Starting phenix.real_space_refine
on Tue Sep 24 19:50:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/09_2024/7yk6_33888.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/09_2024/7yk6_33888.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/09_2024/7yk6_33888.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/09_2024/7yk6_33888.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/09_2024/7yk6_33888.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/09_2024/7yk6_33888.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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
     S      55      5.16       5
     Cl      1      4.86       5
     C    5575      2.51       5
     N    1497      2.21       5
     O    1608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 8736
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "I"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1694
          Classifications: {'peptide': 211}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 208}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2220
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "S"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1771
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'IYF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.44, per 1000 atoms: 0.62
  Number of scatterers: 8736
  At special positions: 0
  Unit cell: (91.035, 118.881, 131.733, 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)
     Cl      1     17.00
     S      55     16.00
     O    1608      8.00
     N    1497      7.00
     C    5575      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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: 2.35
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2084

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      37.6% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 4.148A  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 'I' and resid 6 through 30
    Processing helix  chain 'I' and resid 45 through 53
      removed outlier: 4.331A  pdb=" N   MET I  53 " --> pdb=" O   ILE I  49 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 209 through 214
      removed outlier: 4.172A  pdb=" N   HIS I 214 " --> pdb=" O   LYS I 210 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 215 through 217
      No H-bonds generated for 'chain 'I' and resid 215 through 217'
    Processing helix  chain 'I' and resid 243 through 256
    Processing helix  chain 'I' and resid 271 through 282
      removed outlier: 3.601A  pdb=" N   PHE I 275 " --> pdb=" O   LYS I 271 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLU I 277 " --> pdb=" O   ASP I 273 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   THR I 280 " --> pdb=" O   GLU I 276 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 283 through 287
    Processing helix  chain 'I' and resid 299 through 312
      removed outlier: 3.683A  pdb=" N   ASN I 312 " --> pdb=" O   PHE I 308 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 331 through 352
      removed outlier: 3.789A  pdb=" N   PHE I 335 " --> pdb=" O   LYS I 331 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL I 336 " --> pdb=" O   ASN I 332 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 64
    Processing helix  chain 'R' and resid 75 through 103
      removed outlier: 4.381A  pdb=" N   PHE R  79 " --> pdb=" O   PRO R  75 " (cutoff:3.500A)
      Proline residue:  R  95  - end of helix
    Processing helix  chain 'R' and resid 110 through 144
      removed outlier: 4.266A  pdb=" N   LYS R 115 " --> pdb=" O   GLY R 111 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   MET R 116 " --> pdb=" O   ALA R 112 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   THR R 119 " --> pdb=" O   LYS R 115 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 180
      Proline residue:  R 175  - end of helix
    Processing helix  chain 'R' and resid 202 through 212
    Processing helix  chain 'R' and resid 213 through 233
      removed outlier: 3.662A  pdb=" N   ARG R 233 " --> pdb=" O   ALA R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 237 through 275
      removed outlier: 3.876A  pdb=" N   ARG R 242 " --> pdb=" O   ARG R 238 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   VAL R 243 " --> pdb=" O   GLN R 239 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL R 244 " --> pdb=" O   ASP R 240 " (cutoff:3.500A)
      Proline residue:  R 261  - end of helix
    Processing helix  chain 'R' and resid 282 through 300
      Proline residue:  R 292  - end of helix
      removed outlier: 3.626A  pdb=" N   SER R 300 " --> pdb=" O   CYS R 296 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 310
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 320
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.601A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.116A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.756A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 74 through 77
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.767A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 25
      removed outlier: 3.525A  pdb=" N   CYS T  25 " --> pdb=" O   ALA T  21 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 29 through 35
    Processing sheet with id=AA1, first strand: chain 'I' and resid 186 through 191
      removed outlier: 3.751A  pdb=" N   ALA I 221 " --> pdb=" O   LYS I  35 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   CYS I 225 " --> pdb=" O   LEU I  39 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ILE I 265 " --> pdb=" O   TYR I 321 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   HIS I 323 " --> pdb=" O   ILE I 265 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   LEU I 267 " --> pdb=" O   HIS I 323 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 4 through 7
      removed outlier: 3.573A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU S  20 " --> pdb=" O   LEU S  81 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR S  78 " --> pdb=" O   ASP S  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 11 through 12
    Processing sheet with id=AA4, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.506A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 141
      removed outlier: 3.552A  pdb=" N   ILE S 216 " --> pdb=" O   VAL S 155 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.981A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'T' and resid 46 through 52
      removed outlier: 3.630A  pdb=" N   ARG T  46 " --> pdb=" O   ASN T 340 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASN T 340 " --> pdb=" O   ARG T  46 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE T 338 " --> pdb=" O   ARG T  48 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   THR T  50 " --> pdb=" O   LEU T 336 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   LEU T 336 " --> pdb=" O   THR T  50 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   PHE T 335 " --> pdb=" O   SER T 331 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER T 331 " --> pdb=" O   PHE T 335 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'T' and resid 58 through 63
      removed outlier: 6.957A  pdb=" N   ALA T  73 " --> pdb=" O   TYR T  59 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   MET T  61 " --> pdb=" O   VAL T  71 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL T  71 " --> pdb=" O   MET T  61 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   TRP T  63 " --> pdb=" O   LEU T  69 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   LEU T  69 " --> pdb=" O   TRP T  63 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER T  74 " --> pdb=" O   LYS T  78 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LYS T  78 " --> pdb=" O   SER T  74 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   LEU T  79 " --> pdb=" O   ALA T  92 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ALA T  92 " --> pdb=" O   LEU T  79 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE T  81 " --> pdb=" O   VAL T  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'T' and resid 100 through 105
      removed outlier: 3.795A  pdb=" N   GLY T 115 " --> pdb=" O   THR T 102 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   CYS T 121 " --> pdb=" O   GLU T 138 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   GLU T 138 " --> pdb=" O   CYS T 121 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ILE T 123 " --> pdb=" O   SER T 136 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG T 134 " --> pdb=" O   ASN T 125 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'T' and resid 146 through 151
      removed outlier: 6.760A  pdb=" N   SER T 160 " --> pdb=" O   SER T 147 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   CYS T 149 " --> pdb=" O   VAL T 158 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL T 158 " --> pdb=" O   CYS T 149 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   PHE T 151 " --> pdb=" O   GLN T 156 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   GLN T 156 " --> pdb=" O   PHE T 151 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE T 157 " --> pdb=" O   TRP T 169 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   THR T 165 " --> pdb=" O   SER T 161 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR T 178 " --> pdb=" O   LEU T 168 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ASP T 170 " --> pdb=" O   GLN T 176 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   GLN T 176 " --> pdb=" O   ASP T 170 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'T' and resid 187 through 192
      removed outlier: 6.921A  pdb=" N   GLY T 202 " --> pdb=" O   MET T 188 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   LEU T 190 " --> pdb=" O   VAL T 200 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL T 200 " --> pdb=" O   LEU T 190 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   LEU T 192 " --> pdb=" O   LEU T 198 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   LEU T 198 " --> pdb=" O   LEU T 192 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   SER T 207 " --> pdb=" O   ALA T 203 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLN T 220 " --> pdb=" O   LEU T 210 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'T' and resid 229 through 234
      removed outlier: 4.079A  pdb=" N   THR T 249 " --> pdb=" O   SER T 245 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   CYS T 250 " --> pdb=" O   THR T 263 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   THR T 263 " --> pdb=" O   CYS T 250 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LEU T 252 " --> pdb=" O   LEU T 261 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLN T 259 " --> pdb=" O   ASP T 254 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'T' and resid 276 through 278

    400 hydrogen bonds defined for protein.
    1164 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: 2.43

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2811
        1.34 -     1.46: 2135
        1.46 -     1.58: 3902
        1.58 -     1.70: 0
        1.70 -     1.82: 79
  Bond restraints: 8927
  Sorted by residual:
  bond pdb=" C10 IYF R 601 "
       pdb=" N11 IYF R 601 "
    ideal  model  delta    sigma   weight residual
    1.274  1.475 -0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" C27 IYF R 601 "
       pdb=" N26 IYF R 601 "
    ideal  model  delta    sigma   weight residual
    1.374  1.503 -0.129 2.00e-02 2.50e+03 4.14e+01
  bond pdb=" C25 IYF R 601 "
       pdb=" C9  IYF R 601 "
    ideal  model  delta    sigma   weight residual
    1.376  1.271  0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" C10 IYF R 601 "
       pdb=" C9  IYF R 601 "
    ideal  model  delta    sigma   weight residual
    1.444  1.549 -0.105 2.00e-02 2.50e+03 2.74e+01
  bond pdb=" C13 IYF R 601 "
       pdb=" N12 IYF R 601 "
    ideal  model  delta    sigma   weight residual
    1.380  1.483 -0.103 2.00e-02 2.50e+03 2.64e+01
  ... (remaining 8922 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.74: 12058
        3.74 -     7.47: 39
        7.47 -    11.21: 9
       11.21 -    14.94: 1
       14.94 -    18.68: 2
  Bond angle restraints: 12109
  Sorted by residual:
  angle pdb=" N   PHE R 324 "
        pdb=" CA  PHE R 324 "
        pdb=" C   PHE R 324 "
      ideal   model   delta    sigma   weight residual
     112.23  104.25    7.98 1.26e+00 6.30e-01 4.01e+01
  angle pdb=" C25 IYF R 601 "
        pdb=" C9  IYF R 601 "
        pdb=" C8  IYF R 601 "
      ideal   model   delta    sigma   weight residual
     106.34  125.02  -18.68 3.00e+00 1.11e-01 3.88e+01
  angle pdb=" C13 IYF R 601 "
        pdb=" N15 IYF R 601 "
        pdb=" C16 IYF R 601 "
      ideal   model   delta    sigma   weight residual
     126.12  110.40   15.72 3.00e+00 1.11e-01 2.75e+01
  angle pdb=" C9  IYF R 601 "
        pdb=" C10 IYF R 601 "
        pdb=" N11 IYF R 601 "
      ideal   model   delta    sigma   weight residual
     121.60  110.73   10.87 3.00e+00 1.11e-01 1.31e+01
  angle pdb=" C   LEU R 193 "
        pdb=" N   ARG R 194 "
        pdb=" CA  ARG R 194 "
      ideal   model   delta    sigma   weight residual
     121.54  114.92    6.62 1.91e+00 2.74e-01 1.20e+01
  ... (remaining 12104 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 4714
       17.20 -    34.41: 422
       34.41 -    51.61: 89
       51.61 -    68.82: 12
       68.82 -    86.02: 13
  Dihedral angle restraints: 5250
    sinusoidal: 2021
      harmonic: 3229
  Sorted by residual:
  dihedral pdb=" CA  TRP R 200 "
           pdb=" C   TRP R 200 "
           pdb=" N   LEU R 201 "
           pdb=" CA  LEU R 201 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.18  -27.82     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  LEU R 193 "
           pdb=" C   LEU R 193 "
           pdb=" N   ARG R 194 "
           pdb=" CA  ARG R 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.66  -25.34     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  ARG R 198 "
           pdb=" C   ARG R 198 "
           pdb=" N   TYR R 199 "
           pdb=" CA  TYR R 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.23   22.77     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 5247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1210
       0.072 -    0.144: 160
       0.144 -    0.216: 3
       0.216 -    0.288: 0
       0.288 -    0.360: 1
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" CA  THR R 323 "
            pdb=" N   THR R 323 "
            pdb=" C   THR R 323 "
            pdb=" CB  THR R 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CA  PHE R 324 "
            pdb=" N   PHE R 324 "
            pdb=" C   PHE R 324 "
            pdb=" CB  PHE R 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.58e-01
  chirality pdb=" CA  ARG I  32 "
            pdb=" N   ARG I  32 "
            pdb=" C   ARG I  32 "
            pdb=" CB  ARG I  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.03e-01
  ... (remaining 1371 not shown)

  Planarity restraints: 1528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C13 IYF R 601 "   -0.127 2.00e-02 2.50e+03   3.79e-01 2.15e+03
        pdb=" C16 IYF R 601 "    0.554 2.00e-02 2.50e+03
        pdb=" N11 IYF R 601 "    0.318 2.00e-02 2.50e+03
        pdb=" N12 IYF R 601 "   -0.318 2.00e-02 2.50e+03
        pdb=" N14 IYF R 601 "    0.136 2.00e-02 2.50e+03
        pdb=" N15 IYF R 601 "   -0.563 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 IYF R 601 "    0.259 2.00e-02 2.50e+03   2.69e-01 7.23e+02
        pdb=" C9  IYF R 601 "   -0.255 2.00e-02 2.50e+03
        pdb=" N11 IYF R 601 "    0.278 2.00e-02 2.50e+03
        pdb=" N12 IYF R 601 "   -0.282 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL S 147 "    0.077 5.00e-02 4.00e+02   1.15e-01 2.11e+01
        pdb=" N   PRO S 148 "   -0.199 5.00e-02 4.00e+02
        pdb=" CA  PRO S 148 "    0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO S 148 "    0.061 5.00e-02 4.00e+02
  ... (remaining 1525 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 191
        2.68 -     3.24: 8542
        3.24 -     3.79: 13454
        3.79 -     4.35: 17695
        4.35 -     4.90: 29830
  Nonbonded interactions: 69712
  Sorted by model distance:
  nonbonded pdb=" O   THR R 282 "
            pdb=" OG1 THR R 285 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OG  SER T 245 "
            pdb=" OD1 ASP T 247 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER T 161 "
            pdb=" OD1 ASP T 163 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" OG  SER T 331 "
            pdb=" OD1 ASP T 333 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OD1 ASP T 153 "
            pdb=" N   ASP T 154 "
     model   vdw
     2.207 3.120
  ... (remaining 69707 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:             0.920
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.710
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
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      :  0.006   0.201   8927  Z= 0.397
  Angle     :  0.734  18.678  12109  Z= 0.380
  Chirality :  0.046   0.360   1374
  Planarity :  0.013   0.379   1528
  Dihedral  : 14.225  86.020   3160
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.46 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.85 %
    Favored  : 98.93 %
  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: -0.18 (0.26), residues: 1098
  helix:  1.79 (0.28), residues: 358
  sheet: -0.56 (0.32), residues: 297
  loop : -1.38 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP T 169 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.013   0.002   PHE T 253 
 TYR   0.027   0.002   TYR S 235 
 ARG   0.008   0.001   ARG T 129 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 195
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
REVERT: I   17 LYS cc_start: 0.7556 (mtpt) cc_final: 0.7344 (mtpt)
REVERT: I   29 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7825 (ttmm)
REVERT: I   38 LEU cc_start: 0.8082 (tt) cc_final: 0.7827 (tt)
REVERT: R  107 TRP cc_start: 0.5507 (t-100) cc_final: 0.5071 (t-100)
REVERT: T   61 MET cc_start: 0.7881 (ppp) cc_final: 0.7266 (ppp)
REVERT: T  150 ARG cc_start: 0.8382 (mmt-90) cc_final: 0.8049 (mpt180)
REVERT: T  230 ASN cc_start: 0.7899 (m110) cc_final: 0.7678 (m-40)
  outliers start: 2
  outliers final: 1
  residues processed: 197
  average time/residue: 0.2474
  time to fit residues: 63.8667
Evaluate side-chains
  178 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  323 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** R  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 287 GLN
T  62 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.0956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8927  Z= 0.240
  Angle     :  0.661  20.716  12109  Z= 0.327
  Chirality :  0.044   0.149   1374
  Planarity :  0.005   0.073   1528
  Dihedral  :  6.829  85.618   1217
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.10 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.98 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.15 (0.26), residues: 1098
  helix:  1.96 (0.28), residues: 362
  sheet: -0.12 (0.32), residues: 296
  loop : -1.34 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 268 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.002   PHE I 251 
 TYR   0.013   0.001   TYR S 235 
 ARG   0.005   0.000   ARG T 251 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 215
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: I    9 ASP cc_start: 0.7259 (m-30) cc_final: 0.7040 (m-30)
REVERT: I   17 LYS cc_start: 0.7581 (mtpt) cc_final: 0.7341 (mtpt)
REVERT: I   25 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6889 (mm-30)
REVERT: I   29 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7811 (ttmm)
REVERT: I   38 LEU cc_start: 0.8094 (tt) cc_final: 0.7800 (tt)
REVERT: I   39 LEU cc_start: 0.8035 (mt) cc_final: 0.7831 (mm)
REVERT: I  210 LYS cc_start: 0.8187 (tmmt) cc_final: 0.7930 (tmmt)
REVERT: R  192 LEU cc_start: 0.7931 (tp) cc_final: 0.7706 (tp)
REVERT: R  208 ARG cc_start: 0.8142 (tmm-80) cc_final: 0.7784 (tmm-80)
REVERT: S   79 LEU cc_start: 0.7866 (tp) cc_final: 0.7661 (tp)
REVERT: T   34 THR cc_start: 0.7945 (t) cc_final: 0.7583 (t)
REVERT: T   61 MET cc_start: 0.7881 (ppp) cc_final: 0.7244 (ppp)
REVERT: T   86 THR cc_start: 0.8676 (p) cc_final: 0.8463 (p)
REVERT: T  150 ARG cc_start: 0.8419 (mmt-90) cc_final: 0.8123 (mpt180)
REVERT: T  189 SER cc_start: 0.8345 (p) cc_final: 0.8041 (t)
REVERT: T  230 ASN cc_start: 0.7749 (m110) cc_final: 0.7468 (m-40)
REVERT: T  258 ASP cc_start: 0.7589 (t0) cc_final: 0.7118 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 218
  average time/residue: 0.2335
  time to fit residues: 67.2359
Evaluate side-chains
  214 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 206
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain T residue   65 THR
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  263 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** R  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8927  Z= 0.245
  Angle     :  0.600  14.861  12109  Z= 0.305
  Chirality :  0.044   0.151   1374
  Planarity :  0.005   0.059   1528
  Dihedral  :  6.583  89.184   1216
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.54 %
    Favored  : 84.65 %
  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:  0.18 (0.26), residues: 1098
  helix:  1.94 (0.28), residues: 362
  sheet: -0.03 (0.32), residues: 294
  loop : -1.34 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 268 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.014   0.001   PHE S  29 
 TYR   0.013   0.001   TYR S 235 
 ARG   0.005   0.000   ARG T  49 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 212
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   25 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6874 (mm-30)
REVERT: I   29 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7888 (ttmm)
REVERT: I   38 LEU cc_start: 0.8137 (tt) cc_final: 0.7828 (tt)
REVERT: I   53 MET cc_start: -0.0136 (pmm) cc_final: -0.1887 (pmm)
REVERT: I  210 LYS cc_start: 0.8221 (tmmt) cc_final: 0.7975 (tmmt)
REVERT: R  107 TRP cc_start: 0.5758 (t-100) cc_final: 0.5285 (t-100)
REVERT: R  208 ARG cc_start: 0.8149 (tmm-80) cc_final: 0.7792 (tmm-80)
REVERT: S   59 TYR cc_start: 0.7801 (m-10) cc_final: 0.7571 (m-80)
REVERT: T   34 THR cc_start: 0.7976 (t) cc_final: 0.7629 (t)
REVERT: T   61 MET cc_start: 0.7869 (ppp) cc_final: 0.7356 (ppp)
REVERT: T   86 THR cc_start: 0.8663 (p) cc_final: 0.8425 (p)
REVERT: T  189 SER cc_start: 0.8335 (p) cc_final: 0.8057 (t)
REVERT: T  230 ASN cc_start: 0.7823 (m110) cc_final: 0.7528 (m-40)
REVERT: T  239 ASN cc_start: 0.7878 (m-40) cc_final: 0.7613 (m-40)
REVERT: T  258 ASP cc_start: 0.7668 (t0) cc_final: 0.7078 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 218
  average time/residue: 0.2410
  time to fit residues: 68.9535
Evaluate side-chains
  224 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 211
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain I residue   26 ASP
Chi-restraints excluded: chain I residue  315 LYS
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain T residue   12 GLU
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  263 THR
Chi-restraints excluded: chain T residue  270 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
I 270 ASN
** R  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8927  Z= 0.237
  Angle     :  0.575  11.274  12109  Z= 0.294
  Chirality :  0.043   0.153   1374
  Planarity :  0.004   0.057   1528
  Dihedral  :  6.499  89.780   1216
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.83 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.14 %
    Favored  : 82.09 %
  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:  0.21 (0.26), residues: 1098
  helix:  1.98 (0.28), residues: 361
  sheet: -0.05 (0.32), residues: 300
  loop : -1.30 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 268 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.014   0.001   PHE S  29 
 TYR   0.013   0.001   TYR S 190 
 ARG   0.004   0.000   ARG T  48 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 215
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  198 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7324 (ttmm)
REVERT: I  210 LYS cc_start: 0.8205 (tmmt) cc_final: 0.8004 (tmmt)
REVERT: I  220 THR cc_start: 0.8310 (m) cc_final: 0.8109 (m)
REVERT: R  107 TRP cc_start: 0.5791 (t-100) cc_final: 0.5322 (t-100)
REVERT: R  125 VAL cc_start: 0.7240 (OUTLIER) cc_final: 0.6586 (m)
REVERT: R  192 LEU cc_start: 0.7959 (tp) cc_final: 0.7756 (tp)
REVERT: S   45 LEU cc_start: 0.8360 (mt) cc_final: 0.8148 (mp)
REVERT: T   34 THR cc_start: 0.7985 (t) cc_final: 0.7645 (t)
REVERT: T   50 THR cc_start: 0.8205 (m) cc_final: 0.7905 (t)
REVERT: T   61 MET cc_start: 0.7853 (ppp) cc_final: 0.7395 (ppp)
REVERT: T   86 THR cc_start: 0.8682 (p) cc_final: 0.8421 (p)
REVERT: T  189 SER cc_start: 0.8334 (p) cc_final: 0.8056 (t)
REVERT: T  230 ASN cc_start: 0.7819 (m110) cc_final: 0.7491 (m-40)
REVERT: T  239 ASN cc_start: 0.7892 (m-40) cc_final: 0.7637 (m-40)
REVERT: T  258 ASP cc_start: 0.7731 (t0) cc_final: 0.7099 (t0)
  outliers start: 26
  outliers final: 16
  residues processed: 226
  average time/residue: 0.2500
  time to fit residues: 74.6277
Evaluate side-chains
  227 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 210
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain I residue  258 LYS
Chi-restraints excluded: chain I residue  315 LYS
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain T residue   12 GLU
Chi-restraints excluded: chain T residue   65 THR
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  263 THR
Chi-restraints excluded: chain T residue  270 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0000
   chunk 43 optimal weight:    0.5980
   chunk 90 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** R  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8927  Z= 0.306
  Angle     :  0.610  11.443  12109  Z= 0.312
  Chirality :  0.045   0.159   1374
  Planarity :  0.004   0.057   1528
  Dihedral  :  6.543  87.076   1216
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.84 %
    Favored  : 80.28 %
  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:  0.12 (0.26), residues: 1098
  helix:  1.82 (0.27), residues: 367
  sheet: -0.06 (0.32), residues: 299
  loop : -1.34 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  47 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.014   0.001   PHE T 253 
 TYR   0.017   0.002   TYR S 190 
 ARG   0.011   0.000   ARG R  39 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 214
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   38 MET cc_start: 0.7912 (ttp) cc_final: 0.7705 (ttm)
REVERT: I    9 ASP cc_start: 0.7295 (m-30) cc_final: 0.7010 (m-30)
REVERT: I  210 LYS cc_start: 0.8171 (tmmt) cc_final: 0.7968 (tmmt)
REVERT: R  107 TRP cc_start: 0.5832 (t-100) cc_final: 0.5268 (t-100)
REVERT: R  125 VAL cc_start: 0.7242 (OUTLIER) cc_final: 0.6537 (m)
REVERT: R  192 LEU cc_start: 0.8001 (tp) cc_final: 0.7770 (tp)
REVERT: R  208 ARG cc_start: 0.8130 (tmm-80) cc_final: 0.7881 (tmm-80)
REVERT: T   50 THR cc_start: 0.8193 (m) cc_final: 0.7914 (t)
REVERT: T   61 MET cc_start: 0.7910 (ppp) cc_final: 0.7443 (ppp)
REVERT: T  150 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.8183 (mpt180)
REVERT: T  189 SER cc_start: 0.8386 (p) cc_final: 0.8121 (t)
REVERT: T  230 ASN cc_start: 0.7839 (m110) cc_final: 0.7502 (m110)
REVERT: T  239 ASN cc_start: 0.7922 (m-40) cc_final: 0.7665 (m-40)
REVERT: T  258 ASP cc_start: 0.7769 (t0) cc_final: 0.6983 (t0)
  outliers start: 27
  outliers final: 17
  residues processed: 227
  average time/residue: 0.2378
  time to fit residues: 71.2762
Evaluate side-chains
  230 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 212
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain I residue  258 LYS
Chi-restraints excluded: chain I residue  315 LYS
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain T residue   12 GLU
Chi-restraints excluded: chain T residue   65 THR
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  198 LEU
Chi-restraints excluded: chain T residue  263 THR
Chi-restraints excluded: chain T residue  270 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 95 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** R  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 194 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8927  Z= 0.317
  Angle     :  0.628  16.819  12109  Z= 0.317
  Chirality :  0.045   0.185   1374
  Planarity :  0.004   0.056   1528
  Dihedral  :  6.527  84.548   1216
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.74 %
    Favored  : 80.28 %
  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:  0.10 (0.26), residues: 1098
  helix:  1.65 (0.27), residues: 373
  sheet:  0.01 (0.32), residues: 297
  loop : -1.31 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.015   0.001   PHE T 253 
 TYR   0.017   0.002   TYR S 190 
 ARG   0.005   0.000   ARG T  48 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  210 LYS cc_start: 0.8255 (tmmt) cc_final: 0.8044 (tmmt)
REVERT: R  107 TRP cc_start: 0.5875 (t-100) cc_final: 0.5323 (t-100)
REVERT: R  125 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6532 (m)
REVERT: R  192 LEU cc_start: 0.8040 (tp) cc_final: 0.7801 (tp)
REVERT: T   22 ARG cc_start: 0.7947 (mtt-85) cc_final: 0.7673 (mtm-85)
REVERT: T   50 THR cc_start: 0.8201 (m) cc_final: 0.7946 (t)
REVERT: T   61 MET cc_start: 0.7924 (ppp) cc_final: 0.7476 (ppp)
REVERT: T  150 ARG cc_start: 0.8458 (mmt-90) cc_final: 0.8192 (mpt180)
REVERT: T  189 SER cc_start: 0.8437 (p) cc_final: 0.8110 (t)
REVERT: T  230 ASN cc_start: 0.7837 (m110) cc_final: 0.7497 (m-40)
REVERT: T  239 ASN cc_start: 0.7920 (m-40) cc_final: 0.7668 (m-40)
REVERT: T  258 ASP cc_start: 0.7801 (t0) cc_final: 0.6874 (t0)
REVERT: T  290 ASP cc_start: 0.7381 (m-30) cc_final: 0.7078 (m-30)
  outliers start: 28
  outliers final: 20
  residues processed: 233
  average time/residue: 0.2327
  time to fit residues: 71.7050
Evaluate side-chains
  238 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain I residue  258 LYS
Chi-restraints excluded: chain I residue  315 LYS
Chi-restraints excluded: chain I residue  322 THR
Chi-restraints excluded: chain R residue  114 CYS
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain T residue   12 GLU
Chi-restraints excluded: chain T residue   65 THR
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  217 MET
Chi-restraints excluded: chain T residue  263 THR
Chi-restraints excluded: chain T residue  270 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 77 optimal weight:    8.9990
   chunk 89 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 65 optimal weight:    0.1980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** R  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8927  Z= 0.241
  Angle     :  0.609  14.911  12109  Z= 0.306
  Chirality :  0.044   0.187   1374
  Planarity :  0.004   0.054   1528
  Dihedral  :  6.431  83.732   1216
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.55 %
    Favored  : 78.14 %
  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:  0.12 (0.26), residues: 1098
  helix:  1.62 (0.27), residues: 376
  sheet:  0.10 (0.32), residues: 292
  loop : -1.32 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 268 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.014   0.001   PHE T 253 
 TYR   0.015   0.001   TYR S 190 
 ARG   0.006   0.000   ARG R  39 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  210 LYS cc_start: 0.8195 (tmmt) cc_final: 0.7972 (tmmt)
REVERT: I  331 LYS cc_start: 0.7920 (ptpp) cc_final: 0.7684 (ptpp)
REVERT: I  346 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7346 (ttpt)
REVERT: R  107 TRP cc_start: 0.5844 (t-100) cc_final: 0.5226 (t-100)
REVERT: R  125 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6547 (m)
REVERT: R  192 LEU cc_start: 0.8001 (tp) cc_final: 0.7765 (tp)
REVERT: R  208 ARG cc_start: 0.8074 (tmm-80) cc_final: 0.7808 (tmm-80)
REVERT: T   22 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7624 (mtm-85)
REVERT: T   50 THR cc_start: 0.8167 (m) cc_final: 0.7916 (t)
REVERT: T   61 MET cc_start: 0.7883 (ppp) cc_final: 0.7427 (ppp)
REVERT: T  150 ARG cc_start: 0.8440 (mmt-90) cc_final: 0.8191 (mpt180)
REVERT: T  176 GLN cc_start: 0.8065 (mm110) cc_final: 0.7817 (mm110)
REVERT: T  189 SER cc_start: 0.8470 (p) cc_final: 0.8121 (t)
REVERT: T  230 ASN cc_start: 0.7828 (m110) cc_final: 0.7488 (m-40)
REVERT: T  239 ASN cc_start: 0.7914 (m-40) cc_final: 0.7661 (m-40)
REVERT: T  258 ASP cc_start: 0.7800 (t0) cc_final: 0.6885 (t0)
REVERT: T  290 ASP cc_start: 0.7278 (m-30) cc_final: 0.6978 (m-30)
  outliers start: 31
  outliers final: 19
  residues processed: 219
  average time/residue: 0.2358
  time to fit residues: 67.6942
Evaluate side-chains
  224 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 204
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain I residue   53 MET
Chi-restraints excluded: chain I residue  258 LYS
Chi-restraints excluded: chain I residue  315 LYS
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  114 CYS
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain T residue   12 GLU
Chi-restraints excluded: chain T residue   65 THR
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  234 PHE
Chi-restraints excluded: chain T residue  263 THR
Chi-restraints excluded: chain T residue  270 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 20 optimal weight:    8.9990
   chunk 67 optimal weight:    0.0020
   chunk 72 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0670
   chunk 101 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.4126

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

Flipped N/Q/H residues before XYZ refinement:
** R  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8927  Z= 0.183
  Angle     :  0.589  17.013  12109  Z= 0.294
  Chirality :  0.043   0.189   1374
  Planarity :  0.004   0.052   1528
  Dihedral  :  6.181  80.768   1216
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.98 %
    Favored  : 78.36 %
  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:  0.22 (0.26), residues: 1098
  helix:  1.73 (0.27), residues: 372
  sheet:  0.07 (0.32), residues: 294
  loop : -1.20 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 268 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.013   0.001   PHE R 283 
 TYR   0.012   0.001   TYR S 235 
 ARG   0.006   0.000   ARG R  39 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  210 LYS cc_start: 0.8228 (tmmt) cc_final: 0.7995 (tmmt)
REVERT: I  346 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7357 (ttpt)
REVERT: R  107 TRP cc_start: 0.5781 (t-100) cc_final: 0.5127 (t-100)
REVERT: R  125 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.7006 (t)
REVERT: R  192 LEU cc_start: 0.8009 (tp) cc_final: 0.7755 (tp)
REVERT: T   48 ARG cc_start: 0.7828 (mmt180) cc_final: 0.7588 (mpt180)
REVERT: T   50 THR cc_start: 0.8156 (m) cc_final: 0.7895 (t)
REVERT: T   61 MET cc_start: 0.7866 (ppp) cc_final: 0.7428 (ppp)
REVERT: T   86 THR cc_start: 0.8722 (p) cc_final: 0.8467 (p)
REVERT: T  150 ARG cc_start: 0.8435 (mmt-90) cc_final: 0.8157 (mpt180)
REVERT: T  189 SER cc_start: 0.8479 (p) cc_final: 0.8115 (t)
REVERT: T  198 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7986 (mt)
REVERT: T  230 ASN cc_start: 0.7804 (m110) cc_final: 0.7470 (m-40)
REVERT: T  239 ASN cc_start: 0.7893 (m-40) cc_final: 0.7632 (m-40)
REVERT: T  251 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7683 (mtt90)
REVERT: T  258 ASP cc_start: 0.7788 (t0) cc_final: 0.6978 (t0)
REVERT: T  290 ASP cc_start: 0.7267 (m-30) cc_final: 0.6968 (m-30)
  outliers start: 25
  outliers final: 21
  residues processed: 208
  average time/residue: 0.2474
  time to fit residues: 67.4024
Evaluate side-chains
  224 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 201
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain I residue   53 MET
Chi-restraints excluded: chain I residue  258 LYS
Chi-restraints excluded: chain I residue  315 LYS
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain R residue  279 TRP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain T residue   12 GLU
Chi-restraints excluded: chain T residue   65 THR
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  198 LEU
Chi-restraints excluded: chain T residue  217 MET
Chi-restraints excluded: chain T residue  234 PHE
Chi-restraints excluded: chain T residue  263 THR
Chi-restraints excluded: chain T residue  270 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.2980
   chunk 101 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0970
   chunk 104 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** R  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8927  Z= 0.206
  Angle     :  0.594  16.512  12109  Z= 0.297
  Chirality :  0.043   0.193   1374
  Planarity :  0.004   0.052   1528
  Dihedral  :  6.055  77.472   1216
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.98 %
    Favored  : 78.25 %
  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:  0.25 (0.26), residues: 1098
  helix:  1.76 (0.27), residues: 372
  sheet:  0.10 (0.32), residues: 294
  loop : -1.20 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 268 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.013   0.001   PHE T 234 
 TYR   0.014   0.001   TYR S 190 
 ARG   0.005   0.000   ARG R  39 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   38 LEU cc_start: 0.8275 (tt) cc_final: 0.7891 (tp)
REVERT: I  210 LYS cc_start: 0.8295 (tmmt) cc_final: 0.8064 (tmmt)
REVERT: I  313 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7361 (mmtm)
REVERT: I  346 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7352 (ttpt)
REVERT: R  125 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.7004 (t)
REVERT: R  192 LEU cc_start: 0.8009 (tp) cc_final: 0.7749 (tp)
REVERT: T   32 GLN cc_start: 0.8252 (mt0) cc_final: 0.8044 (mt0)
REVERT: T   48 ARG cc_start: 0.7830 (mmt180) cc_final: 0.7600 (mpt180)
REVERT: T   61 MET cc_start: 0.7882 (ppp) cc_final: 0.7435 (ppp)
REVERT: T   86 THR cc_start: 0.8722 (p) cc_final: 0.8454 (p)
REVERT: T  150 ARG cc_start: 0.8444 (mmt-90) cc_final: 0.8166 (mpt180)
REVERT: T  189 SER cc_start: 0.8471 (p) cc_final: 0.8110 (t)
REVERT: T  198 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8007 (mt)
REVERT: T  230 ASN cc_start: 0.7808 (m110) cc_final: 0.7436 (m-40)
REVERT: T  239 ASN cc_start: 0.7892 (m-40) cc_final: 0.7639 (m-40)
REVERT: T  251 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7701 (mtt90)
REVERT: T  258 ASP cc_start: 0.7748 (t0) cc_final: 0.6906 (t0)
REVERT: T  290 ASP cc_start: 0.7248 (m-30) cc_final: 0.6964 (m-30)
  outliers start: 26
  outliers final: 22
  residues processed: 211
  average time/residue: 0.2320
  time to fit residues: 64.4516
Evaluate side-chains
  224 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 200
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain I residue   53 MET
Chi-restraints excluded: chain I residue  215 CYS
Chi-restraints excluded: chain I residue  315 LYS
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  114 CYS
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain T residue   12 GLU
Chi-restraints excluded: chain T residue   65 THR
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  198 LEU
Chi-restraints excluded: chain T residue  217 MET
Chi-restraints excluded: chain T residue  234 PHE
Chi-restraints excluded: chain T residue  263 THR
Chi-restraints excluded: chain T residue  269 ILE
Chi-restraints excluded: chain T residue  270 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 72 optimal weight:    0.0770
   chunk 109 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0040
   chunk 92 optimal weight:    0.0970
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.1748

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

Flipped N/Q/H residues before XYZ refinement:
R  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8927  Z= 0.151
  Angle     :  0.575  15.897  12109  Z= 0.289
  Chirality :  0.043   0.357   1374
  Planarity :  0.004   0.053   1528
  Dihedral  :  5.781  73.132   1216
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.72 %
    Favored  : 77.93 %
  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:  0.31 (0.26), residues: 1098
  helix:  1.82 (0.27), residues: 370
  sheet:  0.16 (0.32), residues: 290
  loop : -1.17 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 268 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.012   0.001   PHE R 283 
 TYR   0.012   0.001   TYR R 140 
 ARG   0.005   0.000   ARG T 219 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   38 LEU cc_start: 0.8254 (tt) cc_final: 0.7959 (tt)
REVERT: I  210 LYS cc_start: 0.8267 (tmmt) cc_final: 0.8037 (tmmt)
REVERT: I  313 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7334 (mmtm)
REVERT: I  346 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7354 (ttpt)
REVERT: R  192 LEU cc_start: 0.7986 (tp) cc_final: 0.7741 (tp)
REVERT: S   83 MET cc_start: 0.6968 (tmm) cc_final: 0.6602 (tmm)
REVERT: S  217 SER cc_start: 0.8315 (m) cc_final: 0.8059 (p)
REVERT: T   32 GLN cc_start: 0.8119 (mt0) cc_final: 0.7843 (mt0)
REVERT: T   48 ARG cc_start: 0.7771 (mmt180) cc_final: 0.7543 (mpt180)
REVERT: T   61 MET cc_start: 0.7899 (ppp) cc_final: 0.7437 (ppp)
REVERT: T   86 THR cc_start: 0.8693 (p) cc_final: 0.8445 (p)
REVERT: T  150 ARG cc_start: 0.8444 (mmt-90) cc_final: 0.8178 (mpt180)
REVERT: T  176 GLN cc_start: 0.7908 (mm110) cc_final: 0.7612 (mm110)
REVERT: T  189 SER cc_start: 0.8411 (p) cc_final: 0.8072 (t)
REVERT: T  198 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8057 (mt)
REVERT: T  230 ASN cc_start: 0.7733 (m110) cc_final: 0.7382 (m-40)
REVERT: T  239 ASN cc_start: 0.7865 (m-40) cc_final: 0.7517 (m-40)
REVERT: T  258 ASP cc_start: 0.7722 (t0) cc_final: 0.6904 (t0)
REVERT: T  290 ASP cc_start: 0.7208 (m-30) cc_final: 0.6930 (m-30)
  outliers start: 22
  outliers final: 17
  residues processed: 218
  average time/residue: 0.2497
  time to fit residues: 71.4646
Evaluate side-chains
  222 residues out of total 941 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 204
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain I residue   53 MET
Chi-restraints excluded: chain I residue  215 CYS
Chi-restraints excluded: chain I residue  315 LYS
Chi-restraints excluded: chain R residue  254 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain T residue   12 GLU
Chi-restraints excluded: chain T residue   65 THR
Chi-restraints excluded: chain T residue  101 MET
Chi-restraints excluded: chain T residue  135 VAL
Chi-restraints excluded: chain T residue  198 LEU
Chi-restraints excluded: chain T residue  234 PHE
Chi-restraints excluded: chain T residue  263 THR
Chi-restraints excluded: chain T residue  269 ILE
Chi-restraints excluded: chain T residue  270 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0980
   chunk 89 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.152779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.129929 restraints weight = 13616.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.58
r_work: 0.3571 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8927  Z= 0.233
  Angle     :  0.604  16.356  12109  Z= 0.303
  Chirality :  0.044   0.302   1374
  Planarity :  0.004   0.052   1528
  Dihedral  :  5.799  69.920   1216
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.58 %
    Favored  : 77.19 %
  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:  0.29 (0.26), residues: 1098
  helix:  1.80 (0.27), residues: 372
  sheet:  0.10 (0.32), residues: 294
  loop : -1.16 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP T 169 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.014   0.001   PHE T 234 
 TYR   0.014   0.001   TYR S 190 
 ARG   0.011   0.000   ARG T 251 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2347.12 seconds
wall clock time: 42 minutes 19.07 seconds (2539.07 seconds total)