Starting phenix.real_space_refine
on Thu Feb 13 18:40:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wq3_32698/02_2025/7wq3_32698.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wq3_32698/02_2025/7wq3_32698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wq3_32698/02_2025/7wq3_32698.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wq3_32698/02_2025/7wq3_32698.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wq3_32698/02_2025/7wq3_32698.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wq3_32698/02_2025/7wq3_32698.cif"
  }
  resolution = 2.7
  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=   0.006
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      61      5.16       5
     C    5915      2.51       5
     N    1548      2.21       5
     O    1685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9209
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2303
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 13, 'TRANS': 275}
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1787
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 117
          Classifications: {'peptide': 16}
          Link IDs: {'PTRANS': 1, 'TRANS': 14}
    Chain: "R"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 140
          Unusual residues: {'CLR': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.57, per 1000 atoms: 0.60
  Number of scatterers: 9209
  At special positions: 0
  Unit cell: (110.16, 125.46, 123.42, 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      61     16.00
     O    1685      8.00
     N    1548      7.00
     C    5915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 187 " 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: 2.38
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      39.7% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 4.618A  pdb=" N   VAL R  38 " --> pdb=" O   PHE R  34 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER R  61 " --> pdb=" O   VAL R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 98
      removed outlier: 3.754A  pdb=" N   ILE R  89 " --> pdb=" O   LEU R  85 " (cutoff:3.500A)
      Proline residue:  R  90  - end of helix
      removed outlier: 4.257A  pdb=" N   THR R  94 " --> pdb=" O   PRO R  90 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL R  95 " --> pdb=" O   PHE R  91 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR R  96 " --> pdb=" O   GLN R  92 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 103 through 139
      removed outlier: 4.015A  pdb=" N   ILE R 107 " --> pdb=" O   LEU R 103 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   HIS R 112 " --> pdb=" O   CYS R 108 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TYR R 113 " --> pdb=" O   LYS R 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE R 137 " --> pdb=" O   ARG R 133 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   HIS R 139 " --> pdb=" O   VAL R 135 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 142 through 147
    Processing helix  chain 'R' and resid 148 through 167
    Processing helix  chain 'R' and resid 167 through 174
      removed outlier: 3.656A  pdb=" N   ALA R 171 " --> pdb=" O   ALA R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 193 through 209
      removed outlier: 3.715A  pdb=" N   ALA R 199 " --> pdb=" O   ARG R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 231
    Processing helix  chain 'R' and resid 235 through 260
      removed outlier: 4.429A  pdb=" N   TRP R 260 " --> pdb=" O   PHE R 256 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 272
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 3.780A  pdb=" N   SER R 296 " --> pdb=" O   ALA R 292 " (cutoff:3.500A)
      Proline residue:  R 300  - end of helix
    Processing helix  chain 'R' and resid 307 through 318
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 5.078A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.166A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 232 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 232'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.543A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 4.360A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.631A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.631A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.852A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.605A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.884A  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 87 through 91
      removed outlier: 4.184A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.789A  pdb=" N   ASP S 223 " --> pdb=" O   GLU S 220 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 220 through 224'
    Processing helix  chain 'L' and resid 3 through 12
    Processing sheet with id=AA1, first strand: chain 'R' and resid 175 through 177
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.299A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.722A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.973A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.033A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.010A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.789A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.177A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.121A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.620A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.292A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.292A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141
      removed outlier: 3.928A  pdb=" N   THR S 141 " --> pdb=" O   ARG S 160 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG S 160 " --> pdb=" O   THR S 141 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 4.028A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ARG S 191 " --> pdb=" O   ASN S 194 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1311 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: 2.90

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2915
        1.34 -     1.46: 2281
        1.46 -     1.58: 4113
        1.58 -     1.70: 25
        1.70 -     1.81: 91
  Bond restraints: 9425
  Sorted by residual:
  bond pdb=" C5  CLR R 401 "
       pdb=" C6  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.652 -0.320 2.00e-02 2.50e+03 2.56e+02
  bond pdb=" C5  CLR R 402 "
       pdb=" C6  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 405 "
       pdb=" C6  CLR R 405 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 403 "
       pdb=" C6  CLR R 403 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 404 "
       pdb=" C6  CLR R 404 "
    ideal  model  delta    sigma   weight residual
    1.332  1.650 -0.318 2.00e-02 2.50e+03 2.53e+02
  ... (remaining 9420 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 12667
        2.66 -     5.32: 91
        5.32 -     7.98: 19
        7.98 -    10.64: 10
       10.64 -    13.30: 10
  Bond angle restraints: 12797
  Sorted by residual:
  angle pdb=" C5  CLR R 405 "
        pdb=" C6  CLR R 405 "
        pdb=" C7  CLR R 405 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C5  CLR R 403 "
        pdb=" C6  CLR R 403 "
        pdb=" C7  CLR R 403 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C5  CLR R 402 "
        pdb=" C6  CLR R 402 "
        pdb=" C7  CLR R 402 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C5  CLR R 404 "
        pdb=" C6  CLR R 404 "
        pdb=" C7  CLR R 404 "
      ideal   model   delta    sigma   weight residual
     125.11  111.82   13.29 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C4  CLR R 401 "
        pdb=" C5  CLR R 401 "
        pdb=" C6  CLR R 401 "
      ideal   model   delta    sigma   weight residual
     120.33  107.93   12.40 3.00e+00 1.11e-01 1.71e+01
  ... (remaining 12792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.56: 5564
       15.56 -    31.12: 165
       31.12 -    46.68: 53
       46.68 -    62.24: 23
       62.24 -    77.79: 3
  Dihedral angle restraints: 5808
    sinusoidal: 2443
      harmonic: 3365
  Sorted by residual:
  dihedral pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
           pdb=" CB  ARG S 191 "
           pdb=" CG  ARG S 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.85   59.85     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   PHE B 234 "
           pdb=" CA  PHE B 234 "
           pdb=" CB  PHE B 234 "
           pdb=" CG  PHE B 234 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.95  -57.05     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" N   PHE R 114 "
           pdb=" CA  PHE R 114 "
           pdb=" CB  PHE R 114 "
           pdb=" CG  PHE R 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.13   53.13     3      1.50e+01 4.44e-03 9.18e+00
  ... (remaining 5805 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1408
       0.112 -    0.223: 29
       0.223 -    0.335: 11
       0.335 -    0.446: 4
       0.446 -    0.558: 5
  Chirality restraints: 1457
  Sorted by residual:
  chirality pdb=" C13 CLR R 405 "
            pdb=" C12 CLR R 405 "
            pdb=" C14 CLR R 405 "
            pdb=" C17 CLR R 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.37   -0.56 2.00e-01 2.50e+01 7.78e+00
  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   -2.38   -0.56 2.00e-01 2.50e+01 7.74e+00
  chirality pdb=" C13 CLR R 401 "
            pdb=" C12 CLR R 401 "
            pdb=" C14 CLR R 401 "
            pdb=" C17 CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.38   -0.55 2.00e-01 2.50e+01 7.69e+00
  ... (remaining 1454 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 299 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO R 300 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO R 300 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 300 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO S  41 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO B 236 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 435
        2.73 -     3.27: 9049
        3.27 -     3.82: 14930
        3.82 -     4.36: 17758
        4.36 -     4.90: 31232
  Nonbonded interactions: 73404
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 248 "
            pdb=" OD1 ASP A 251 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   PHE S  29 "
            pdb=" NH2 ARG S  72 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.269 3.040
  ... (remaining 73399 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:             0.580
  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:             0.000
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.550
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:15.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4588
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      :  0.011   0.320   9425  Z= 0.733
  Angle     :  0.724  13.301  12797  Z= 0.335
  Chirality :  0.061   0.558   1457
  Planarity :  0.003   0.032   1586
  Dihedral  :  9.420  77.794   3633
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  2.43 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -1.34 (0.23), residues: 1144
  helix:  0.07 (0.25), residues: 408
  sheet: -1.00 (0.27), residues: 292
  loop : -1.59 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.008   0.001   PHE A 274 
 TYR   0.006   0.001   TYR S 102 
 ARG   0.002   0.000   ARG B  68 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 227
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 ASN cc_start: 0.6883 (m110) cc_final: 0.6622 (m110)
REVERT: R  244 LYS cc_start: 0.6246 (mttt) cc_final: 0.5999 (mtmm)
REVERT: A  248 LYS cc_start: 0.6669 (ttmm) cc_final: 0.6377 (tmmm)
REVERT: A  266 LEU cc_start: 0.5029 (tp) cc_final: 0.4807 (tm)
REVERT: A  276 GLU cc_start: 0.7628 (mp0) cc_final: 0.7292 (mp0)
REVERT: A  305 CYS cc_start: 0.6720 (m) cc_final: 0.6438 (m)
REVERT: A  314 LYS cc_start: 0.6025 (mttt) cc_final: 0.5625 (tppt)
REVERT: A  342 VAL cc_start: 0.6855 (t) cc_final: 0.6526 (m)
REVERT: G   20 LYS cc_start: 0.7013 (ptpp) cc_final: 0.6256 (pttm)
REVERT: G   60 PRO cc_start: 0.6335 (Cg_endo) cc_final: 0.6097 (Cg_exo)
REVERT: S   53 SER cc_start: 0.6534 (t) cc_final: 0.6274 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 231
  average time/residue: 1.0938
  time to fit residues: 272.1590
Evaluate side-chains
  136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0170
   chunk 65 optimal weight:    3.9990
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
R  71 ASN
R 173 HIS
R 190 GLN
A 204 GLN
B  91 HIS
B 142 HIS
B 176 GLN
G  18 GLN
G  59 ASN
S  39 GLN
S 194 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.196991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.168633 restraints weight = 11616.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 1.83
r_work: 0.3868 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3765 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9425  Z= 0.229
  Angle     :  0.691  10.469  12797  Z= 0.349
  Chirality :  0.044   0.173   1457
  Planarity :  0.005   0.054   1586
  Dihedral  :  6.943  55.688   1574
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.94 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.24), residues: 1144
  helix:  1.30 (0.27), residues: 396
  sheet: -0.31 (0.28), residues: 288
  loop : -1.06 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP S  36 
 HIS   0.014   0.002   HIS R 173 
 PHE   0.028   0.002   PHE R  91 
 TYR   0.015   0.002   TYR G  40 
 ARG   0.006   0.001   ARG S 191 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 181
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 SER cc_start: 0.7237 (m) cc_final: 0.6464 (p)
REVERT: R  129 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7007 (mtm)
REVERT: A  198 MET cc_start: 0.8001 (mtp) cc_final: 0.7785 (mtm)
REVERT: A  248 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7537 (tmmm)
REVERT: A  305 CYS cc_start: 0.7631 (m) cc_final: 0.7355 (m)
REVERT: B  134 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7357 (mtp-110)
REVERT: B  190 LEU cc_start: 0.8606 (mt) cc_final: 0.8318 (pp)
REVERT: B  219 ARG cc_start: 0.8464 (mmt180) cc_final: 0.8070 (mpt-90)
REVERT: G   38 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5684 (mmm)
REVERT: S   46 GLU cc_start: 0.7592 (pt0) cc_final: 0.7329 (pt0)
REVERT: S   58 ILE cc_start: 0.6448 (mt) cc_final: 0.6031 (mt)
REVERT: S   83 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8088 (ptp)
  outliers start: 30
  outliers final: 10
  residues processed: 200
  average time/residue: 1.1151
  time to fit residues: 239.5612
Evaluate side-chains
  127 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  129 MET
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  164 SER
Chi-restraints excluded: chain S residue  204 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0000
   chunk 79 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0270
   chunk 81 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.5844

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
R 228 HIS
R 299 ASN
A 204 GLN
B  88 ASN
B 125 ASN
B 156 GLN
L   5 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.185532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152698 restraints weight = 10841.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.02
r_work: 0.3608 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.6779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9425  Z= 0.179
  Angle     :  0.552   7.802  12797  Z= 0.283
  Chirality :  0.041   0.143   1457
  Planarity :  0.004   0.038   1586
  Dihedral  :  5.668  43.032   1574
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.47 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.25), residues: 1144
  helix:  1.94 (0.28), residues: 400
  sheet:  0.06 (0.29), residues: 288
  loop : -0.81 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.009   0.001   HIS S  35 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.009   0.001   TYR G  40 
 ARG   0.006   0.001   ARG A  21 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7833 (mttt) cc_final: 0.7546 (mtmt)
REVERT: A   28 GLU cc_start: 0.7626 (tt0) cc_final: 0.7050 (mt-10)
REVERT: A  209 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7529 (tttm)
REVERT: A  232 LEU cc_start: 0.6943 (mt) cc_final: 0.6624 (mp)
REVERT: B   16 ASN cc_start: 0.6476 (m-40) cc_final: 0.6211 (m110)
REVERT: B   19 ARG cc_start: 0.6351 (ttp80) cc_final: 0.6134 (ttp80)
REVERT: B   98 SER cc_start: 0.8745 (m) cc_final: 0.8386 (t)
REVERT: B  134 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7624 (mtp-110)
REVERT: B  137 ARG cc_start: 0.7683 (mmp80) cc_final: 0.7344 (tpp-160)
REVERT: B  268 ASN cc_start: 0.7299 (t0) cc_final: 0.6927 (m-40)
REVERT: B  293 ASN cc_start: 0.7666 (p0) cc_final: 0.7151 (m-40)
REVERT: S    3 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7934 (tt0)
REVERT: S   46 GLU cc_start: 0.8309 (pt0) cc_final: 0.7980 (pt0)
REVERT: S   93 MET cc_start: 0.7890 (tpp) cc_final: 0.7684 (tpt)
REVERT: S  191 ARG cc_start: 0.2748 (OUTLIER) cc_final: 0.1825 (tpp80)
  outliers start: 36
  outliers final: 14
  residues processed: 178
  average time/residue: 1.1509
  time to fit residues: 219.7400
Evaluate side-chains
  144 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  119 MET
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  191 ARG
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    7.9990
   chunk 103 optimal weight:    0.0370
   chunk 68 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0040
   chunk 83 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.7672

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
A 204 GLN
B 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.177278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143497 restraints weight = 10626.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 1.97
r_work: 0.3490 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.8503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9425  Z= 0.169
  Angle     :  0.539   9.183  12797  Z= 0.279
  Chirality :  0.041   0.191   1457
  Planarity :  0.004   0.044   1586
  Dihedral  :  5.828  56.921   1574
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 16.50 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.94 (0.25), residues: 1144
  helix:  2.29 (0.27), residues: 390
  sheet:  0.30 (0.30), residues: 282
  loop : -0.57 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 160 
 HIS   0.003   0.001   HIS R 263 
 PHE   0.019   0.002   PHE R 115 
 TYR   0.009   0.001   TYR S 173 
 ARG   0.004   0.000   ARG S 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 163
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
REVERT: R  252 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7097 (m)
REVERT: A   22 ASN cc_start: 0.8114 (m-40) cc_final: 0.7886 (m110)
REVERT: A   24 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7653 (ttm110)
REVERT: A   28 GLU cc_start: 0.7856 (tt0) cc_final: 0.7319 (mt-10)
REVERT: A  209 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7720 (mptt)
REVERT: B   16 ASN cc_start: 0.6619 (m-40) cc_final: 0.6210 (m110)
REVERT: B   19 ARG cc_start: 0.6663 (ttp80) cc_final: 0.6440 (ttp80)
REVERT: B   98 SER cc_start: 0.8975 (m) cc_final: 0.8704 (t)
REVERT: B  130 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6696 (mp0)
REVERT: B  134 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7847 (ptp90)
REVERT: B  215 GLU cc_start: 0.7981 (mp0) cc_final: 0.7551 (mt-10)
REVERT: B  268 ASN cc_start: 0.7376 (t0) cc_final: 0.7095 (m-40)
REVERT: B  312 ASP cc_start: 0.8512 (m-30) cc_final: 0.8288 (m-30)
REVERT: G   46 LYS cc_start: 0.7824 (tppt) cc_final: 0.7544 (pmtt)
REVERT: G   58 GLU cc_start: 0.7078 (mp0) cc_final: 0.6276 (tm-30)
REVERT: S   46 GLU cc_start: 0.8543 (pt0) cc_final: 0.8170 (pt0)
REVERT: S   65 LYS cc_start: 0.7670 (ttmt) cc_final: 0.7121 (tttm)
REVERT: S   71 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7876 (p)
REVERT: S   78 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7124 (t)
REVERT: S  160 ARG cc_start: 0.7573 (ptt90) cc_final: 0.6382 (mtm-85)
  outliers start: 45
  outliers final: 19
  residues processed: 186
  average time/residue: 1.1729
  time to fit residues: 233.7247
Evaluate side-chains
  155 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  119 MET
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  32 GLN
B  44 GLN
B 156 GLN
B 176 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.173461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.142351 restraints weight = 11407.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.88
r_work: 0.3555 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.9888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9425  Z= 0.220
  Angle     :  0.562   8.185  12797  Z= 0.293
  Chirality :  0.042   0.148   1457
  Planarity :  0.004   0.047   1586
  Dihedral  :  5.341  46.805   1574
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 18.42 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.95 (0.25), residues: 1144
  helix:  2.32 (0.27), residues: 391
  sheet:  0.24 (0.31), residues: 277
  loop : -0.54 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.009   0.001   HIS B  54 
 PHE   0.022   0.002   PHE R 110 
 TYR   0.011   0.001   TYR S  95 
 ARG   0.003   0.001   ARG A 313 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 148
  time to evaluate  : 1.007 
Fit side-chains
REVERT: R   78 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7770 (m)
REVERT: R  252 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7434 (m)
REVERT: R  261 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7886 (tm)
REVERT: A   22 ASN cc_start: 0.8164 (m-40) cc_final: 0.7961 (m110)
REVERT: A   25 GLU cc_start: 0.7614 (tt0) cc_final: 0.6927 (tm-30)
REVERT: A   28 GLU cc_start: 0.7866 (tt0) cc_final: 0.7478 (mt-10)
REVERT: A  209 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7809 (mppt)
REVERT: A  273 LEU cc_start: 0.8009 (tp) cc_final: 0.7614 (tp)
REVERT: B   16 ASN cc_start: 0.6870 (m-40) cc_final: 0.6567 (m110)
REVERT: B   42 ARG cc_start: 0.6827 (tpt170) cc_final: 0.6568 (tmt170)
REVERT: B   46 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7544 (mmt90)
REVERT: B  130 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7213 (mp0)
REVERT: B  134 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7945 (ptp90)
REVERT: B  172 GLU cc_start: 0.7513 (tp30) cc_final: 0.7226 (mt-10)
REVERT: B  215 GLU cc_start: 0.8023 (mp0) cc_final: 0.7749 (mt-10)
REVERT: G   46 LYS cc_start: 0.8024 (tppt) cc_final: 0.7781 (pmtt)
REVERT: G   58 GLU cc_start: 0.7273 (mp0) cc_final: 0.6287 (tm-30)
REVERT: S   46 GLU cc_start: 0.8735 (pt0) cc_final: 0.8336 (pt0)
REVERT: S   65 LYS cc_start: 0.7585 (ttmt) cc_final: 0.7143 (tttm)
REVERT: S   78 THR cc_start: 0.8010 (t) cc_final: 0.7531 (m)
REVERT: S  160 ARG cc_start: 0.7646 (ptt90) cc_final: 0.6615 (mtm-85)
REVERT: S  186 GLN cc_start: 0.8031 (tt0) cc_final: 0.7679 (tm-30)
  outliers start: 52
  outliers final: 17
  residues processed: 178
  average time/residue: 1.2535
  time to fit residues: 238.4504
Evaluate side-chains
  161 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  151 ASN
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0370
   chunk 60 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0270
   chunk 84 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  32 GLN
S  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.175223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.145138 restraints weight = 11268.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 1.79
r_work: 0.3564 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          1.0067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9425  Z= 0.138
  Angle     :  0.490   6.632  12797  Z= 0.255
  Chirality :  0.040   0.140   1457
  Planarity :  0.004   0.059   1586
  Dihedral  :  5.060  59.476   1574
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 19.43 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.19 (0.26), residues: 1144
  helix:  2.60 (0.28), residues: 388
  sheet:  0.40 (0.31), residues: 277
  loop : -0.48 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.006   0.001   HIS R 173 
 PHE   0.014   0.001   PHE R 110 
 TYR   0.009   0.001   TYR R  84 
 ARG   0.004   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 0.962 
Fit side-chains
REVERT: R   78 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7784 (m)
REVERT: R  252 VAL cc_start: 0.7676 (p) cc_final: 0.7418 (m)
REVERT: A   22 ASN cc_start: 0.8131 (m-40) cc_final: 0.7928 (m110)
REVERT: A   25 GLU cc_start: 0.7628 (tt0) cc_final: 0.6996 (tm-30)
REVERT: A   28 GLU cc_start: 0.7822 (tt0) cc_final: 0.7490 (mt-10)
REVERT: A  209 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7917 (mptt)
REVERT: A  272 ASP cc_start: 0.7004 (m-30) cc_final: 0.6726 (m-30)
REVERT: A  273 LEU cc_start: 0.8006 (tp) cc_final: 0.7655 (tp)
REVERT: B   16 ASN cc_start: 0.6954 (m-40) cc_final: 0.6593 (m110)
REVERT: B   42 ARG cc_start: 0.6916 (tpt170) cc_final: 0.6627 (tmt170)
REVERT: B   46 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7550 (mmt90)
REVERT: B   76 ASP cc_start: 0.7734 (m-30) cc_final: 0.7504 (m-30)
REVERT: B  130 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7251 (mp0)
REVERT: B  215 GLU cc_start: 0.7991 (mp0) cc_final: 0.7753 (mt-10)
REVERT: B  296 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8398 (p)
REVERT: G   58 GLU cc_start: 0.7287 (mp0) cc_final: 0.6259 (tm-30)
REVERT: S   46 GLU cc_start: 0.8775 (pt0) cc_final: 0.8472 (pt0)
REVERT: S   65 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7187 (tttm)
REVERT: S   78 THR cc_start: 0.7951 (t) cc_final: 0.7513 (m)
REVERT: S  160 ARG cc_start: 0.7643 (ptt90) cc_final: 0.6893 (mtm-85)
REVERT: S  186 GLN cc_start: 0.8083 (tt0) cc_final: 0.7815 (tm-30)
  outliers start: 38
  outliers final: 16
  residues processed: 165
  average time/residue: 1.1313
  time to fit residues: 200.9520
Evaluate side-chains
  157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 15 optimal weight:    7.9990
   chunk 102 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  32 GLN
S  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.171483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.140845 restraints weight = 11398.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 1.89
r_work: 0.3507 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          1.0451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9425  Z= 0.172
  Angle     :  0.526   6.769  12797  Z= 0.273
  Chirality :  0.041   0.143   1457
  Planarity :  0.004   0.052   1586
  Dihedral  :  4.919  55.275   1574
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 20.45 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.18 (0.25), residues: 1144
  helix:  2.52 (0.27), residues: 392
  sheet:  0.39 (0.31), residues: 278
  loop : -0.44 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R 173 
 PHE   0.019   0.001   PHE R 115 
 TYR   0.009   0.001   TYR S  95 
 ARG   0.003   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 134
  time to evaluate  : 0.873 
Fit side-chains
REVERT: R   78 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7674 (m)
REVERT: R  252 VAL cc_start: 0.7806 (p) cc_final: 0.7533 (m)
REVERT: A   22 ASN cc_start: 0.8136 (m-40) cc_final: 0.7933 (m110)
REVERT: A   25 GLU cc_start: 0.7708 (tt0) cc_final: 0.7019 (tm-30)
REVERT: A   28 GLU cc_start: 0.7875 (tt0) cc_final: 0.7526 (mt-10)
REVERT: A  273 LEU cc_start: 0.7995 (tp) cc_final: 0.7746 (tp)
REVERT: B   46 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7570 (mmt90)
REVERT: B   76 ASP cc_start: 0.7657 (m-30) cc_final: 0.7421 (m-30)
REVERT: B  130 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7304 (mp0)
REVERT: B  135 VAL cc_start: 0.8971 (t) cc_final: 0.8644 (p)
REVERT: G   58 GLU cc_start: 0.7305 (mp0) cc_final: 0.6259 (tm-30)
REVERT: S   46 GLU cc_start: 0.8700 (pt0) cc_final: 0.8375 (pt0)
REVERT: S   65 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7410 (ttpt)
REVERT: S   76 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7309 (ttmt)
REVERT: S   78 THR cc_start: 0.8075 (t) cc_final: 0.7668 (m)
REVERT: S  118 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7887 (p)
REVERT: S  140 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.6815 (mmm)
REVERT: S  160 ARG cc_start: 0.7629 (ptt90) cc_final: 0.6820 (mtm-85)
REVERT: L   14 HIS cc_start: 0.5270 (m-70) cc_final: 0.4928 (m-70)
  outliers start: 38
  outliers final: 22
  residues processed: 158
  average time/residue: 1.1495
  time to fit residues: 195.2909
Evaluate side-chains
  157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:   40.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  32 GLN
B 266 HIS
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.165964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.135104 restraints weight = 11477.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 1.88
r_work: 0.3439 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          1.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9425  Z= 0.265
  Angle     :  0.609   8.807  12797  Z= 0.313
  Chirality :  0.044   0.204   1457
  Planarity :  0.004   0.049   1586
  Dihedral  :  5.296  54.859   1574
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.66 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.00 (0.25), residues: 1144
  helix:  2.41 (0.27), residues: 391
  sheet:  0.21 (0.30), residues: 288
  loop : -0.53 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 211 
 HIS   0.007   0.001   HIS B  54 
 PHE   0.029   0.002   PHE R 115 
 TYR   0.012   0.002   TYR S  95 
 ARG   0.005   0.001   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 139
  time to evaluate  : 0.964 
Fit side-chains
REVERT: R  252 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7768 (m)
REVERT: R  271 GLU cc_start: 0.7784 (tp30) cc_final: 0.7422 (mm-30)
REVERT: R  308 GLU cc_start: 0.7794 (mp0) cc_final: 0.7355 (mt-10)
REVERT: A   25 GLU cc_start: 0.7771 (tt0) cc_final: 0.7025 (tm-30)
REVERT: A   28 GLU cc_start: 0.7842 (tt0) cc_final: 0.7479 (mt-10)
REVERT: A  273 LEU cc_start: 0.7986 (tp) cc_final: 0.7750 (tp)
REVERT: A  345 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8327 (mttp)
REVERT: B   46 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7640 (mmt90)
REVERT: B   76 ASP cc_start: 0.7886 (m-30) cc_final: 0.7673 (m-30)
REVERT: B  130 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7308 (mp0)
REVERT: G   58 GLU cc_start: 0.7420 (mp0) cc_final: 0.6314 (tm-30)
REVERT: S   46 GLU cc_start: 0.8723 (pt0) cc_final: 0.8420 (pt0)
REVERT: S   65 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7498 (ttpt)
REVERT: S   78 THR cc_start: 0.8253 (t) cc_final: 0.7935 (m)
REVERT: S  118 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7808 (p)
REVERT: S  140 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7015 (mmm)
  outliers start: 40
  outliers final: 26
  residues processed: 163
  average time/residue: 1.1905
  time to fit residues: 207.8994
Evaluate side-chains
  165 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain L residue    6 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    0.0060
   chunk 109 optimal weight:    7.9990
   chunk 108 optimal weight:    6.9990
   chunk 95 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.9600

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  32 GLN
G  18 GLN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.169781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.138567 restraints weight = 11335.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 1.91
r_work: 0.3485 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          1.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9425  Z= 0.172
  Angle     :  0.533   8.379  12797  Z= 0.273
  Chirality :  0.041   0.212   1457
  Planarity :  0.004   0.051   1586
  Dihedral  :  4.939  58.472   1574
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 22.57 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.14 (0.26), residues: 1144
  helix:  2.60 (0.27), residues: 389
  sheet:  0.39 (0.30), residues: 276
  loop : -0.56 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 228 
 PHE   0.019   0.001   PHE R 115 
 TYR   0.008   0.001   TYR S  95 
 ARG   0.002   0.000   ARG B  68 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 140
  time to evaluate  : 1.074 
Fit side-chains
REVERT: R   51 ASN cc_start: 0.7417 (m-40) cc_final: 0.6877 (m110)
REVERT: R  252 VAL cc_start: 0.7911 (p) cc_final: 0.7644 (m)
REVERT: R  271 GLU cc_start: 0.7758 (tp30) cc_final: 0.7468 (mm-30)
REVERT: R  308 GLU cc_start: 0.7779 (mp0) cc_final: 0.7321 (mt-10)
REVERT: A   25 GLU cc_start: 0.7816 (tt0) cc_final: 0.7510 (tt0)
REVERT: A   28 GLU cc_start: 0.7906 (tt0) cc_final: 0.7506 (mt-10)
REVERT: A  273 LEU cc_start: 0.7948 (tp) cc_final: 0.7685 (tp)
REVERT: B   42 ARG cc_start: 0.7144 (tmt170) cc_final: 0.6557 (mmm-85)
REVERT: B   46 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7603 (mtp180)
REVERT: B   76 ASP cc_start: 0.7779 (m-30) cc_final: 0.7533 (m-30)
REVERT: B  130 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7351 (mp0)
REVERT: B  135 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8669 (p)
REVERT: B  296 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8471 (p)
REVERT: G   58 GLU cc_start: 0.7348 (mp0) cc_final: 0.6301 (tm-30)
REVERT: S   46 GLU cc_start: 0.8721 (pt0) cc_final: 0.8476 (pt0)
REVERT: S   65 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7499 (ttpt)
REVERT: S   78 THR cc_start: 0.8227 (t) cc_final: 0.7962 (m)
REVERT: S  118 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7822 (p)
REVERT: S  192 MET cc_start: 0.4736 (mpp) cc_final: 0.3068 (mtm)
  outliers start: 37
  outliers final: 21
  residues processed: 165
  average time/residue: 1.1600
  time to fit residues: 207.0910
Evaluate side-chains
  161 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  32 GLN
B 268 ASN
G  18 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.166155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.135773 restraints weight = 11392.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.90
r_work: 0.3443 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          1.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9425  Z= 0.267
  Angle     :  0.624   9.466  12797  Z= 0.318
  Chirality :  0.044   0.162   1457
  Planarity :  0.004   0.050   1586
  Dihedral  :  5.249  54.842   1574
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 23.48 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.98 (0.26), residues: 1144
  helix:  2.40 (0.27), residues: 391
  sheet:  0.21 (0.30), residues: 287
  loop : -0.56 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 211 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.029   0.002   PHE R 115 
 TYR   0.012   0.002   TYR S  95 
 ARG   0.004   0.001   ARG B  68 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 1.080 
Fit side-chains
REVERT: R  252 VAL cc_start: 0.8089 (p) cc_final: 0.7744 (m)
REVERT: R  271 GLU cc_start: 0.7801 (tp30) cc_final: 0.7494 (mm-30)
REVERT: R  308 GLU cc_start: 0.7796 (mp0) cc_final: 0.7358 (mt-10)
REVERT: A   25 GLU cc_start: 0.7818 (tt0) cc_final: 0.7038 (tm-30)
REVERT: A   28 GLU cc_start: 0.7858 (tt0) cc_final: 0.7514 (mt-10)
REVERT: A  273 LEU cc_start: 0.8039 (tp) cc_final: 0.7716 (tp)
REVERT: B   46 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7612 (mmt90)
REVERT: B  130 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7261 (mp0)
REVERT: B  215 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7997 (mt-10)
REVERT: G   58 GLU cc_start: 0.7381 (mp0) cc_final: 0.6340 (tm-30)
REVERT: S   46 GLU cc_start: 0.8718 (pt0) cc_final: 0.8412 (pt0)
REVERT: S   65 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7575 (ttpt)
REVERT: S   76 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7339 (ttmt)
REVERT: S   78 THR cc_start: 0.8334 (t) cc_final: 0.8101 (m)
REVERT: S  118 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7811 (p)
REVERT: S  192 MET cc_start: 0.4875 (mpp) cc_final: 0.3321 (mtm)
  outliers start: 31
  outliers final: 23
  residues processed: 155
  average time/residue: 1.1787
  time to fit residues: 196.3484
Evaluate side-chains
  152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 11 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  32 GLN
B 268 ASN
G  18 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.168128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.137107 restraints weight = 11344.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 1.87
r_work: 0.3469 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3361 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          1.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9425  Z= 0.196
  Angle     :  0.571   9.319  12797  Z= 0.291
  Chirality :  0.042   0.135   1457
  Planarity :  0.004   0.050   1586
  Dihedral  :  5.051  57.779   1574
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 23.58 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.10 (0.26), residues: 1144
  helix:  2.54 (0.27), residues: 389
  sheet:  0.29 (0.30), residues: 285
  loop : -0.52 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 211 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.021   0.001   PHE R 115 
 TYR   0.009   0.001   TYR A 302 
 ARG   0.003   0.000   ARG B 251 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7754.30 seconds
wall clock time: 137 minutes 18.43 seconds (8238.43 seconds total)