Starting phenix.real_space_refine
on Fri Nov 15 06:47:37 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/11_2024/8hdp_34677.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/11_2024/8hdp_34677.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/11_2024/8hdp_34677.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/11_2024/8hdp_34677.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/11_2024/8hdp_34677.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/11_2024/8hdp_34677.cif"
  }
  resolution = 3.2
  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=   0.004
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: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5280      2.51       5
     N    1430      2.21       5
     O    1519      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8282
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1985
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2594
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 2166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2166
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 11, 'TRANS': 268}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 131
          Unusual residues: {'ADN%rna3p': 1, 'CLR': 4}
          Classifications: {'undetermined': 5}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 4}
  Time building chain proxies: 5.13, per 1000 atoms: 0.62
  Number of scatterers: 8282
  At special positions: 0
  Unit cell: (95.68, 76.96, 130, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1519      8.00
     N    1430      7.00
     C    5280      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  78 " - pdb=" SG  CYS R 171 " 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: 2.42
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      42.8% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 4.267A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 114 through 130
      removed outlier: 3.636A  pdb=" N   GLN A 119 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   GLU A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 156
      removed outlier: 3.511A  pdb=" N   GLY A 156 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.243A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
      removed outlier: 3.537A  pdb=" N   TYR A 170 " --> pdb=" O   PHE A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 203
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.556A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.777A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.702A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.825A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 6 through 35
    Processing helix  chain 'R' and resid 40 through 59
    Processing helix  chain 'R' and resid 59 through 69
    Processing helix  chain 'R' and resid 74 through 109
      removed outlier: 3.583A  pdb=" N   LEU R  81 " --> pdb=" O   GLY R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 117
    Processing helix  chain 'R' and resid 118 through 138
    Processing helix  chain 'R' and resid 138 through 144
      removed outlier: 3.814A  pdb=" N   LEU R 142 " --> pdb=" O   LEU R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 184
    Processing helix  chain 'R' and resid 186 through 191
    Processing helix  chain 'R' and resid 191 through 214
    Processing helix  chain 'R' and resid 225 through 260
      removed outlier: 3.572A  pdb=" N   PHE R 243 " --> pdb=" O   ILE R 239 " (cutoff:3.500A)
      Proline residue:  R 249  - end of helix
    Processing helix  chain 'R' and resid 267 through 291
      removed outlier: 4.472A  pdb=" N   ASN R 273 " --> pdb=" O   LYS R 269 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   SER R 283 " --> pdb=" O   SER R 279 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   VAL R 284 " --> pdb=" O   HIS R 280 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
    Processing helix  chain 'R' and resid 294 through 309
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65
      removed outlier: 6.317A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.605A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.965A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103
      removed outlier: 6.891A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 5.651A  pdb=" N   CYS B 149 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   PHE B 151 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL B 158 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.613A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.809A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.625A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.784A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    436 hydrogen bonds defined for protein.
    1236 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: 2.52

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1448
        1.33 -     1.45: 2236
        1.45 -     1.57: 4701
        1.57 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 8458
  Sorted by residual:
  bond pdb=" C4  ADN R 401 "
       pdb=" C5  ADN R 401 "
    ideal  model  delta    sigma   weight residual
    1.385  1.467 -0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" C5  ADN R 401 "
       pdb=" C6  ADN R 401 "
    ideal  model  delta    sigma   weight residual
    1.408  1.482 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C   MET R 238 "
       pdb=" O   MET R 238 "
    ideal  model  delta    sigma   weight residual
    1.236  1.202  0.033 1.17e-02 7.31e+03 8.14e+00
  bond pdb=" N   TRP R 247 "
       pdb=" CA  TRP R 247 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.84e+00
  bond pdb=" N   GLU R 174 "
       pdb=" CA  GLU R 174 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.27e-02 6.20e+03 6.58e+00
  ... (remaining 8453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.13: 11482
        6.13 -    12.26: 12
       12.26 -    18.38: 1
       18.38 -    24.51: 1
       24.51 -    30.64: 2
  Bond angle restraints: 11498
  Sorted by residual:
  angle pdb=" C17 CLR R 404 "
        pdb=" C13 CLR R 404 "
        pdb=" C18 CLR R 404 "
      ideal   model   delta    sigma   weight residual
     110.18   79.54   30.64 3.00e+00 1.11e-01 1.04e+02
  angle pdb=" C12 CLR R 404 "
        pdb=" C13 CLR R 404 "
        pdb=" C18 CLR R 404 "
      ideal   model   delta    sigma   weight residual
     111.01   81.73   29.28 3.00e+00 1.11e-01 9.52e+01
  angle pdb=" C14 CLR R 404 "
        pdb=" C13 CLR R 404 "
        pdb=" C18 CLR R 404 "
      ideal   model   delta    sigma   weight residual
     112.24   90.75   21.49 3.00e+00 1.11e-01 5.13e+01
  angle pdb=" C12 CLR R 404 "
        pdb=" C13 CLR R 404 "
        pdb=" C17 CLR R 404 "
      ideal   model   delta    sigma   weight residual
     116.52  130.09  -13.57 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" C1' ADN R 401 "
        pdb=" C2' ADN R 401 "
        pdb=" C3' ADN R 401 "
      ideal   model   delta    sigma   weight residual
     101.30  105.27   -3.97 1.00e+00 1.00e+00 1.58e+01
  ... (remaining 11493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.51: 5158
       34.51 -    69.01: 71
       69.01 -   103.52: 5
      103.52 -   138.02: 1
      138.02 -   172.53: 5
  Dihedral angle restraints: 5240
    sinusoidal: 2209
      harmonic: 3031
  Sorted by residual:
  dihedral pdb=" C16 CLR R 404 "
           pdb=" C13 CLR R 404 "
           pdb=" C17 CLR R 404 "
           pdb=" C18 CLR R 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -78.02   94.51 -172.53     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C18 CLR R 404 "
           pdb=" C13 CLR R 404 "
           pdb=" C17 CLR R 404 "
           pdb=" C20 CLR R 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     312.73  144.58  168.15     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" C15 CLR R 404 "
           pdb=" C13 CLR R 404 "
           pdb=" C14 CLR R 404 "
           pdb=" C18 CLR R 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.18  -96.05  165.23     1      3.00e+01 1.11e-03 2.10e+01
  ... (remaining 5237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.383: 1317
       0.383 -    0.766: 1
       0.766 -    1.149: 0
       1.149 -    1.532: 0
       1.532 -    1.914: 2
  Chirality restraints: 1320
  Sorted by residual:
  chirality pdb=" C13 CLR R 404 "
            pdb=" C12 CLR R 404 "
            pdb=" C14 CLR R 404 "
            pdb=" C17 CLR R 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -1.02   -1.91 2.00e-01 2.50e+01 9.16e+01
  chirality pdb=" CG  LEU R   3 "
            pdb=" CB  LEU R   3 "
            pdb=" CD1 LEU R   3 "
            pdb=" CD2 LEU R   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.89   -1.70 2.00e-01 2.50e+01 7.20e+01
  chirality pdb=" CA  GLN R   6 "
            pdb=" N   GLN R   6 "
            pdb=" C   GLN R   6 "
            pdb=" CB  GLN R   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.43 2.00e-01 2.50e+01 4.52e+00
  ... (remaining 1317 not shown)

  Planarity restraints: 1446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 237 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   ALA R 237 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ALA R 237 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   MET R 238 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 173 "    0.010 2.00e-02 2.50e+03   2.14e-02 4.57e+00
        pdb=" C   PHE R 173 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   PHE R 173 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU R 174 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 178 "    0.011 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   PRO R 178 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   PRO R 178 "    0.014 2.00e-02 2.50e+03
        pdb=" N   MET R 179 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1443 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 108
        2.58 -     3.16: 7464
        3.16 -     3.74: 13104
        3.74 -     4.32: 18541
        4.32 -     4.90: 30724
  Nonbonded interactions: 69941
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 170 "
            pdb=" OD2 ASP A 195 "
     model   vdw
     2.006 3.040
  nonbonded pdb=" OG  SER R 235 "
            pdb=" NH2 ARG R 293 "
     model   vdw
     2.022 3.120
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.080 3.120
  nonbonded pdb=" OD1 ASP A 111 "
            pdb=" OG  SER A 113 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OG1 THR R  40 "
            pdb=" OD1 ASN R  43 "
     model   vdw
     2.136 3.040
  ... (remaining 69936 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.130
  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:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
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      :  0.003   0.082   8458  Z= 0.211
  Angle     :  0.755  30.642  11498  Z= 0.343
  Chirality :  0.085   1.914   1320
  Planarity :  0.003   0.041   1446
  Dihedral  : 12.508 172.528   3271
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.04 %
    Favored  : 93.39 %
  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: -1.79 (0.25), residues: 1027
  helix:  0.17 (0.25), residues: 401
  sheet: -2.09 (0.31), residues: 207
  loop : -1.98 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 247 
 HIS   0.005   0.001   HIS R 251 
 PHE   0.014   0.001   PHE R 173 
 TYR   0.005   0.001   TYR R  10 
 ARG   0.002   0.000   ARG A 237 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 289
  time to evaluate  : 1.014 
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: symmetry clash
REVERT: A   62 ILE cc_start: 0.8121 (tt) cc_final: 0.7907 (pt)
REVERT: A  212 TYR cc_start: 0.8614 (m-80) cc_final: 0.7915 (m-80)
REVERT: B    9 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8586 (pp30)
REVERT: B   10 GLU cc_start: 0.8695 (tp30) cc_final: 0.8409 (tp30)
REVERT: B   63 TRP cc_start: 0.8484 (m100) cc_final: 0.8248 (m100)
REVERT: B  171 ILE cc_start: 0.6986 (mp) cc_final: 0.6614 (mm)
REVERT: B  280 LYS cc_start: 0.8845 (tttm) cc_final: 0.8560 (ttpp)
REVERT: B  289 TYR cc_start: 0.8423 (m-80) cc_final: 0.7748 (m-80)
REVERT: B  297 TRP cc_start: 0.7497 (m100) cc_final: 0.7256 (m100)
REVERT: N   60 TYR cc_start: 0.8323 (m-80) cc_final: 0.7396 (m-80)
REVERT: N   87 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8048 (mtmm)
REVERT: R  227 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7691 (pt0)
  outliers start: 5
  outliers final: 1
  residues processed: 293
  average time/residue: 0.2486
  time to fit residues: 94.9143
Evaluate side-chains
  179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  239 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
A  75 GLN
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 GLN
A 123 ASN
B  62 HIS
B  91 HIS
B 119 ASN
B 156 GLN
B 230 ASN
B 295 ASN
R 175 ASN
R 280 HIS
** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8458  Z= 0.223
  Angle     :  0.766  30.957  11498  Z= 0.342
  Chirality :  0.067   1.897   1320
  Planarity :  0.004   0.057   1446
  Dihedral  : 11.972 166.520   1421
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 12.31 %
    Favored  : 84.83 %
  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: -0.55 (0.26), residues: 1027
  helix:  1.15 (0.26), residues: 392
  sheet: -1.46 (0.31), residues: 214
  loop : -1.15 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.019   0.001   PHE R 173 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.005   0.001   ARG B  19 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.910 
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: symmetry clash
REVERT: A  230 ASP cc_start: 0.8051 (m-30) cc_final: 0.7783 (m-30)
REVERT: B    9 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8642 (pp30)
REVERT: B   10 GLU cc_start: 0.8693 (tp30) cc_final: 0.8476 (tp30)
REVERT: B   15 LYS cc_start: 0.9203 (ptpt) cc_final: 0.8918 (ptpp)
REVERT: B  280 LYS cc_start: 0.8958 (tttm) cc_final: 0.8565 (ttpp)
REVERT: N   32 TYR cc_start: 0.8267 (m-80) cc_final: 0.7926 (m-80)
REVERT: N   60 TYR cc_start: 0.8392 (m-80) cc_final: 0.8060 (m-80)
REVERT: N   65 LYS cc_start: 0.8723 (tptm) cc_final: 0.8417 (tppp)
REVERT: N   87 LYS cc_start: 0.8395 (mtpt) cc_final: 0.7980 (mtmm)
REVERT: N   90 ASP cc_start: 0.6961 (m-30) cc_final: 0.6676 (m-30)
REVERT: R  227 GLN cc_start: 0.8215 (mm-40) cc_final: 0.8009 (pt0)
REVERT: R  229 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7092 (tm-30)
  outliers start: 25
  outliers final: 17
  residues processed: 194
  average time/residue: 0.2604
  time to fit residues: 65.9686
Evaluate side-chains
  156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  303 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 28 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   chunk 62 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 91 optimal weight:    0.8980
   chunk 99 optimal weight:    0.2980
   chunk 81 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8458  Z= 0.248
  Angle     :  0.759  31.188  11498  Z= 0.336
  Chirality :  0.065   1.835   1320
  Planarity :  0.004   0.056   1446
  Dihedral  : 11.650 168.543   1419
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 13.91 %
    Favored  : 83.01 %
  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: -0.16 (0.26), residues: 1027
  helix:  1.39 (0.26), residues: 395
  sheet: -1.12 (0.32), residues: 218
  loop : -0.93 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.018   0.001   PHE B 199 
 TYR   0.012   0.001   TYR N 115 
 ARG   0.006   0.001   ARG N  72 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.7984 (tt) cc_final: 0.7612 (pt)
REVERT: A  230 ASP cc_start: 0.8099 (m-30) cc_final: 0.7853 (m-30)
REVERT: B    9 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8619 (pp30)
REVERT: B   10 GLU cc_start: 0.8737 (tp30) cc_final: 0.8397 (tp30)
REVERT: B   15 LYS cc_start: 0.9205 (ptpt) cc_final: 0.8970 (ptpp)
REVERT: B   23 LYS cc_start: 0.9164 (pttt) cc_final: 0.8957 (pttp)
REVERT: B   35 ASN cc_start: 0.8631 (m110) cc_final: 0.8391 (m-40)
REVERT: B  138 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7683 (mm-30)
REVERT: B  280 LYS cc_start: 0.8944 (tttm) cc_final: 0.8502 (ttpp)
REVERT: N   51 ILE cc_start: 0.8072 (pt) cc_final: 0.7814 (pt)
REVERT: R  227 GLN cc_start: 0.8249 (mm-40) cc_final: 0.8018 (pt0)
REVERT: R  229 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7196 (tm-30)
  outliers start: 27
  outliers final: 24
  residues processed: 171
  average time/residue: 0.2698
  time to fit residues: 60.1721
Evaluate side-chains
  156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  256 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 47 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 61 optimal weight:   20.0000
   chunk 92 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8458  Z= 0.244
  Angle     :  0.750  31.077  11498  Z= 0.330
  Chirality :  0.065   1.819   1320
  Planarity :  0.004   0.059   1446
  Dihedral  : 11.458 169.990   1419
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 14.37 %
    Favored  : 81.87 %
  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:  0.08 (0.26), residues: 1027
  helix:  1.54 (0.26), residues: 391
  sheet: -0.98 (0.32), residues: 222
  loop : -0.70 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.015   0.001   PHE A  74 
 TYR   0.018   0.001   TYR R 308 
 ARG   0.004   0.000   ARG G  13 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 1.005 
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: A   57 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8079 (m)
REVERT: A   62 ILE cc_start: 0.8056 (tt) cc_final: 0.7649 (pt)
REVERT: A  230 ASP cc_start: 0.8104 (m-30) cc_final: 0.7865 (m-30)
REVERT: B    9 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8625 (pp30)
REVERT: B   10 GLU cc_start: 0.8769 (tp30) cc_final: 0.8424 (tp30)
REVERT: B   15 LYS cc_start: 0.9160 (ptpt) cc_final: 0.8955 (ptpp)
REVERT: B  280 LYS cc_start: 0.8960 (tttm) cc_final: 0.8730 (ttpp)
REVERT: G   22 GLU cc_start: 0.9072 (tp30) cc_final: 0.8817 (tp30)
REVERT: R  177 VAL cc_start: 0.8949 (t) cc_final: 0.8626 (m)
REVERT: R  227 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8018 (pt0)
REVERT: R  229 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6996 (tm-30)
  outliers start: 33
  outliers final: 22
  residues processed: 165
  average time/residue: 0.2509
  time to fit residues: 54.4298
Evaluate side-chains
  147 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 83 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 87 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 146 GLN
B  88 ASN
B 340 ASN
** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.5607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   8458  Z= 0.468
  Angle     :  0.843  31.442  11498  Z= 0.388
  Chirality :  0.067   1.809   1320
  Planarity :  0.005   0.061   1446
  Dihedral  : 11.676 169.012   1419
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.74 %
    Favored  : 80.39 %
  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: -0.09 (0.26), residues: 1027
  helix:  1.15 (0.26), residues: 396
  sheet: -1.01 (0.32), residues: 222
  loop : -0.57 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 144 
 HIS   0.005   0.001   HIS A  41 
 PHE   0.018   0.002   PHE A  74 
 TYR   0.019   0.002   TYR N 115 
 ARG   0.004   0.001   ARG G  27 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8689 (pp30)
REVERT: B   10 GLU cc_start: 0.8904 (tp30) cc_final: 0.8564 (tp30)
REVERT: B   35 ASN cc_start: 0.8756 (m-40) cc_final: 0.8503 (m-40)
REVERT: B  127 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8188 (mmtt)
REVERT: N   46 GLU cc_start: 0.7550 (tt0) cc_final: 0.7124 (tt0)
REVERT: N   53 GLN cc_start: 0.8441 (mp10) cc_final: 0.8134 (mp10)
REVERT: N   60 TYR cc_start: 0.8438 (m-80) cc_final: 0.8034 (m-80)
REVERT: R  229 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7093 (tm-30)
  outliers start: 34
  outliers final: 26
  residues processed: 164
  average time/residue: 0.2571
  time to fit residues: 55.6682
Evaluate side-chains
  151 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 94 optimal weight:    0.5980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
B 340 ASN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.5568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8458  Z= 0.222
  Angle     :  0.770  30.697  11498  Z= 0.341
  Chirality :  0.065   1.814   1320
  Planarity :  0.004   0.061   1446
  Dihedral  : 11.478 172.185   1419
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.42 %
    Favored  : 80.50 %
  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:  0.28 (0.26), residues: 1027
  helix:  1.46 (0.26), residues: 391
  sheet: -0.68 (0.33), residues: 224
  loop : -0.44 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.014   0.001   TYR N 115 
 ARG   0.005   0.000   ARG R 293 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.848 
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: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8068 (tt) cc_final: 0.7664 (pt)
REVERT: B    9 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8724 (pp30)
REVERT: B   10 GLU cc_start: 0.8869 (tp30) cc_final: 0.8495 (tp30)
REVERT: B  280 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8423 (ttmm)
REVERT: N   38 ARG cc_start: 0.8528 (ptt90) cc_final: 0.8303 (ptt-90)
REVERT: N   46 GLU cc_start: 0.7520 (tt0) cc_final: 0.7186 (tt0)
REVERT: N   60 TYR cc_start: 0.8434 (m-80) cc_final: 0.7413 (m-80)
REVERT: N   87 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8122 (tppt)
REVERT: R   39 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7104 (mp10)
  outliers start: 27
  outliers final: 21
  residues processed: 163
  average time/residue: 0.2710
  time to fit residues: 58.0087
Evaluate side-chains
  150 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0980
   chunk 59 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.5569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8458  Z= 0.179
  Angle     :  0.752  30.592  11498  Z= 0.331
  Chirality :  0.064   1.817   1320
  Planarity :  0.004   0.059   1446
  Dihedral  : 11.383 172.398   1419
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.45 %
    Favored  : 79.48 %
  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:  0.52 (0.27), residues: 1027
  helix:  1.69 (0.26), residues: 390
  sheet: -0.56 (0.33), residues: 224
  loop : -0.32 (0.33), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.003   0.000   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.021   0.001   TYR R 308 
 ARG   0.008   0.000   ARG G  13 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  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: A   62 ILE cc_start: 0.7974 (tt) cc_final: 0.7578 (pt)
REVERT: A  230 ASP cc_start: 0.8135 (m-30) cc_final: 0.7911 (m-30)
REVERT: B    9 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8724 (pp30)
REVERT: B   10 GLU cc_start: 0.8840 (tp30) cc_final: 0.8488 (tp30)
REVERT: B  280 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8417 (ttmm)
REVERT: N    5 GLN cc_start: 0.7975 (mp10) cc_final: 0.7674 (mp10)
REVERT: N   19 ARG cc_start: 0.8511 (ttt90) cc_final: 0.8238 (ttt90)
REVERT: N   46 GLU cc_start: 0.7527 (tt0) cc_final: 0.7206 (tt0)
REVERT: N   53 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8090 (mm-40)
REVERT: N   60 TYR cc_start: 0.8449 (m-80) cc_final: 0.7527 (m-80)
REVERT: N   78 THR cc_start: 0.9121 (m) cc_final: 0.8507 (p)
REVERT: N  122 THR cc_start: 0.8485 (m) cc_final: 0.8147 (p)
REVERT: R   39 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.6958 (mp10)
  outliers start: 27
  outliers final: 21
  residues processed: 167
  average time/residue: 0.2452
  time to fit residues: 53.8649
Evaluate side-chains
  161 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  283 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0980
   chunk 9 optimal weight:    0.0970
   chunk 76 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.5635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8458  Z= 0.193
  Angle     :  0.754  30.613  11498  Z= 0.334
  Chirality :  0.064   1.812   1320
  Planarity :  0.004   0.059   1446
  Dihedral  : 11.333 172.743   1419
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.36 %
    Favored  : 78.56 %
  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:  0.59 (0.27), residues: 1027
  helix:  1.72 (0.26), residues: 390
  sheet: -0.45 (0.33), residues: 224
  loop : -0.32 (0.33), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.003   0.000   HIS A 209 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.020   0.001   TYR N 115 
 ARG   0.007   0.000   ARG G  13 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.956 
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: A   62 ILE cc_start: 0.8025 (tt) cc_final: 0.7623 (pt)
REVERT: B    9 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8735 (pp30)
REVERT: B   10 GLU cc_start: 0.8840 (tp30) cc_final: 0.8480 (tp30)
REVERT: B  280 LYS cc_start: 0.8987 (ttpp) cc_final: 0.8393 (ttmm)
REVERT: G   13 ARG cc_start: 0.8884 (ptp-110) cc_final: 0.8512 (ptp90)
REVERT: G   32 LYS cc_start: 0.8873 (tppt) cc_final: 0.8636 (tppt)
REVERT: N    5 GLN cc_start: 0.7967 (mp10) cc_final: 0.7660 (mp10)
REVERT: N   19 ARG cc_start: 0.8527 (ttt90) cc_final: 0.8288 (ttt90)
REVERT: N   38 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.8279 (ptt90)
REVERT: N   46 GLU cc_start: 0.7506 (tt0) cc_final: 0.7207 (tt0)
REVERT: N   53 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8148 (mm-40)
REVERT: N   60 TYR cc_start: 0.8549 (m-80) cc_final: 0.7612 (m-80)
REVERT: N   78 THR cc_start: 0.9066 (m) cc_final: 0.8458 (p)
REVERT: N   87 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8169 (mmtp)
REVERT: N  122 THR cc_start: 0.8504 (m) cc_final: 0.8035 (p)
REVERT: R   39 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.6958 (mp10)
  outliers start: 27
  outliers final: 21
  residues processed: 163
  average time/residue: 0.2519
  time to fit residues: 54.1269
Evaluate side-chains
  153 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  283 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 93 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.5742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8458  Z= 0.186
  Angle     :  0.756  30.583  11498  Z= 0.336
  Chirality :  0.064   1.812   1320
  Planarity :  0.004   0.058   1446
  Dihedral  : 11.299 172.917   1419
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.93 %
    Favored  : 78.45 %
  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:  0.60 (0.27), residues: 1027
  helix:  1.70 (0.25), residues: 396
  sheet: -0.34 (0.33), residues: 223
  loop : -0.38 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.000   HIS A 209 
 PHE   0.028   0.001   PHE R 187 
 TYR   0.023   0.001   TYR N 115 
 ARG   0.005   0.000   ARG G  13 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.998 
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: A   62 ILE cc_start: 0.7975 (tt) cc_final: 0.7572 (pt)
REVERT: B    9 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8718 (pp30)
REVERT: B   10 GLU cc_start: 0.8833 (tp30) cc_final: 0.8486 (tp30)
REVERT: B  280 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8381 (ttmm)
REVERT: B  289 TYR cc_start: 0.8550 (m-80) cc_final: 0.8192 (m-80)
REVERT: G   32 LYS cc_start: 0.8931 (tppt) cc_final: 0.8670 (tppt)
REVERT: N    5 GLN cc_start: 0.8023 (mp10) cc_final: 0.7649 (mp10)
REVERT: N   19 ARG cc_start: 0.8532 (ttt90) cc_final: 0.8305 (ttt90)
REVERT: N   38 ARG cc_start: 0.8669 (ptt-90) cc_final: 0.8249 (ptt90)
REVERT: N   46 GLU cc_start: 0.7523 (tt0) cc_final: 0.7215 (tt0)
REVERT: N   60 TYR cc_start: 0.8571 (m-80) cc_final: 0.7621 (m-80)
REVERT: N   78 THR cc_start: 0.9005 (m) cc_final: 0.8424 (p)
REVERT: N   87 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8254 (mmtp)
REVERT: N  122 THR cc_start: 0.8437 (m) cc_final: 0.8104 (p)
REVERT: R   39 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6911 (mp10)
  outliers start: 23
  outliers final: 20
  residues processed: 162
  average time/residue: 0.2348
  time to fit residues: 50.6063
Evaluate side-chains
  157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  283 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 92 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 61 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.5847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8458  Z= 0.212
  Angle     :  0.776  30.629  11498  Z= 0.348
  Chirality :  0.065   1.807   1320
  Planarity :  0.004   0.066   1446
  Dihedral  : 11.328 172.997   1419
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.50 %
    Favored  : 77.99 %
  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:  0.57 (0.27), residues: 1027
  helix:  1.67 (0.25), residues: 396
  sheet: -0.42 (0.33), residues: 225
  loop : -0.34 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.023   0.001   PHE R 187 
 TYR   0.024   0.001   TYR N 115 
 ARG   0.010   0.000   ARG B 129 

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.943 
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: symmetry clash
REVERT: A   62 ILE cc_start: 0.7983 (tt) cc_final: 0.7571 (pt)
REVERT: B    9 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8717 (pp30)
REVERT: B   10 GLU cc_start: 0.8838 (tp30) cc_final: 0.8486 (tp30)
REVERT: B  280 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8406 (ttmm)
REVERT: B  289 TYR cc_start: 0.8680 (m-80) cc_final: 0.8306 (m-80)
REVERT: G   32 LYS cc_start: 0.8969 (tppt) cc_final: 0.8716 (tppt)
REVERT: N    5 GLN cc_start: 0.8016 (mp10) cc_final: 0.7652 (mp10)
REVERT: N   19 ARG cc_start: 0.8566 (ttt90) cc_final: 0.8345 (ttt90)
REVERT: N   38 ARG cc_start: 0.8686 (ptt-90) cc_final: 0.8276 (ptt90)
REVERT: N   46 GLU cc_start: 0.7537 (tt0) cc_final: 0.7226 (tt0)
REVERT: N   51 ILE cc_start: 0.7596 (pt) cc_final: 0.7308 (pt)
REVERT: N   60 TYR cc_start: 0.8674 (m-80) cc_final: 0.8205 (m-80)
REVERT: N   78 THR cc_start: 0.8977 (m) cc_final: 0.8427 (p)
REVERT: N   87 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8267 (mmtp)
REVERT: N  122 THR cc_start: 0.8432 (m) cc_final: 0.8057 (p)
REVERT: R   39 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.6953 (mp10)
  outliers start: 22
  outliers final: 19
  residues processed: 153
  average time/residue: 0.2438
  time to fit residues: 49.5184
Evaluate side-chains
  152 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  283 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    8.9990
   chunk 70 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 286 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 = 0.3726 r_free = 0.3726 target = 0.102841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.077950 restraints weight = 16627.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 3.11
r_work: 0.3133 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.5867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8458  Z= 0.198
  Angle     :  0.766  30.581  11498  Z= 0.341
  Chirality :  0.064   1.808   1320
  Planarity :  0.004   0.063   1446
  Dihedral  : 11.311 173.170   1419
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.73 %
    Favored  : 77.99 %
  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:  0.56 (0.27), residues: 1027
  helix:  1.66 (0.25), residues: 399
  sheet: -0.35 (0.33), residues: 224
  loop : -0.41 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.000   HIS A 209 
 PHE   0.020   0.001   PHE R 187 
 TYR   0.023   0.001   TYR N 115 
 ARG   0.008   0.000   ARG G  13 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2106.15 seconds
wall clock time: 39 minutes 7.09 seconds (2347.09 seconds total)