2.21 -     4.42: 340
        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=" O4'   A T  28 "
        pdb=" C1'   A T  28 "
        pdb=" N9    A T  28 "
      ideal   model   delta    sigma   weight residual
     108.20  111.01   -2.81 8.00e-01 1.56e+00 1.24e+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
  ... (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: 1702
       0.104 -    0.207: 195
       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:             14.110
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.200
  Find NCS groups from input model:        0.140
  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:             0.010
  Load rotamer database and sin/cos tables:6.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.760
-------------------------------------------------------------------------------
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= 0.514
  Angle     :  0.894  11.062  15948  Z= 0.563
  Chirality :  0.065   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        0.00790 /  0.51 (11542)
  covalent geometry    : angle       0.89440 /  0.56 (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  : 0.328 
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: 0.8026
  time to fit residues: 143.9604
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  : 0.367 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    4.9990
   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:    0.6180

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.130799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.096397 restraints weight = 10131.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 0.77
r_work: 0.3073 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9116
moved from start:          0.1029

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= 0.174
  Angle     :  0.596   7.524  15948  Z= 0.317
  Chirality :  0.043   0.161   1901
  Planarity :  0.005   0.045   1826
  Dihedral  : 17.289 177.664   2415
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.74 %
    Favored  : 92.77 %
  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:  1.81 (0.23), residues: 1292
  helix:  2.26 (0.21), residues: 610
  sheet: -0.56 (0.32), residues: 193
  loop :  0.75 (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   0.019   0.002   PHE C 223 
 TRP   0.012   0.002   TRP F 183 
 HIS   0.007   0.001   HIS F 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.17 (11542)
  covalent geometry    : angle       0.59565 /  0.32 (15948)
  hydrogen bonds       : bond        0.06311 /  4.40 (  571)
  hydrogen bonds       : angle       5.46845 /  4.08 ( 1610)
  Misc. bond           : bond        0.00001 /  0.00 (    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
  146 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 0.382 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 141
  average time/residue: 0.7310
  time to fit residues: 109.3762
Evaluate side-chains
  141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 GLU
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:    0.9990
   chunk 11 optimal weight:    0.2980
   chunk 106 optimal weight:    7.9990
   chunk 83 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0030
   chunk 4 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.3368

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.132529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.098481 restraints weight = 10332.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 0.77
r_work: 0.3109 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 2.13 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9086
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11543  Z= 0.127
  Angle     :  0.523   7.471  15948  Z= 0.278
  Chirality :  0.041   0.146   1901
  Planarity :  0.004   0.035   1826
  Dihedral  : 17.189 178.495   2415
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.62 %
    Favored  : 91.59 %
  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:  1.83 (0.23), residues: 1292
  helix:  2.43 (0.21), residues: 607
  sheet: -0.77 (0.31), residues: 213
  loop :  0.71 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 106 
 TYR   0.007   0.001   TYR F 135 
 PHE   0.013   0.002   PHE F  97 
 TRP   0.009   0.001   TRP F 183 
 HIS   0.004   0.001   HIS F 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.13 (11542)
  covalent geometry    : angle       0.52349 /  0.28 (15948)
  hydrogen bonds       : bond        0.05102 /  3.57 (  571)
  hydrogen bonds       : angle       5.11384 /  3.80 ( 1610)
  Misc. bond           : bond        0.00155 /  0.08 (    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
  158 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8438 (mptt)
REVERT: F  141 LYS cc_start: 0.7291 (tmmt) cc_final: 0.7087 (ttmm)
  outliers start: 8
  outliers final: 5
  residues processed: 153
  average time/residue: 0.7639
  time to fit residues: 123.4601
Evaluate side-chains
  135 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 80 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  56 ASN
F 221 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.129482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.095035 restraints weight = 10256.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 0.77
r_work: 0.3049 rms_B_bonded: 1.35 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:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  11543  Z= 0.227
  Angle     :  0.645   6.883  15948  Z= 0.342
  Chirality :  0.045   0.266   1901
  Planarity :  0.006   0.068   1826
  Dihedral  : 17.248 176.603   2415
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  7.72 %
    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:  1.61 (0.23), residues: 1292
  helix:  2.15 (0.21), residues: 610
  sheet: -0.72 (0.32), residues: 199
  loop :  0.61 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 130 
 TYR   0.014   0.002   TYR F 135 
 PHE   0.020   0.003   PHE B 223 
 TRP   0.011   0.002   TRP F 183 
 HIS   0.005   0.002   HIS C 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00490 /  0.23 (11542)
  covalent geometry    : angle       0.64466 /  0.34 (15948)
  hydrogen bonds       : bond        0.06332 /  4.42 (  571)
  hydrogen bonds       : angle       5.42497 /  4.05 ( 1610)
  Misc. bond           : bond        0.00072 /  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
  147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.272 
Fit side-chains
REVERT: F  152 MET cc_start: 0.6856 (ppp) cc_final: 0.5712 (pp-130)
REVERT: F  153 LYS cc_start: 0.6155 (mmmt) cc_final: 0.5766 (ptpp)
  outliers start: 14
  outliers final: 7
  residues processed: 138
  average time/residue: 0.7003
  time to fit residues: 102.5105
Evaluate side-chains
  136 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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  121 MET
Chi-restraints excluded: chain F residue  133 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 87 optimal weight:    0.2980
   chunk 112 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 103 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 65 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 220 GLN
C  56 ASN
F 221 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.131011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.096897 restraints weight = 10247.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 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: 2.11 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9110
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  11543  Z= 0.151
  Angle     :  0.566   7.092  15948  Z= 0.299
  Chirality :  0.042   0.189   1901
  Planarity :  0.004   0.036   1826
  Dihedral  : 17.227 177.560   2415
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.41 %
    Favored  : 90.62 %
  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:  2.27 (0.21), residues: 609
  sheet: -0.82 (0.32), residues: 193
  loop :  0.59 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 147 
 TYR   0.012   0.001   TYR F 137 
 PHE   0.016   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        0.00320 /  0.15 (11542)
  covalent geometry    : angle       0.56565 /  0.30 (15948)
  hydrogen bonds       : bond        0.05363 /  3.74 (  571)
  hydrogen bonds       : angle       5.21433 /  3.89 ( 1610)
  Misc. bond           : bond        0.00097 /  0.05 (    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
  147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.385 
Fit side-chains
REVERT: F  152 MET cc_start: 0.6882 (ppp) cc_final: 0.5836 (pp-130)
REVERT: F  153 LYS cc_start: 0.6154 (mmmt) cc_final: 0.5774 (ptpp)
  outliers start: 10
  outliers final: 5
  residues processed: 141
  average time/residue: 0.7129
  time to fit residues: 106.7774
Evaluate side-chains
  139 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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  133 LEU
Chi-restraints excluded: chain F residue  330 ASN
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:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 130 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  56 ASN
F 221 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.128847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.094805 restraints weight = 10293.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 0.76
r_work: 0.3050 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 2.09 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9135
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  11543  Z= 0.225
  Angle     :  0.646   7.948  15948  Z= 0.342
  Chirality :  0.045   0.289   1901
  Planarity :  0.006   0.065   1826
  Dihedral  : 17.261 176.632   2415
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  8.60 %
    Favored  : 90.22 %
  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:  1.51 (0.23), residues: 1292
  helix:  2.10 (0.21), residues: 604
  sheet: -0.78 (0.32), residues: 199
  loop :  0.55 (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   0.011   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       0.64559 /  0.34 (15948)
  hydrogen bonds       : bond        0.06212 /  4.34 (  571)
  hydrogen bonds       : angle       5.41284 /  4.04 ( 1610)
  Misc. bond           : bond        0.00093 /  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
  147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.366 
Fit side-chains
REVERT: F  152 MET cc_start: 0.6798 (ppp) cc_final: 0.5761 (pp-130)
REVERT: F  153 LYS cc_start: 0.6153 (mmmt) cc_final: 0.5753 (ptpp)
  outliers start: 12
  outliers final: 6
  residues processed: 140
  average time/residue: 0.6824
  time to fit residues: 101.4290
Evaluate side-chains
  145 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0270
   chunk 20 optimal weight:    0.0270
   chunk 95 optimal weight:    0.8980
   chunk 120 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 127 optimal weight:    0.5980
   chunk 88 optimal weight:    0.5980
   chunk 53 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.2496

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.132122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.098424 restraints weight = 10295.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 0.76
r_work: 0.3112 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9081
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      :  0.003   0.039  11543  Z= 0.120
  Angle     :  0.530   8.836  15948  Z= 0.279
  Chirality :  0.041   0.143   1901
  Planarity :  0.004   0.034   1826
  Dihedral  : 17.200 178.243   2415
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.38 %
    Favored  : 89.74 %
  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 (0.24), residues: 1292
  helix:  2.36 (0.21), residues: 609
  sheet: -0.88 (0.31), residues: 213
  loop :  0.69 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 147 
 TYR   0.009   0.001   TYR F 135 
 PHE   0.012   0.002   PHE F 179 
 TRP   0.008   0.001   TRP F 183 
 HIS   0.002   0.001   HIS F 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 (11542)
  covalent geometry    : angle       0.52965 /  0.28 (15948)
  hydrogen bonds       : bond        0.04662 /  3.25 (  571)
  hydrogen bonds       : angle       5.04763 /  3.75 ( 1610)
  Misc. bond           : bond        0.00089 /  0.05 (    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
  158 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.339 
Fit side-chains
REVERT: F  152 MET cc_start: 0.6813 (ppp) cc_final: 0.6121 (ppp)
REVERT: F  153 LYS cc_start: 0.6116 (mmmt) cc_final: 0.5887 (ptpp)
  outliers start: 9
  outliers final: 5
  residues processed: 156
  average time/residue: 0.6735
  time to fit residues: 111.3437
Evaluate side-chains
  139 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  212 LYS
Chi-restraints excluded: chain D residue   16 THR
Chi-restraints excluded: chain F residue  100 MET
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:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 133 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 132 optimal weight:    7.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  56 ASN
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 = 0.3675 r_free = 0.3675 target = 0.129271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.095214 restraints weight = 10192.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 0.76
r_work: 0.3057 rms_B_bonded: 1.33 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 2.09 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9127
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  11543  Z= 0.208
  Angle     :  0.628   8.258  15948  Z= 0.331
  Chirality :  0.044   0.248   1901
  Planarity :  0.005   0.061   1826
  Dihedral  : 17.206 176.939   2415
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.97 %
    Favored  : 89.15 %
  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:  1.62 (0.23), residues: 1292
  helix:  2.23 (0.21), residues: 604
  sheet: -0.78 (0.32), residues: 193
  loop :  0.55 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 147 
 TYR   0.012   0.002   TYR F 135 
 PHE   0.019   0.003   PHE B 223 
 TRP   0.010   0.002   TRP F 183 
 HIS   0.004   0.002   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.21 (11542)
  covalent geometry    : angle       0.62804 /  0.33 (15948)
  hydrogen bonds       : bond        0.05938 /  4.15 (  571)
  hydrogen bonds       : angle       5.32694 /  3.97 ( 1610)
  Misc. bond           : bond        0.00075 /  0.04 (    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
  139 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.305 
Fit side-chains
REVERT: F  152 MET cc_start: 0.6796 (ppp) cc_final: 0.6101 (ppp)
REVERT: F  153 LYS cc_start: 0.6115 (mmmt) cc_final: 0.5836 (ptpp)
  outliers start: 9
  outliers final: 6
  residues processed: 135
  average time/residue: 0.6300
  time to fit residues: 90.4460
Evaluate side-chains
  137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 104 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 120 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 117 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  56 ASN
C  56 ASN
F 221 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.129681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.095867 restraints weight = 10173.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 0.75
r_work: 0.3068 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 2.07 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9119
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  11543  Z= 0.181
  Angle     :  0.632  20.725  15948  Z= 0.324
  Chirality :  0.043   0.225   1901
  Planarity :  0.005   0.047   1826
  Dihedral  : 17.225 177.187   2415
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  9.97 %
    Favored  : 89.25 %
  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:  1.60 (0.23), residues: 1292
  helix:  2.22 (0.21), residues: 604
  sheet: -0.82 (0.32), residues: 193
  loop :  0.54 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 147 
 TYR   0.012   0.002   TYR F 135 
 PHE   0.018   0.002   PHE B 223 
 TRP   0.009   0.001   TRP F 183 
 HIS   0.004   0.001   HIS F 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.18 (11542)
  covalent geometry    : angle       0.63218 /  0.32 (15948)
  hydrogen bonds       : bond        0.05652 /  3.95 (  571)
  hydrogen bonds       : angle       5.27097 /  3.93 ( 1610)
  Misc. bond           : bond        0.00082 /  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
  146 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 138
  time to evaluate  : 0.304 
Fit side-chains
REVERT: F  152 MET cc_start: 0.6768 (ppp) cc_final: 0.6065 (ppp)
REVERT: F  153 LYS cc_start: 0.6036 (mmmt) cc_final: 0.5787 (ptpp)
  outliers start: 8
  outliers final: 6
  residues processed: 142
  average time/residue: 0.6950
  time to fit residues: 104.4844
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  : 0.374 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 133 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0060
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   overall best weight:    0.5998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  56 ASN
C  56 ASN
F 221 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.096379 restraints weight = 10230.115|
|-----------------------------------------------------------------------------|
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: 0.2992 rms_B_bonded: 2.07 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9111
moved from start:          0.1473

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= 0.163
  Angle     :  0.610  18.056  15948  Z= 0.315
  Chirality :  0.043   0.201   1901
  Planarity :  0.005   0.040   1826
  Dihedral  : 17.175 177.521   2415
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.87 %
    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:  1.62 (0.23), residues: 1292
  helix:  2.24 (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   0.005   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   0.003   0.001   HIS F 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.16 (11542)
  covalent geometry    : angle       0.61042 /  0.31 (15948)
  hydrogen bonds       : bond        0.05398 /  3.77 (  571)
  hydrogen bonds       : angle       5.21774 /  3.88 ( 1610)
  Misc. bond           : bond        0.00080 /  0.04 (    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
  144 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 0.462 
Fit side-chains
REVERT: F  152 MET cc_start: 0.6762 (ppp) cc_final: 0.6043 (ppp)
REVERT: F  153 LYS cc_start: 0.6075 (mmmt) cc_final: 0.5842 (ptpp)
  outliers start: 7
  outliers final: 6
  residues processed: 141
  average time/residue: 0.6628
  time to fit residues: 99.3322
Evaluate side-chains
  140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 134
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 133 optimal weight:    9.9990
   chunk 92 optimal weight:    0.8980
   chunk 105 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 101 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9980
   chunk 111 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  56 ASN
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 = 0.3686 r_free = 0.3686 target = 0.130057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.096168 restraints weight = 10300.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 0.76
r_work: 0.3073 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 2.08 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9112
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11543  Z= 0.167
  Angle     :  0.613  16.459  15948  Z= 0.318
  Chirality :  0.043   0.207   1901
  Planarity :  0.005   0.046   1826
  Dihedral  : 17.088 177.390   2415
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  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:  1.60 (0.23), residues: 1292
  helix:  2.22 (0.21), residues: 604
  sheet: -0.80 (0.32), residues: 193
  loop :  0.53 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   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   0.003   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.17 (11542)
  covalent geometry    : angle       0.61348 /  0.32 (15948)
  hydrogen bonds       : bond        0.05481 /  3.83 (  571)
  hydrogen bonds       : angle       5.23115 /  3.89 ( 1610)
  Misc. bond           : bond        0.00070 /  0.04 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6052.16 seconds
wall clock time: 103 minutes 17.83 seconds (6197.83 seconds total)