Starting phenix.real_space_refine
on Thu Jul  2 09:40:16 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7f4i_31453/07_2026/7f4i_31453.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f4i_31453/07_2026/7f4i_31453.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f4i_31453/07_2026/7f4i_31453.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f4i_31453/07_2026/7f4i_31453.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f4i_31453/07_2026/7f4i_31453.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f4i_31453/07_2026/7f4i_31453.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7f4i_31453/07_2026/7f4i_31453.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7f4i_31453/07_2026/7f4i_31453.cif"
  }
  resolution = 3.1
  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=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      55      5.16       5
     C    5099      2.51       5
     N    1407      2.21       5
     O    1469      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  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: 8031
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "G"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 427
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "A"
      Number of atoms: 1936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1936
          Classifications: {'peptide': 234}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 963
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2577
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 38
    Chain: "R"
      Number of atoms: 2053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2053
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 259}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "U"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 74
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'NLE:plan-1': 1, 'ASP:plan': 1, '4J2:plan-2': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.38, per 1000 atoms: 0.17
  Number of scatterers: 8031
  At special positions: 0
  Unit cell: (85.68, 128.52, 93.177, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      55     16.00
     O    1469      8.00
     N    1407      7.00
     C    5099      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 267 " - pdb=" SG  CYS R 273 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 325.6 milliseconds
  

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  4J2 U   4 "
  Number of C-beta restraints generated:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      43.8% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'G' and resid 11 through 24
      removed outlier: 3.804A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.572A  pdb=" N   LYS A  17 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 60 through 64
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.605A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 279
      removed outlier: 4.403A  pdb=" N   GLN A 267 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.373A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.767A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.961A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'R' and resid 43 through 65
    Processing helix  chain 'R' and resid 66 through 70
    Processing helix  chain 'R' and resid 71 through 102
    Processing helix  chain 'R' and resid 109 through 147
      removed outlier: 4.407A  pdb=" N   GLN R 115 " --> pdb=" O   ALA R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 156
    Processing helix  chain 'R' and resid 157 through 182
    Processing helix  chain 'R' and resid 185 through 226
      removed outlier: 4.071A  pdb=" N   LEU R 189 " --> pdb=" O   HIS R 185 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 270 through 272
      No H-bonds generated for 'chain 'R' and resid 270 through 272'
    Processing helix  chain 'R' and resid 273 through 278
    Processing helix  chain 'R' and resid 279 through 299
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 302 through 311
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.316A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.624A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.800A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.643A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AA3, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.937A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.678A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.572A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.061A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.580A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.742A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.684A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.618A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 0.69 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: 2507
        1.34 -     1.47: 2037
        1.47 -     1.60: 3568
        1.60 -     1.73: 0
        1.73 -     1.86: 75
  Bond restraints: 8187
  Sorted by residual:
  bond pdb=" C   4J2 U   4 "
       pdb=" N   ARG U   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.455 -0.126 1.40e-02 5.10e+03 8.13e+01
  bond pdb=" CA  ASN B 340 "
       pdb=" C   ASN B 340 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 1.23e-02 6.61e+03 1.04e+01
  bond pdb=" CE2 4J2 U   4 "
       pdb=" CZ1 4J2 U   4 "
    ideal  model  delta    sigma   weight residual
    1.419  1.364  0.055 2.00e-02 2.50e+03 7.69e+00
  bond pdb=" CA  4J2 U   4 "
       pdb=" C   4J2 U   4 "
    ideal  model  delta    sigma   weight residual
    1.525  1.476  0.049 2.10e-02 2.27e+03 5.53e+00
  bond pdb=" CA  SER B 343 "
       pdb=" CB  SER B 343 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.042 2.00e-02 2.50e+03 4.46e+00
  ... (remaining 8182 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.36: 11084
        7.36 -    14.72: 4
       14.72 -    22.08: 1
       22.08 -    29.45: 1
       29.45 -    36.81: 2
  Bond angle restraints: 11092
  Sorted by residual:
  angle pdb=" O   4J2 U   4 "
        pdb=" C   4J2 U   4 "
        pdb=" N   ARG U   5 "
      ideal   model   delta    sigma   weight residual
     123.00   86.19   36.81 1.60e+00 3.91e-01 5.29e+02
  angle pdb=" CA  4J2 U   4 "
        pdb=" C   4J2 U   4 "
        pdb=" N   ARG U   5 "
      ideal   model   delta    sigma   weight residual
     116.20  148.84  -32.64 2.00e+00 2.50e-01 2.66e+02
  angle pdb=" C   4J2 U   4 "
        pdb=" N   ARG U   5 "
        pdb=" CA  ARG U   5 "
      ideal   model   delta    sigma   weight residual
     121.70  144.60  -22.90 1.80e+00 3.09e-01 1.62e+02
  angle pdb=" C   HIS U   3 "
        pdb=" N   4J2 U   4 "
        pdb=" CA  4J2 U   4 "
      ideal   model   delta    sigma   weight residual
     121.70  103.47   18.23 1.80e+00 3.09e-01 1.03e+02
  angle pdb=" O   ASN B 340 "
        pdb=" C   ASN B 340 "
        pdb=" N   GLY B 341 "
      ideal   model   delta    sigma   weight residual
     123.25  117.60    5.65 1.14e+00 7.69e-01 2.46e+01
  ... (remaining 11087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 4554
       17.65 -    35.30: 272
       35.30 -    52.95: 36
       52.95 -    70.60: 5
       70.60 -    88.25: 6
  Dihedral angle restraints: 4873
    sinusoidal: 1878
      harmonic: 2995
  Sorted by residual:
  dihedral pdb=" CA  ILE R  40 "
           pdb=" C   ILE R  40 "
           pdb=" N   SER R  41 "
           pdb=" CA  SER R  41 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.05  -27.95     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  GLY B  53 "
           pdb=" C   GLY B  53 "
           pdb=" N   HIS B  54 "
           pdb=" CA  HIS B  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.53   27.47     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  ASP B 195 "
           pdb=" C   ASP B 195 "
           pdb=" N   THR B 196 "
           pdb=" CA  THR B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.92  -27.08     0      5.00e+00 4.00e-02 2.93e+01
  ... (remaining 4870 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 757
       0.049 -    0.098: 385
       0.098 -    0.147: 112
       0.147 -    0.196: 20
       0.196 -    0.245: 1
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  ARG U   5 "
            pdb=" N   ARG U   5 "
            pdb=" C   ARG U   5 "
            pdb=" CB  ARG U   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  ASP N 109 "
            pdb=" N   ASP N 109 "
            pdb=" C   ASP N 109 "
            pdb=" CB  ASP N 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.76e-01
  chirality pdb=" CB  ILE R 144 "
            pdb=" CA  ILE R 144 "
            pdb=" CG1 ILE R 144 "
            pdb=" CG2 ILE R 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.40e-01
  ... (remaining 1272 not shown)

  Planarity restraints: 1406
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 340 "   -0.043 2.00e-02 2.50e+03   8.29e-02 6.87e+01
        pdb=" C   ASN B 340 "    0.143 2.00e-02 2.50e+03
        pdb=" O   ASN B 340 "   -0.053 2.00e-02 2.50e+03
        pdb=" N   GLY B 341 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  4J2 U   4 "    0.045 2.00e-02 2.50e+03   6.37e-02 4.06e+01
        pdb=" C   4J2 U   4 "   -0.110 2.00e-02 2.50e+03
        pdb=" O   4J2 U   4 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ARG U   5 "    0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS U   3 "   -0.030 2.00e-02 2.50e+03   5.70e-02 3.25e+01
        pdb=" C   HIS U   3 "    0.099 2.00e-02 2.50e+03
        pdb=" O   HIS U   3 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   4J2 U   4 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 1403 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 333
        2.72 -     3.26: 8217
        3.26 -     3.81: 12867
        3.81 -     4.35: 16759
        4.35 -     4.90: 28254
  Nonbonded interactions: 66430
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OD1 ASN N  84 "
            pdb=" OG  SER N  85 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" NH2 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.360 3.120
  nonbonded pdb=" OG  SER B 227 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" OE2 GLU R  94 "
            pdb="CA    CA R 501 "
     model   vdw
     2.389 2.510
  ... (remaining 66425 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.520
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.680
  Find NCS groups from input model:        0.020
  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:0.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
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      :  0.009   0.126   8188  Z= 0.500
  Angle     :  1.215  36.806  11094  Z= 0.711
  Chirality :  0.060   0.245   1275
  Planarity :  0.011   0.147   1406
  Dihedral  : 11.957  88.253   2930
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.25), residues: 1010
  helix: -0.05 (0.23), residues: 403
  sheet:  0.59 (0.36), residues: 211
  loop : -0.80 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.057   0.006   ARG A 385 
 TYR   0.038   0.006   TYR B 111 
 PHE   0.028   0.005   PHE R  76 
 TRP   0.065   0.009   TRP B  63 
 HIS   0.018   0.005   HIS G  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00916 /  0.50 ( 8187)
  covalent geometry    : angle       1.21463 /  0.71 (11092)
  SS BOND              : bond        0.00384 /  0.20 (    1)
  SS BOND              : angle       0.21076 /  0.12 (    2)
  hydrogen bonds       : bond        0.15064 / 10.24 (  438)
  hydrogen bonds       : angle       6.62921 /  4.59 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9240 (tp30) cc_final: 0.9038 (tp30)
REVERT: G   21 MET cc_start: 0.9286 (mmm) cc_final: 0.8997 (mtp)
REVERT: G   38 MET cc_start: 0.9111 (ptt) cc_final: 0.8884 (ptp)
REVERT: G   48 ASP cc_start: 0.8694 (t0) cc_final: 0.8479 (t0)
REVERT: A   25 MET cc_start: 0.7593 (tmm) cc_final: 0.7387 (tmm)
REVERT: A  271 ASN cc_start: 0.9029 (m-40) cc_final: 0.8785 (m110)
REVERT: A  330 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8799 (mp0)
REVERT: N   18 LEU cc_start: 0.8431 (mt) cc_final: 0.7957 (mp)
REVERT: N   46 GLU cc_start: 0.8071 (pt0) cc_final: 0.7626 (pt0)
REVERT: N   99 CYS cc_start: 0.8432 (m) cc_final: 0.8101 (m)
REVERT: N  124 VAL cc_start: 0.9271 (t) cc_final: 0.8802 (t)
REVERT: B   10 GLU cc_start: 0.9498 (tt0) cc_final: 0.9123 (tp30)
REVERT: B   15 LYS cc_start: 0.9571 (ttmt) cc_final: 0.9332 (tptp)
REVERT: B   43 ILE cc_start: 0.9256 (mm) cc_final: 0.9024 (mt)
REVERT: B  156 GLN cc_start: 0.8613 (mt0) cc_final: 0.8386 (mt0)
REVERT: B  175 GLN cc_start: 0.8388 (pt0) cc_final: 0.8115 (pt0)
REVERT: B  209 LYS cc_start: 0.8686 (mttt) cc_final: 0.8164 (mtmt)
REVERT: B  280 LYS cc_start: 0.9311 (ttmm) cc_final: 0.8904 (ttmt)
REVERT: B  337 LYS cc_start: 0.8356 (mttt) cc_final: 0.8092 (mttt)
REVERT: R  290 ASN cc_start: 0.8101 (t0) cc_final: 0.7788 (t0)
REVERT: R  294 ASP cc_start: 0.8734 (m-30) cc_final: 0.8389 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0936
  time to fit residues: 25.0141
Evaluate side-chains
  138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 HIS
N   3 GLN
N 120 GLN
B 259 GLN
R  70 HIS
R 219 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.083905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.062007 restraints weight = 20391.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 3.58
r_work: 0.2862 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8188  Z= 0.136
  Angle     :  0.621   8.011  11094  Z= 0.330
  Chirality :  0.043   0.194   1275
  Planarity :  0.004   0.062   1406
  Dihedral  :  5.124  22.066   1122
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.44 %
    Favored  : 91.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.27), residues: 1010
  helix:  1.83 (0.26), residues: 406
  sheet:  0.27 (0.34), residues: 224
  loop :  0.03 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  38 
 TYR   0.013   0.001   TYR B 105 
 PHE   0.022   0.002   PHE G  61 
 TRP   0.024   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 ( 8187)
  covalent geometry    : angle       0.62124 /  0.33 (11092)
  SS BOND              : bond        0.00027 /  0.01 (    1)
  SS BOND              : angle       1.06436 /  0.57 (    2)
  hydrogen bonds       : bond        0.04306 /  2.87 (  438)
  hydrogen bonds       : angle       4.60278 /  3.21 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8840 (mtm110)
REVERT: G   18 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8783 (tp40)
REVERT: G   21 MET cc_start: 0.9322 (mmm) cc_final: 0.9066 (mmm)
REVERT: G   32 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9028 (mmmm)
REVERT: G   47 GLU cc_start: 0.8698 (mp0) cc_final: 0.8158 (mp0)
REVERT: G   48 ASP cc_start: 0.8785 (t0) cc_final: 0.8459 (t0)
REVERT: A  271 ASN cc_start: 0.9222 (m-40) cc_final: 0.8953 (m110)
REVERT: A  330 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8897 (mp0)
REVERT: N   18 LEU cc_start: 0.8058 (mt) cc_final: 0.7801 (mp)
REVERT: N   34 MET cc_start: 0.8532 (mtp) cc_final: 0.8212 (mtp)
REVERT: N   73 ASP cc_start: 0.7922 (t0) cc_final: 0.7616 (t0)
REVERT: N   76 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9141 (ptmm)
REVERT: N   93 VAL cc_start: 0.9149 (t) cc_final: 0.8765 (p)
REVERT: N  107 CYS cc_start: 0.8787 (m) cc_final: 0.8549 (m)
REVERT: B   38 ASP cc_start: 0.9104 (t0) cc_final: 0.8727 (p0)
REVERT: B  172 GLU cc_start: 0.9193 (pt0) cc_final: 0.8974 (pp20)
REVERT: B  209 LYS cc_start: 0.8565 (mttt) cc_final: 0.8163 (mttp)
REVERT: B  254 ASP cc_start: 0.8808 (t70) cc_final: 0.8422 (t0)
REVERT: B  280 LYS cc_start: 0.9278 (ttmm) cc_final: 0.8689 (ttmt)
REVERT: R   83 SER cc_start: 0.9066 (m) cc_final: 0.8815 (t)
REVERT: U    7 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7252 (mtpt)
  outliers start: 10
  outliers final: 4
  residues processed: 160
  average time/residue: 0.1010
  time to fit residues: 20.7987
Evaluate side-chains
  139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain R residue  289 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 32 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0020
   chunk 89 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 35 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.8994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N   1 GLN
R  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.079921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.058421 restraints weight = 21016.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.37
r_work: 0.2811 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8188  Z= 0.156
  Angle     :  0.584   6.608  11094  Z= 0.306
  Chirality :  0.042   0.134   1275
  Planarity :  0.004   0.030   1406
  Dihedral  :  4.712  20.196   1122
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  8.84 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.27), residues: 1010
  helix:  2.09 (0.26), residues: 409
  sheet:  0.36 (0.35), residues: 200
  loop :  0.09 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 223 
 TYR   0.010   0.001   TYR R  74 
 PHE   0.018   0.001   PHE G  61 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.16 ( 8187)
  covalent geometry    : angle       0.58418 /  0.31 (11092)
  SS BOND              : bond        0.00077 /  0.04 (    1)
  SS BOND              : angle       0.71600 /  0.40 (    2)
  hydrogen bonds       : bond        0.04017 /  2.65 (  438)
  hydrogen bonds       : angle       4.30463 /  2.98 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8842 (mm-30)
REVERT: G   20 LYS cc_start: 0.9436 (ptmm) cc_final: 0.9065 (pttp)
REVERT: G   21 MET cc_start: 0.9337 (mmm) cc_final: 0.9093 (mmm)
REVERT: G   32 LYS cc_start: 0.9376 (mmmm) cc_final: 0.9140 (mmmm)
REVERT: G   46 LYS cc_start: 0.9448 (ptpp) cc_final: 0.9199 (ptpp)
REVERT: G   48 ASP cc_start: 0.8916 (t0) cc_final: 0.8657 (t0)
REVERT: A  271 ASN cc_start: 0.9274 (m-40) cc_final: 0.9001 (m110)
REVERT: A  317 ARG cc_start: 0.8637 (mpp80) cc_final: 0.8334 (mpp80)
REVERT: A  330 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8884 (mp0)
REVERT: N   18 LEU cc_start: 0.8206 (mt) cc_final: 0.7956 (mp)
REVERT: N   33 LYS cc_start: 0.8942 (tttt) cc_final: 0.8356 (tttm)
REVERT: N   34 MET cc_start: 0.8588 (mtp) cc_final: 0.8195 (mtp)
REVERT: N   73 ASP cc_start: 0.8424 (t0) cc_final: 0.8081 (t0)
REVERT: N   83 MET cc_start: 0.8987 (mtm) cc_final: 0.8701 (ptp)
REVERT: N   93 VAL cc_start: 0.9306 (t) cc_final: 0.8844 (p)
REVERT: N  107 CYS cc_start: 0.8849 (m) cc_final: 0.8600 (m)
REVERT: N  120 GLN cc_start: 0.8966 (mm110) cc_final: 0.8260 (mm-40)
REVERT: B    8 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8501 (mtt-85)
REVERT: B   15 LYS cc_start: 0.9528 (ttmt) cc_final: 0.9301 (tptp)
REVERT: B   23 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8890 (mttp)
REVERT: B   38 ASP cc_start: 0.9165 (t0) cc_final: 0.8865 (p0)
REVERT: B  209 LYS cc_start: 0.8873 (mttt) cc_final: 0.8463 (mttp)
REVERT: B  217 MET cc_start: 0.8643 (ppp) cc_final: 0.8260 (ppp)
REVERT: B  254 ASP cc_start: 0.8906 (t70) cc_final: 0.8534 (t0)
REVERT: B  280 LYS cc_start: 0.9337 (ttmm) cc_final: 0.8953 (ttmm)
REVERT: R  262 THR cc_start: 0.9371 (m) cc_final: 0.9168 (t)
REVERT: R  307 ARG cc_start: 0.7515 (mmp80) cc_final: 0.7312 (mmp80)
  outliers start: 14
  outliers final: 7
  residues processed: 147
  average time/residue: 0.0994
  time to fit residues: 18.6877
Evaluate side-chains
  138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.081559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.059928 restraints weight = 21001.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 3.51
r_work: 0.2830 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8188  Z= 0.138
  Angle     :  0.551   6.358  11094  Z= 0.288
  Chirality :  0.041   0.143   1275
  Planarity :  0.003   0.031   1406
  Dihedral  :  4.461  18.109   1122
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.51 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.27), residues: 1010
  helix:  2.28 (0.26), residues: 408
  sheet:  0.46 (0.36), residues: 198
  loop :  0.13 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  38 
 TYR   0.011   0.001   TYR B 264 
 PHE   0.016   0.001   PHE G  61 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 ( 8187)
  covalent geometry    : angle       0.55141 /  0.29 (11092)
  SS BOND              : bond        0.00078 /  0.04 (    1)
  SS BOND              : angle       0.70593 /  0.39 (    2)
  hydrogen bonds       : bond        0.03802 /  2.52 (  438)
  hydrogen bonds       : angle       4.18217 /  2.90 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8924 (mm-30)
REVERT: G   20 LYS cc_start: 0.9431 (ptmm) cc_final: 0.9058 (pttp)
REVERT: G   21 MET cc_start: 0.9364 (mmm) cc_final: 0.9075 (mmm)
REVERT: G   48 ASP cc_start: 0.8805 (t0) cc_final: 0.8495 (t0)
REVERT: A   64 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7570 (p-80)
REVERT: A  271 ASN cc_start: 0.9217 (m-40) cc_final: 0.8918 (m110)
REVERT: A  330 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8892 (mp0)
REVERT: N    2 VAL cc_start: 0.9305 (p) cc_final: 0.9043 (t)
REVERT: N    3 GLN cc_start: 0.8345 (pt0) cc_final: 0.8116 (pt0)
REVERT: N   18 LEU cc_start: 0.8134 (mt) cc_final: 0.7879 (mp)
REVERT: N   38 ARG cc_start: 0.8985 (ptt180) cc_final: 0.8605 (ptt90)
REVERT: N   73 ASP cc_start: 0.8217 (t0) cc_final: 0.7822 (t0)
REVERT: N   83 MET cc_start: 0.8949 (mtm) cc_final: 0.8724 (ptp)
REVERT: N   93 VAL cc_start: 0.9033 (t) cc_final: 0.8695 (p)
REVERT: N  120 GLN cc_start: 0.9057 (mm110) cc_final: 0.8311 (mm-40)
REVERT: B    8 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8546 (mtt-85)
REVERT: B   38 ASP cc_start: 0.9224 (t0) cc_final: 0.8847 (p0)
REVERT: B  209 LYS cc_start: 0.8560 (mttt) cc_final: 0.8075 (mttp)
REVERT: B  217 MET cc_start: 0.8594 (ppp) cc_final: 0.8203 (ppp)
REVERT: B  254 ASP cc_start: 0.8864 (t70) cc_final: 0.8358 (t0)
REVERT: B  280 LYS cc_start: 0.9145 (ttmm) cc_final: 0.8712 (ttmm)
REVERT: R   84 ASP cc_start: 0.9165 (m-30) cc_final: 0.8089 (t70)
REVERT: R  262 THR cc_start: 0.9295 (m) cc_final: 0.9094 (t)
  outliers start: 14
  outliers final: 9
  residues processed: 154
  average time/residue: 0.0872
  time to fit residues: 17.4176
Evaluate side-chains
  141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  289 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0370
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.9462

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.082493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.060962 restraints weight = 20976.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.51
r_work: 0.2856 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8188  Z= 0.113
  Angle     :  0.555   7.797  11094  Z= 0.286
  Chirality :  0.041   0.146   1275
  Planarity :  0.003   0.032   1406
  Dihedral  :  4.217  16.775   1122
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.37 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.65 (0.27), residues: 1010
  helix:  2.51 (0.25), residues: 402
  sheet:  0.38 (0.36), residues: 198
  loop :  0.10 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  38 
 TYR   0.011   0.001   TYR B 264 
 PHE   0.013   0.001   PHE G  61 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 8187)
  covalent geometry    : angle       0.55486 /  0.29 (11092)
  SS BOND              : bond        0.00005 /  0.00 (    1)
  SS BOND              : angle       0.88668 /  0.51 (    2)
  hydrogen bonds       : bond        0.03554 /  2.37 (  438)
  hydrogen bonds       : angle       4.04141 /  2.80 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9043 (mm-30)
REVERT: G   20 LYS cc_start: 0.9437 (ptmm) cc_final: 0.9044 (pttp)
REVERT: G   21 MET cc_start: 0.9362 (mmm) cc_final: 0.9081 (mmm)
REVERT: G   22 GLU cc_start: 0.8721 (tt0) cc_final: 0.8421 (tt0)
REVERT: G   48 ASP cc_start: 0.8815 (t0) cc_final: 0.8495 (t0)
REVERT: A   64 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7541 (p-80)
REVERT: A  271 ASN cc_start: 0.9211 (m-40) cc_final: 0.8903 (m110)
REVERT: A  330 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8842 (mp0)
REVERT: N    3 GLN cc_start: 0.8360 (pt0) cc_final: 0.8143 (pt0)
REVERT: N    5 GLN cc_start: 0.8733 (tp40) cc_final: 0.8483 (tp40)
REVERT: N   18 LEU cc_start: 0.8139 (mt) cc_final: 0.7892 (mp)
REVERT: N   38 ARG cc_start: 0.8950 (ptt180) cc_final: 0.8657 (ptm160)
REVERT: N   73 ASP cc_start: 0.8191 (t0) cc_final: 0.7747 (t0)
REVERT: N   76 LYS cc_start: 0.9374 (ptmm) cc_final: 0.9108 (ptmm)
REVERT: N   93 VAL cc_start: 0.9135 (t) cc_final: 0.8684 (p)
REVERT: B   10 GLU cc_start: 0.9536 (tt0) cc_final: 0.9278 (mt-10)
REVERT: B   31 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.8991 (p)
REVERT: B  209 LYS cc_start: 0.8622 (mttt) cc_final: 0.8178 (mttp)
REVERT: B  217 MET cc_start: 0.8653 (ppp) cc_final: 0.8254 (ppp)
REVERT: B  254 ASP cc_start: 0.9069 (t70) cc_final: 0.8651 (t70)
REVERT: B  280 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8829 (ttmm)
REVERT: R   84 ASP cc_start: 0.9169 (m-30) cc_final: 0.8033 (t70)
REVERT: R  307 ARG cc_start: 0.7509 (mmp80) cc_final: 0.7289 (mmp80)
  outliers start: 15
  outliers final: 7
  residues processed: 155
  average time/residue: 0.0814
  time to fit residues: 16.1944
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  289 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 75 optimal weight:   20.0000
   chunk 36 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.082271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.060704 restraints weight = 20701.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 3.59
r_work: 0.2850 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8188  Z= 0.128
  Angle     :  0.550   8.427  11094  Z= 0.285
  Chirality :  0.041   0.153   1275
  Planarity :  0.003   0.031   1406
  Dihedral  :  4.167  17.144   1122
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.02 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.27), residues: 1010
  helix:  2.64 (0.25), residues: 396
  sheet:  0.42 (0.36), residues: 198
  loop :  0.17 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 129 
 TYR   0.013   0.001   TYR B 264 
 PHE   0.012   0.001   PHE G  61 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 ( 8187)
  covalent geometry    : angle       0.54950 /  0.28 (11092)
  SS BOND              : bond        0.00012 /  0.01 (    1)
  SS BOND              : angle       0.56862 /  0.32 (    2)
  hydrogen bonds       : bond        0.03560 /  2.35 (  438)
  hydrogen bonds       : angle       4.03406 /  2.80 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9109 (mm-30)
REVERT: G   21 MET cc_start: 0.9374 (mmm) cc_final: 0.9100 (mmm)
REVERT: G   47 GLU cc_start: 0.8705 (mp0) cc_final: 0.8500 (mp0)
REVERT: G   48 ASP cc_start: 0.8807 (t0) cc_final: 0.8490 (t0)
REVERT: A  266 LEU cc_start: 0.9441 (mt) cc_final: 0.9237 (mt)
REVERT: A  271 ASN cc_start: 0.9218 (m-40) cc_final: 0.8914 (m110)
REVERT: A  330 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8851 (mp0)
REVERT: N    5 GLN cc_start: 0.8739 (tp40) cc_final: 0.8496 (tp40)
REVERT: N   18 LEU cc_start: 0.8165 (mt) cc_final: 0.7866 (mp)
REVERT: N   38 ARG cc_start: 0.8932 (ptt180) cc_final: 0.8439 (ptm-80)
REVERT: N   73 ASP cc_start: 0.8240 (t0) cc_final: 0.7642 (t0)
REVERT: N   80 TYR cc_start: 0.8512 (m-80) cc_final: 0.8241 (m-80)
REVERT: N   93 VAL cc_start: 0.9167 (t) cc_final: 0.8704 (p)
REVERT: N   99 CYS cc_start: 0.9265 (m) cc_final: 0.8590 (m)
REVERT: B   38 ASP cc_start: 0.9194 (t0) cc_final: 0.8931 (p0)
REVERT: B  209 LYS cc_start: 0.8644 (mttt) cc_final: 0.8140 (mttp)
REVERT: B  217 MET cc_start: 0.8699 (ppp) cc_final: 0.8312 (ppp)
REVERT: B  254 ASP cc_start: 0.9120 (t70) cc_final: 0.8692 (t70)
REVERT: B  280 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8873 (ttmm)
REVERT: B  292 PHE cc_start: 0.9116 (m-10) cc_final: 0.8635 (m-80)
  outliers start: 17
  outliers final: 8
  residues processed: 147
  average time/residue: 0.0797
  time to fit residues: 15.3390
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  289 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0570
   chunk 48 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 81 optimal weight:    8.9990
   chunk 76 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    1.1702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.082621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.061142 restraints weight = 20874.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 3.56
r_work: 0.2844 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8188  Z= 0.122
  Angle     :  0.560   7.944  11094  Z= 0.288
  Chirality :  0.041   0.158   1275
  Planarity :  0.004   0.033   1406
  Dihedral  :  4.106  17.985   1122
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.02 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.27), residues: 1010
  helix:  2.65 (0.25), residues: 396
  sheet:  0.42 (0.36), residues: 199
  loop :  0.17 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 129 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.012   0.001   PHE G  61 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 8187)
  covalent geometry    : angle       0.56009 /  0.29 (11092)
  SS BOND              : bond        0.00012 /  0.01 (    1)
  SS BOND              : angle       0.63513 /  0.35 (    2)
  hydrogen bonds       : bond        0.03494 /  2.31 (  438)
  hydrogen bonds       : angle       3.99686 /  2.78 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9121 (mm-30)
REVERT: G   21 MET cc_start: 0.9380 (mmm) cc_final: 0.9109 (mmm)
REVERT: G   48 ASP cc_start: 0.8730 (t0) cc_final: 0.8455 (t0)
REVERT: A   64 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7507 (p-80)
REVERT: A  266 LEU cc_start: 0.9436 (mt) cc_final: 0.9231 (mt)
REVERT: A  271 ASN cc_start: 0.9189 (m-40) cc_final: 0.8871 (m110)
REVERT: A  330 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8839 (mp0)
REVERT: N    5 GLN cc_start: 0.8735 (tp40) cc_final: 0.8497 (tp40)
REVERT: N   18 LEU cc_start: 0.8107 (mt) cc_final: 0.7847 (mp)
REVERT: N   38 ARG cc_start: 0.8877 (ptt180) cc_final: 0.8384 (ptm-80)
REVERT: N   73 ASP cc_start: 0.8187 (t0) cc_final: 0.7512 (t0)
REVERT: N   76 LYS cc_start: 0.9382 (ptmm) cc_final: 0.9129 (ptmm)
REVERT: N   80 TYR cc_start: 0.8442 (m-80) cc_final: 0.8156 (m-80)
REVERT: B   10 GLU cc_start: 0.9533 (tt0) cc_final: 0.9271 (mt-10)
REVERT: B   38 ASP cc_start: 0.9214 (t0) cc_final: 0.8909 (p0)
REVERT: B  209 LYS cc_start: 0.8632 (mttt) cc_final: 0.8138 (mttp)
REVERT: B  217 MET cc_start: 0.8728 (ppp) cc_final: 0.8319 (ppp)
REVERT: B  254 ASP cc_start: 0.9123 (t70) cc_final: 0.8692 (t70)
REVERT: B  280 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8831 (ttmm)
REVERT: B  292 PHE cc_start: 0.9133 (m-10) cc_final: 0.8613 (m-80)
REVERT: R   55 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8550 (mm-30)
REVERT: R   84 ASP cc_start: 0.9115 (m-30) cc_final: 0.8121 (t70)
  outliers start: 16
  outliers final: 11
  residues processed: 146
  average time/residue: 0.0840
  time to fit residues: 16.1202
Evaluate side-chains
  138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  289 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 65 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 24 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.082485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.061086 restraints weight = 20805.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 3.51
r_work: 0.2876 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8188  Z= 0.115
  Angle     :  0.572   9.124  11094  Z= 0.291
  Chirality :  0.040   0.157   1275
  Planarity :  0.003   0.033   1406
  Dihedral  :  4.049  17.598   1122
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.60 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.82 (0.27), residues: 1010
  helix:  2.70 (0.25), residues: 396
  sheet:  0.50 (0.36), residues: 199
  loop :  0.15 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 129 
 TYR   0.012   0.001   TYR B 264 
 PHE   0.011   0.001   PHE A 212 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 301 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.11 ( 8187)
  covalent geometry    : angle       0.57247 /  0.29 (11092)
  SS BOND              : bond        0.00005 /  0.00 (    1)
  SS BOND              : angle       0.56400 /  0.31 (    2)
  hydrogen bonds       : bond        0.03377 /  2.24 (  438)
  hydrogen bonds       : angle       3.94417 /  2.74 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9176 (mm-30)
REVERT: G   21 MET cc_start: 0.9358 (mmm) cc_final: 0.9095 (mmm)
REVERT: G   48 ASP cc_start: 0.8713 (t0) cc_final: 0.8342 (t0)
REVERT: A   64 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7391 (p-80)
REVERT: A  266 LEU cc_start: 0.9457 (mt) cc_final: 0.9249 (mt)
REVERT: A  271 ASN cc_start: 0.9195 (m-40) cc_final: 0.8867 (m110)
REVERT: A  330 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8810 (mp0)
REVERT: N    5 GLN cc_start: 0.8747 (tp40) cc_final: 0.8522 (tp40)
REVERT: N   18 LEU cc_start: 0.8176 (mt) cc_final: 0.7888 (mp)
REVERT: N   38 ARG cc_start: 0.8888 (ptt180) cc_final: 0.8396 (ptm-80)
REVERT: N   39 GLN cc_start: 0.9284 (tt0) cc_final: 0.8539 (tp40)
REVERT: N   73 ASP cc_start: 0.8260 (t0) cc_final: 0.7575 (t0)
REVERT: N   76 LYS cc_start: 0.9444 (ptmm) cc_final: 0.9145 (ptmm)
REVERT: N   80 TYR cc_start: 0.8435 (m-80) cc_final: 0.8158 (m-80)
REVERT: N   93 VAL cc_start: 0.9155 (t) cc_final: 0.8805 (p)
REVERT: N   99 CYS cc_start: 0.9228 (m) cc_final: 0.8779 (m)
REVERT: B   10 GLU cc_start: 0.9554 (tt0) cc_final: 0.9260 (mt-10)
REVERT: B   38 ASP cc_start: 0.9215 (t0) cc_final: 0.8907 (p0)
REVERT: B  217 MET cc_start: 0.8696 (ppp) cc_final: 0.8267 (ppp)
REVERT: B  254 ASP cc_start: 0.9099 (t70) cc_final: 0.8817 (t0)
REVERT: B  280 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8582 (ttmm)
REVERT: B  292 PHE cc_start: 0.9073 (m-10) cc_final: 0.8543 (m-80)
REVERT: U    7 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8215 (mtmm)
  outliers start: 13
  outliers final: 10
  residues processed: 144
  average time/residue: 0.0926
  time to fit residues: 17.5235
Evaluate side-chains
  136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   45 PHE
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  289 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 38 optimal weight:    0.3980
   chunk 87 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    3.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.079876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.057881 restraints weight = 21351.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 3.55
r_work: 0.2780 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8188  Z= 0.223
  Angle     :  0.637   8.651  11094  Z= 0.327
  Chirality :  0.042   0.171   1275
  Planarity :  0.004   0.033   1406
  Dihedral  :  4.410  18.699   1122
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.42 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.27), residues: 1010
  helix:  2.46 (0.25), residues: 405
  sheet:  0.33 (0.35), residues: 205
  loop : -0.03 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 129 
 TYR   0.018   0.001   TYR B 264 
 PHE   0.015   0.001   PHE R 258 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 301 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00510 /  0.22 ( 8187)
  covalent geometry    : angle       0.63712 /  0.33 (11092)
  SS BOND              : bond        0.00018 /  0.01 (    1)
  SS BOND              : angle       0.66812 /  0.39 (    2)
  hydrogen bonds       : bond        0.03928 /  2.57 (  438)
  hydrogen bonds       : angle       4.13004 /  2.87 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8761 (ptp-110) cc_final: 0.8469 (ptp-170)
REVERT: G   17 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9217 (mm-30)
REVERT: G   21 MET cc_start: 0.9384 (mmm) cc_final: 0.9115 (mmm)
REVERT: G   48 ASP cc_start: 0.8822 (t0) cc_final: 0.8579 (t0)
REVERT: A  271 ASN cc_start: 0.9267 (m-40) cc_final: 0.8933 (m110)
REVERT: A  330 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8865 (mp0)
REVERT: N    5 GLN cc_start: 0.8774 (tp40) cc_final: 0.8556 (tp40)
REVERT: N   38 ARG cc_start: 0.8967 (ptt180) cc_final: 0.8690 (ptm160)
REVERT: N   73 ASP cc_start: 0.8274 (t0) cc_final: 0.7689 (t0)
REVERT: N   76 LYS cc_start: 0.9416 (ptmm) cc_final: 0.9108 (ptmm)
REVERT: N   83 MET cc_start: 0.8252 (mpp) cc_final: 0.8005 (mpp)
REVERT: N   99 CYS cc_start: 0.9261 (m) cc_final: 0.8792 (m)
REVERT: B   10 GLU cc_start: 0.9577 (tt0) cc_final: 0.9263 (mt-10)
REVERT: B  254 ASP cc_start: 0.9176 (t70) cc_final: 0.8784 (t70)
REVERT: B  256 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.9107 (mtm-85)
REVERT: B  280 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8805 (ttmm)
REVERT: R   55 GLU cc_start: 0.8186 (tt0) cc_final: 0.7947 (tt0)
REVERT: U    7 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8212 (mtmm)
  outliers start: 14
  outliers final: 11
  residues processed: 134
  average time/residue: 0.0970
  time to fit residues: 16.9087
Evaluate side-chains
  131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  192 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  289 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 16 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0970
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.082549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.061027 restraints weight = 21149.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.54
r_work: 0.2854 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8188  Z= 0.109
  Angle     :  0.590   9.609  11094  Z= 0.298
  Chirality :  0.041   0.156   1275
  Planarity :  0.004   0.034   1406
  Dihedral  :  4.128  24.169   1122
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.88 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.27), residues: 1010
  helix:  2.76 (0.26), residues: 398
  sheet:  0.66 (0.36), residues: 191
  loop : -0.02 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 129 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.011   0.001   PHE A 376 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 301 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 8187)
  covalent geometry    : angle       0.58955 /  0.30 (11092)
  SS BOND              : bond        0.00014 /  0.01 (    1)
  SS BOND              : angle       0.55113 /  0.30 (    2)
  hydrogen bonds       : bond        0.03367 /  2.23 (  438)
  hydrogen bonds       : angle       3.94048 /  2.72 ( 1233)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8769 (ptp-110) cc_final: 0.8497 (ptp-170)
REVERT: G   17 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9206 (mm-30)
REVERT: G   21 MET cc_start: 0.9385 (mmm) cc_final: 0.9137 (mmm)
REVERT: G   48 ASP cc_start: 0.8799 (t0) cc_final: 0.8518 (t0)
REVERT: A  271 ASN cc_start: 0.9203 (m-40) cc_final: 0.8848 (m110)
REVERT: A  330 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8830 (mp0)
REVERT: N    1 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: N    3 GLN cc_start: 0.8374 (pt0) cc_final: 0.8045 (pt0)
REVERT: N    5 GLN cc_start: 0.8763 (tp40) cc_final: 0.8543 (tp40)
REVERT: N   38 ARG cc_start: 0.8862 (ptt180) cc_final: 0.8606 (ptm-80)
REVERT: N   39 GLN cc_start: 0.9292 (tt0) cc_final: 0.8533 (tp40)
REVERT: N   73 ASP cc_start: 0.8207 (t0) cc_final: 0.7881 (t0)
REVERT: N   76 LYS cc_start: 0.9393 (ptmm) cc_final: 0.8989 (ptmm)
REVERT: N   83 MET cc_start: 0.8279 (mpp) cc_final: 0.8043 (mpp)
REVERT: N   99 CYS cc_start: 0.9267 (m) cc_final: 0.8790 (m)
REVERT: B   10 GLU cc_start: 0.9572 (tt0) cc_final: 0.9268 (mt-10)
REVERT: B   38 ASP cc_start: 0.9183 (t0) cc_final: 0.8980 (p0)
REVERT: B  254 ASP cc_start: 0.9125 (t70) cc_final: 0.8899 (t0)
REVERT: B  280 LYS cc_start: 0.9150 (ttmm) cc_final: 0.8666 (ttmm)
REVERT: B  292 PHE cc_start: 0.9053 (m-10) cc_final: 0.8526 (m-80)
REVERT: R   84 ASP cc_start: 0.9195 (m-30) cc_final: 0.8194 (t70)
REVERT: U    7 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8128 (mtmm)
  outliers start: 12
  outliers final: 10
  residues processed: 136
  average time/residue: 0.1023
  time to fit residues: 18.2164
Evaluate side-chains
  134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  289 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 59 optimal weight:    0.4980
   chunk 73 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    4.2988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.078740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.056357 restraints weight = 21322.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 3.58
r_work: 0.2752 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   8188  Z= 0.292
  Angle     :  0.687   8.651  11094  Z= 0.354
  Chirality :  0.044   0.175   1275
  Planarity :  0.004   0.035   1406
  Dihedral  :  4.512  20.304   1122
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.47 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.42 (0.27), residues: 1010
  helix:  2.39 (0.25), residues: 405
  sheet:  0.35 (0.35), residues: 200
  loop : -0.19 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 129 
 TYR   0.022   0.002   TYR B 264 
 PHE   0.019   0.002   PHE R 258 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00664 /  0.29 ( 8187)
  covalent geometry    : angle       0.68673 /  0.35 (11092)
  SS BOND              : bond        0.00004 /  0.00 (    1)
  SS BOND              : angle       0.68344 /  0.40 (    2)
  hydrogen bonds       : bond        0.04114 /  2.69 (  438)
  hydrogen bonds       : angle       4.24164 /  2.95 ( 1233)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1592.04 seconds
wall clock time: 28 minutes 5.95 seconds (1685.95 seconds total)