Starting phenix.real_space_refine
on Wed Mar 12 18:00:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f4i_31453/03_2025/7f4i_31453.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f4i_31453/03_2025/7f4i_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_31453/03_2025/7f4i_31453.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f4i_31453/03_2025/7f4i_31453.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f4i_31453/03_2025/7f4i_31453.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f4i_31453/03_2025/7f4i_31453.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 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: {'4J2:plan-2': 1, 'NLE:plan-1': 1, 'ASP:plan': 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: 4.78, per 1000 atoms: 0.60
  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: 2.33
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.89
  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: 2.15

  Time building geometry restraints manager: 2.65 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:             0.530
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.340
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
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   8187  Z= 0.604
  Angle     :  1.215  36.806  11092  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.065   0.009   TRP B  63 
 HIS   0.018   0.005   HIS G  44 
 PHE   0.028   0.005   PHE R  76 
 TYR   0.038   0.006   TYR B 111 
 ARG   0.057   0.006   ARG A 385 

*********************** 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  : 0.980 
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: 0.7956 (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: 0.8093 (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: 0.3013
  time to fit residues: 79.7196
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  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3470 r_free = 0.3470 target = 0.082267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.060258 restraints weight = 20219.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 3.55
r_work: 0.2841 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8187  Z= 0.253
  Angle     :  0.635   7.493  11092  Z= 0.338
  Chirality :  0.044   0.194   1275
  Planarity :  0.004   0.053   1406
  Dihedral  :  5.210  22.590   1122
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.67 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.27), residues: 1010
  helix:  1.65 (0.25), residues: 412
  sheet:  0.36 (0.34), residues: 223
  loop : -0.07 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 362 
 PHE   0.023   0.002   PHE G  61 
 TYR   0.014   0.001   TYR B 105 
 ARG   0.005   0.001   ARG N  19 

*********************** 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
  154 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 0.928 
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   13 ARG cc_start: 0.9223 (ttm110) cc_final: 0.8897 (mtm110)
REVERT: G   21 MET cc_start: 0.9318 (mmm) cc_final: 0.9063 (mmm)
REVERT: G   22 GLU cc_start: 0.8873 (tt0) cc_final: 0.8668 (tt0)
REVERT: G   32 LYS cc_start: 0.9386 (mmmm) cc_final: 0.9058 (mmmm)
REVERT: G   42 GLU cc_start: 0.8530 (pp20) cc_final: 0.8329 (pp20)
REVERT: G   48 ASP cc_start: 0.8804 (t0) cc_final: 0.8508 (t0)
REVERT: A  271 ASN cc_start: 0.9247 (m-40) cc_final: 0.8970 (m110)
REVERT: A  330 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8901 (mp0)
REVERT: N   18 LEU cc_start: 0.8126 (mt) cc_final: 0.7858 (mp)
REVERT: N   34 MET cc_start: 0.8525 (mtp) cc_final: 0.8193 (mtp)
REVERT: N   73 ASP cc_start: 0.7967 (t0) cc_final: 0.7678 (t0)
REVERT: N   93 VAL cc_start: 0.9190 (t) cc_final: 0.8802 (p)
REVERT: B   38 ASP cc_start: 0.9109 (t0) cc_final: 0.8748 (p0)
REVERT: B  172 GLU cc_start: 0.9186 (pt0) cc_final: 0.8951 (pp20)
REVERT: B  254 ASP cc_start: 0.8888 (t70) cc_final: 0.8498 (t0)
REVERT: B  280 LYS cc_start: 0.9277 (ttmm) cc_final: 0.9043 (ttmm)
REVERT: R   83 SER cc_start: 0.9112 (m) cc_final: 0.8865 (t)
REVERT: U    7 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7310 (mtpt)
  outliers start: 9
  outliers final: 4
  residues processed: 150
  average time/residue: 0.3098
  time to fit residues: 59.4931
Evaluate side-chains
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
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 R residue  289 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0570
   chunk 65 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 96 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.9302

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3468 r_free = 0.3468 target = 0.081445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.059959 restraints weight = 21111.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 3.42
r_work: 0.2854 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8187  Z= 0.165
  Angle     :  0.570   6.537  11092  Z= 0.297
  Chirality :  0.042   0.158   1275
  Planarity :  0.004   0.034   1406
  Dihedral  :  4.594  19.157   1122
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  8.95 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.27), residues: 1010
  helix:  2.18 (0.26), residues: 408
  sheet:  0.43 (0.35), residues: 198
  loop :  0.14 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R  70 
 PHE   0.016   0.001   PHE G  61 
 TYR   0.008   0.001   TYR N  95 
 ARG   0.009   0.001   ARG R 223 

*********************** 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
  160 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.917 
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: 0.9237 (mm-30) cc_final: 0.8896 (mm-30)
REVERT: G   20 LYS cc_start: 0.9459 (ptmm) cc_final: 0.9078 (pttp)
REVERT: G   21 MET cc_start: 0.9377 (mmm) cc_final: 0.9113 (mmm)
REVERT: G   32 LYS cc_start: 0.9348 (mmmm) cc_final: 0.9110 (mmmm)
REVERT: G   42 GLU cc_start: 0.8563 (pp20) cc_final: 0.8287 (pp20)
REVERT: G   46 LYS cc_start: 0.9428 (ptpp) cc_final: 0.9185 (ptpp)
REVERT: G   48 ASP cc_start: 0.8930 (t0) cc_final: 0.8682 (t0)
REVERT: A   60 MET cc_start: 0.9165 (mmm) cc_final: 0.8959 (mmm)
REVERT: A   64 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7760 (p-80)
REVERT: A  271 ASN cc_start: 0.9262 (m-40) cc_final: 0.8984 (m110)
REVERT: A  330 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8885 (mp0)
REVERT: N    2 VAL cc_start: 0.9510 (p) cc_final: 0.8893 (t)
REVERT: N   18 LEU cc_start: 0.8332 (mt) cc_final: 0.8077 (mp)
REVERT: N   34 MET cc_start: 0.8544 (mtp) cc_final: 0.8219 (mtp)
REVERT: N   73 ASP cc_start: 0.8360 (t0) cc_final: 0.8005 (t0)
REVERT: N   93 VAL cc_start: 0.9249 (t) cc_final: 0.8806 (p)
REVERT: B   23 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8881 (mttp)
REVERT: B   38 ASP cc_start: 0.9166 (t0) cc_final: 0.8854 (p0)
REVERT: B  209 LYS cc_start: 0.8829 (mttt) cc_final: 0.8513 (mttp)
REVERT: B  217 MET cc_start: 0.8577 (ppp) cc_final: 0.8174 (ppp)
REVERT: B  254 ASP cc_start: 0.8891 (t70) cc_final: 0.8522 (t0)
REVERT: R   83 SER cc_start: 0.9141 (m) cc_final: 0.8913 (t)
  outliers start: 12
  outliers final: 3
  residues processed: 155
  average time/residue: 0.2703
  time to fit residues: 54.3229
Evaluate side-chains
  133 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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  187 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    0.0010
   chunk 21 optimal weight:   20.0000
   chunk 15 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   overall best weight:    1.7790

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

Flipped N/Q/H residues before XYZ refinement:
N  82 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 = 0.3465 r_free = 0.3465 target = 0.081852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.060172 restraints weight = 20566.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 3.58
r_work: 0.2839 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8187  Z= 0.225
  Angle     :  0.570   7.264  11092  Z= 0.297
  Chirality :  0.042   0.191   1275
  Planarity :  0.004   0.034   1406
  Dihedral  :  4.467  18.575   1122
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.40 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.27), residues: 1010
  helix:  2.28 (0.26), residues: 408
  sheet:  0.51 (0.36), residues: 198
  loop :  0.08 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R  70 
 PHE   0.015   0.001   PHE G  61 
 TYR   0.012   0.001   TYR B 264 
 ARG   0.006   0.000   ARG A  38 

*********************** 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
  154 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.900 
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: 0.9369 (mm-30) cc_final: 0.9058 (mm-30)
REVERT: G   20 LYS cc_start: 0.9438 (ptmm) cc_final: 0.9034 (pttp)
REVERT: G   21 MET cc_start: 0.9379 (mmm) cc_final: 0.9107 (mmm)
REVERT: G   42 GLU cc_start: 0.8621 (pp20) cc_final: 0.8338 (pp20)
REVERT: G   48 ASP cc_start: 0.8879 (t0) cc_final: 0.8639 (t0)
REVERT: A   60 MET cc_start: 0.9161 (mmm) cc_final: 0.8887 (mmm)
REVERT: A  271 ASN cc_start: 0.9225 (m-40) cc_final: 0.8912 (m110)
REVERT: A  330 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8873 (mp0)
REVERT: N    2 VAL cc_start: 0.9299 (p) cc_final: 0.8987 (m)
REVERT: N   18 LEU cc_start: 0.8262 (mt) cc_final: 0.8013 (mp)
REVERT: N   38 ARG cc_start: 0.8970 (ptt180) cc_final: 0.8624 (ptt90)
REVERT: N   73 ASP cc_start: 0.8152 (t0) cc_final: 0.7718 (t0)
REVERT: N   76 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9057 (ptmm)
REVERT: N   93 VAL cc_start: 0.9143 (t) cc_final: 0.8800 (p)
REVERT: B   38 ASP cc_start: 0.9237 (t0) cc_final: 0.8843 (p0)
REVERT: B  209 LYS cc_start: 0.8568 (mttt) cc_final: 0.8174 (mttp)
REVERT: B  217 MET cc_start: 0.8534 (ppp) cc_final: 0.8155 (ppp)
REVERT: B  254 ASP cc_start: 0.8936 (t70) cc_final: 0.8478 (t0)
  outliers start: 14
  outliers final: 8
  residues processed: 144
  average time/residue: 0.3319
  time to fit residues: 62.8042
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  : 1.922 
-------------------------------------------------------------------------------
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   64 VAL
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 81 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3448 r_free = 0.3448 target = 0.080962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.059200 restraints weight = 20820.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 3.56
r_work: 0.2802 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8187  Z= 0.249
  Angle     :  0.577   6.498  11092  Z= 0.300
  Chirality :  0.042   0.176   1275
  Planarity :  0.004   0.035   1406
  Dihedral  :  4.406  17.471   1122
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.74 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.27), residues: 1010
  helix:  2.46 (0.26), residues: 402
  sheet:  0.32 (0.35), residues: 200
  loop :  0.11 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R  70 
 PHE   0.015   0.001   PHE G  61 
 TYR   0.014   0.001   TYR B 264 
 ARG   0.007   0.000   ARG A  38 

*********************** 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
  155 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.865 
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: 0.9410 (mm-30) cc_final: 0.9104 (mm-30)
REVERT: G   20 LYS cc_start: 0.9436 (ptmm) cc_final: 0.9037 (pttp)
REVERT: G   21 MET cc_start: 0.9389 (mmm) cc_final: 0.9106 (mmm)
REVERT: G   42 GLU cc_start: 0.8677 (pp20) cc_final: 0.8346 (pp20)
REVERT: G   48 ASP cc_start: 0.8810 (t0) cc_final: 0.8514 (t0)
REVERT: A  271 ASN cc_start: 0.9235 (m-40) cc_final: 0.8899 (m110)
REVERT: A  330 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8898 (mp0)
REVERT: N   18 LEU cc_start: 0.8211 (mt) cc_final: 0.7899 (mp)
REVERT: N   38 ARG cc_start: 0.8968 (ptt180) cc_final: 0.8644 (ptm160)
REVERT: N   73 ASP cc_start: 0.8181 (t0) cc_final: 0.7730 (t0)
REVERT: N   76 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9032 (ptmm)
REVERT: N   93 VAL cc_start: 0.9179 (t) cc_final: 0.8720 (p)
REVERT: B    8 ARG cc_start: 0.9105 (mmm-85) cc_final: 0.8856 (ttm110)
REVERT: B   23 LYS cc_start: 0.9360 (tppt) cc_final: 0.9155 (mttp)
REVERT: B  209 LYS cc_start: 0.8573 (mttt) cc_final: 0.8068 (mttp)
REVERT: B  217 MET cc_start: 0.8580 (ppp) cc_final: 0.8219 (ppp)
REVERT: B  254 ASP cc_start: 0.9142 (t70) cc_final: 0.8703 (t70)
REVERT: B  280 LYS cc_start: 0.9197 (ttmm) cc_final: 0.8849 (ttmm)
REVERT: U    7 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8355 (mtmm)
  outliers start: 21
  outliers final: 12
  residues processed: 144
  average time/residue: 0.2527
  time to fit residues: 46.6917
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
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   64 VAL
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue   83 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3428 r_free = 0.3428 target = 0.080219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.057939 restraints weight = 20832.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 3.59
r_work: 0.2779 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8187  Z= 0.329
  Angle     :  0.607   8.155  11092  Z= 0.316
  Chirality :  0.043   0.287   1275
  Planarity :  0.004   0.034   1406
  Dihedral  :  4.542  18.378   1122
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.33 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.27), residues: 1010
  helix:  2.41 (0.25), residues: 405
  sheet:  0.14 (0.35), residues: 205
  loop :  0.01 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R  70 
 PHE   0.016   0.001   PHE G  61 
 TYR   0.019   0.001   TYR B 264 
 ARG   0.007   0.001   ARG B 129 

*********************** 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
  155 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 1.047 
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: 0.9478 (mm-30) cc_final: 0.9257 (mm-30)
REVERT: G   21 MET cc_start: 0.9373 (mmm) cc_final: 0.9105 (mmm)
REVERT: G   42 GLU cc_start: 0.8735 (pp20) cc_final: 0.8359 (pp20)
REVERT: G   48 ASP cc_start: 0.8800 (t0) cc_final: 0.8532 (t0)
REVERT: A  271 ASN cc_start: 0.9269 (m-40) cc_final: 0.8913 (m110)
REVERT: A  330 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8892 (mp0)
REVERT: N    5 GLN cc_start: 0.8747 (tp40) cc_final: 0.8480 (tp40)
REVERT: N   18 LEU cc_start: 0.8350 (mt) cc_final: 0.8060 (mp)
REVERT: N   73 ASP cc_start: 0.8220 (t0) cc_final: 0.7766 (t0)
REVERT: N   76 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9096 (ptmm)
REVERT: B   10 GLU cc_start: 0.9582 (tt0) cc_final: 0.9187 (mt-10)
REVERT: B   15 LYS cc_start: 0.9663 (ttmt) cc_final: 0.9303 (tptp)
REVERT: B   23 LYS cc_start: 0.9460 (tppt) cc_final: 0.9223 (mtmt)
REVERT: B   38 ASP cc_start: 0.9232 (t0) cc_final: 0.9022 (p0)
REVERT: B  209 LYS cc_start: 0.8658 (mttt) cc_final: 0.8243 (mttp)
REVERT: B  217 MET cc_start: 0.8594 (ppp) cc_final: 0.8283 (ppp)
REVERT: B  254 ASP cc_start: 0.9190 (t70) cc_final: 0.8745 (t70)
REVERT: U    7 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8414 (mtmm)
  outliers start: 21
  outliers final: 13
  residues processed: 143
  average time/residue: 0.2534
  time to fit residues: 46.4780
Evaluate side-chains
  139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
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   64 VAL
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue  172 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 72 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0770
   chunk 98 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    1.1342

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3462 r_free = 0.3462 target = 0.081486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.059853 restraints weight = 20768.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 3.53
r_work: 0.2840 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8187  Z= 0.183
  Angle     :  0.569   7.794  11092  Z= 0.295
  Chirality :  0.041   0.153   1275
  Planarity :  0.003   0.038   1406
  Dihedral  :  4.288  17.100   1122
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.19 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.27), residues: 1010
  helix:  2.49 (0.25), residues: 405
  sheet:  0.27 (0.35), residues: 200
  loop : -0.01 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  70 
 PHE   0.012   0.001   PHE G  61 
 TYR   0.012   0.001   TYR B 264 
 ARG   0.008   0.000   ARG B 129 

*********************** 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
  149 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.872 
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: 0.9437 (mm-30) cc_final: 0.9197 (mm-30)
REVERT: G   21 MET cc_start: 0.9374 (mmm) cc_final: 0.9108 (mmm)
REVERT: G   22 GLU cc_start: 0.8751 (tt0) cc_final: 0.8391 (tt0)
REVERT: G   42 GLU cc_start: 0.8713 (pp20) cc_final: 0.8308 (pp20)
REVERT: G   48 ASP cc_start: 0.8827 (t0) cc_final: 0.8448 (t0)
REVERT: A  271 ASN cc_start: 0.9250 (m-40) cc_final: 0.8916 (m110)
REVERT: A  330 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8845 (mp0)
REVERT: N    5 GLN cc_start: 0.8733 (tp40) cc_final: 0.8481 (tp40)
REVERT: N   18 LEU cc_start: 0.8357 (mt) cc_final: 0.8003 (mp)
REVERT: N   38 ARG cc_start: 0.8959 (ptt180) cc_final: 0.8715 (ptm160)
REVERT: N   73 ASP cc_start: 0.8227 (t0) cc_final: 0.7615 (t0)
REVERT: N   76 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9078 (ptmm)
REVERT: N   80 TYR cc_start: 0.8527 (m-80) cc_final: 0.8226 (m-80)
REVERT: N   99 CYS cc_start: 0.9229 (m) cc_final: 0.8641 (m)
REVERT: B   10 GLU cc_start: 0.9565 (tt0) cc_final: 0.9284 (mt-10)
REVERT: B   15 LYS cc_start: 0.9642 (ttmt) cc_final: 0.9293 (tptp)
REVERT: B   31 SER cc_start: 0.9234 (m) cc_final: 0.8936 (p)
REVERT: B   38 ASP cc_start: 0.9243 (t0) cc_final: 0.8972 (p0)
REVERT: B  217 MET cc_start: 0.8608 (ppp) cc_final: 0.8291 (ppp)
REVERT: B  254 ASP cc_start: 0.9163 (t70) cc_final: 0.8750 (t70)
REVERT: B  280 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8655 (ttmm)
  outliers start: 12
  outliers final: 9
  residues processed: 142
  average time/residue: 0.2815
  time to fit residues: 50.7353
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
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   64 VAL
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain B residue  154 ASP
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 28 optimal weight:   20.0000
   chunk 91 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0970
   chunk 9 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3459 r_free = 0.3459 target = 0.083239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.060607 restraints weight = 21780.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 3.57
r_work: 0.2818 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8187  Z= 0.231
  Angle     :  0.577   8.072  11092  Z= 0.296
  Chirality :  0.041   0.162   1275
  Planarity :  0.003   0.036   1406
  Dihedral  :  4.282  18.377   1122
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.07 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.27), residues: 1010
  helix:  2.51 (0.25), residues: 405
  sheet:  0.34 (0.35), residues: 200
  loop : -0.01 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  70 
 PHE   0.013   0.001   PHE G  61 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.010   0.001   ARG B 129 

*********************** 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
  142 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.939 
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: 0.9444 (mm-30) cc_final: 0.9202 (mm-30)
REVERT: G   21 MET cc_start: 0.9374 (mmm) cc_final: 0.9109 (mmm)
REVERT: G   42 GLU cc_start: 0.8734 (pp20) cc_final: 0.8328 (pp20)
REVERT: G   48 ASP cc_start: 0.8820 (t0) cc_final: 0.8438 (t0)
REVERT: A  271 ASN cc_start: 0.9234 (m-40) cc_final: 0.8886 (m110)
REVERT: A  330 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8851 (mp0)
REVERT: N    5 GLN cc_start: 0.8759 (tp40) cc_final: 0.8524 (tp40)
REVERT: N   18 LEU cc_start: 0.8268 (mt) cc_final: 0.7937 (mp)
REVERT: N   38 ARG cc_start: 0.8974 (ptt180) cc_final: 0.8753 (ptm160)
REVERT: N   73 ASP cc_start: 0.8237 (t0) cc_final: 0.7615 (t0)
REVERT: N   76 LYS cc_start: 0.9350 (ptmm) cc_final: 0.9038 (ptmm)
REVERT: N   80 TYR cc_start: 0.8552 (m-80) cc_final: 0.8128 (m-80)
REVERT: N   81 LEU cc_start: 0.8837 (tp) cc_final: 0.8551 (tt)
REVERT: N   99 CYS cc_start: 0.9233 (m) cc_final: 0.8648 (m)
REVERT: B   10 GLU cc_start: 0.9578 (tt0) cc_final: 0.9275 (mt-10)
REVERT: B   15 LYS cc_start: 0.9648 (ttmt) cc_final: 0.9293 (tptp)
REVERT: B   38 ASP cc_start: 0.9244 (t0) cc_final: 0.8986 (p0)
REVERT: B  217 MET cc_start: 0.8587 (ppp) cc_final: 0.8225 (ppp)
REVERT: B  254 ASP cc_start: 0.9140 (t70) cc_final: 0.8744 (t70)
  outliers start: 13
  outliers final: 10
  residues processed: 138
  average time/residue: 0.2626
  time to fit residues: 46.4321
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
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   64 VAL
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
N 120 GLN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.082220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.060309 restraints weight = 21360.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 3.61
r_work: 0.2849 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8187  Z= 0.179
  Angle     :  0.584   8.495  11092  Z= 0.296
  Chirality :  0.041   0.161   1275
  Planarity :  0.003   0.038   1406
  Dihedral  :  4.168  20.566   1122
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.27), residues: 1010
  helix:  2.71 (0.25), residues: 398
  sheet:  0.39 (0.35), residues: 200
  loop :  0.09 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.010   0.000   ARG B 129 

*********************** 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
  150 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.768 
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: 0.9446 (mm-30) cc_final: 0.9243 (mm-30)
REVERT: G   21 MET cc_start: 0.9364 (mmm) cc_final: 0.9113 (mmm)
REVERT: G   22 GLU cc_start: 0.8772 (tt0) cc_final: 0.8396 (tt0)
REVERT: G   42 GLU cc_start: 0.8701 (pp20) cc_final: 0.8292 (pp20)
REVERT: G   48 ASP cc_start: 0.8786 (t0) cc_final: 0.8437 (t0)
REVERT: A  271 ASN cc_start: 0.9241 (m-40) cc_final: 0.8888 (m110)
REVERT: A  284 THR cc_start: 0.9613 (OUTLIER) cc_final: 0.9261 (t)
REVERT: A  330 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8805 (mp0)
REVERT: N    5 GLN cc_start: 0.8745 (tp40) cc_final: 0.8495 (tp40)
REVERT: N   18 LEU cc_start: 0.8322 (mt) cc_final: 0.7936 (mp)
REVERT: N   38 ARG cc_start: 0.8885 (ptt180) cc_final: 0.8662 (ptm160)
REVERT: N   39 GLN cc_start: 0.9297 (tt0) cc_final: 0.8604 (tp40)
REVERT: N   73 ASP cc_start: 0.8282 (t0) cc_final: 0.7677 (t0)
REVERT: N   76 LYS cc_start: 0.9401 (ptmm) cc_final: 0.9141 (ptmm)
REVERT: N   80 TYR cc_start: 0.8514 (m-80) cc_final: 0.8197 (m-80)
REVERT: N   99 CYS cc_start: 0.9233 (m) cc_final: 0.8627 (m)
REVERT: B   15 LYS cc_start: 0.9646 (ttmt) cc_final: 0.9296 (tptp)
REVERT: B   23 LYS cc_start: 0.9490 (tppt) cc_final: 0.9195 (mtmt)
REVERT: B   38 ASP cc_start: 0.9267 (t0) cc_final: 0.9002 (p0)
REVERT: B  254 ASP cc_start: 0.9181 (t70) cc_final: 0.8741 (t70)
REVERT: B  277 SER cc_start: 0.9193 (t) cc_final: 0.8986 (m)
REVERT: B  292 PHE cc_start: 0.9079 (m-10) cc_final: 0.8624 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 147
  average time/residue: 0.2492
  time to fit residues: 47.3164
Evaluate side-chains
  141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  172 SER
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 50 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 46 optimal weight:    0.4980
   chunk 73 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 92 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3491 r_free = 0.3491 target = 0.082838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.061513 restraints weight = 20962.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 3.50
r_work: 0.2880 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.4371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8187  Z= 0.168
  Angle     :  0.588   9.361  11092  Z= 0.296
  Chirality :  0.041   0.160   1275
  Planarity :  0.004   0.038   1406
  Dihedral  :  4.094  21.032   1122
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.53 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.27), residues: 1010
  helix:  2.78 (0.25), residues: 398
  sheet:  0.55 (0.35), residues: 193
  loop :  0.07 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.011   0.001   ARG B 129 

********************** 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
  149 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.976 
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: 0.9466 (mm-30) cc_final: 0.9250 (mm-30)
REVERT: G   21 MET cc_start: 0.9348 (mmm) cc_final: 0.9116 (mmm)
REVERT: G   42 GLU cc_start: 0.8705 (pp20) cc_final: 0.8302 (pp20)
REVERT: G   48 ASP cc_start: 0.8743 (t0) cc_final: 0.8388 (t0)
REVERT: A  271 ASN cc_start: 0.9209 (m-40) cc_final: 0.8830 (m110)
REVERT: A  284 THR cc_start: 0.9628 (OUTLIER) cc_final: 0.9292 (t)
REVERT: A  330 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8786 (mp0)
REVERT: N    5 GLN cc_start: 0.8733 (tp40) cc_final: 0.8474 (tp40)
REVERT: N   18 LEU cc_start: 0.8313 (mt) cc_final: 0.7896 (mp)
REVERT: N   38 ARG cc_start: 0.8882 (ptt180) cc_final: 0.8551 (ptm160)
REVERT: N   39 GLN cc_start: 0.9322 (tt0) cc_final: 0.8607 (tp40)
REVERT: N   73 ASP cc_start: 0.8330 (t0) cc_final: 0.7862 (t0)
REVERT: N   76 LYS cc_start: 0.9363 (ptmm) cc_final: 0.9006 (ptmm)
REVERT: N   99 CYS cc_start: 0.9213 (m) cc_final: 0.8641 (m)
REVERT: B   10 GLU cc_start: 0.9581 (tt0) cc_final: 0.9272 (mt-10)
REVERT: B   15 LYS cc_start: 0.9648 (ttmt) cc_final: 0.9303 (tptp)
REVERT: B   38 ASP cc_start: 0.9241 (t0) cc_final: 0.9011 (p0)
REVERT: B  254 ASP cc_start: 0.9120 (t70) cc_final: 0.8813 (t0)
REVERT: B  292 PHE cc_start: 0.9021 (m-10) cc_final: 0.8560 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 146
  average time/residue: 0.2521
  time to fit residues: 47.6819
Evaluate side-chains
  141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  172 SER
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 66 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0970
   chunk 17 optimal weight:    4.9990
   overall best weight:    2.6184

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

Flipped N/Q/H residues before XYZ refinement:
N 120 GLN
** R  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.081696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.059186 restraints weight = 21828.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 3.58
r_work: 0.2778 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8187  Z= 0.310
  Angle     :  0.647   8.911  11092  Z= 0.330
  Chirality :  0.043   0.167   1275
  Planarity :  0.004   0.054   1406
  Dihedral  :  4.374  21.451   1122
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.12 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.27), residues: 1010
  helix:  2.57 (0.26), residues: 405
  sheet:  0.40 (0.35), residues: 195
  loop : -0.05 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.016   0.001   PHE G  61 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.011   0.001   ARG B 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4052.65 seconds
wall clock time: 72 minutes 57.59 seconds (4377.59 seconds total)