Starting phenix.real_space_refine
on Sat Aug 23 00:39:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlr_36405/08_2025/8jlr_36405_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlr_36405/08_2025/8jlr_36405.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlr_36405/08_2025/8jlr_36405_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlr_36405/08_2025/8jlr_36405_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlr_36405/08_2025/8jlr_36405.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlr_36405/08_2025/8jlr_36405.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 sd=   0.100
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      67      5.16       5
     C    5695      2.51       5
     N    1522      2.21       5
     O    1650      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8934
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1928
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2593
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 2160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2160
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 11, 'TRANS': 256}
          Chain breaks: 2
    Chain: "Y"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1784
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'VRK': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.26, per 1000 atoms: 0.25
  Number of scatterers: 8934
  At special positions: 0
  Unit cell: (109.2, 102.96, 124.8, 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      67     16.00
     O    1650      8.00
     N    1522      7.00
     C    5695      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 348.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 14 sheets defined
      37.9% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 211 through 215
      removed outlier: 3.555A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.628A  pdb=" N   PHE A 282 " --> pdb=" O   PHE A 279 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA A 283 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 279 through 283'
    Processing helix  chain 'A' and resid 298 through 319
      removed outlier: 3.606A  pdb=" N   PHE A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
      removed outlier: 3.782A  pdb=" N   ARG A 341 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 56 through 84
      removed outlier: 4.482A  pdb=" N   MET R  77 " --> pdb=" O   GLY R  73 " (cutoff:3.500A)
      Proline residue:  R  78  - end of helix
      removed outlier: 3.844A  pdb=" N   VAL R  82 " --> pdb=" O   PRO R  78 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG R  83 " --> pdb=" O   TYR R  79 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 127
      removed outlier: 3.802A  pdb=" N   ILE R  98 " --> pdb=" O   VAL R  94 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 160
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 187 through 199
      removed outlier: 3.637A  pdb=" N   VAL R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 200 through 228
      removed outlier: 4.269A  pdb=" N   MET R 206 " --> pdb=" O   PRO R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 277
      removed outlier: 3.935A  pdb=" N   PHE R 260 " --> pdb=" O   VAL R 256 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   CYS R 265 " --> pdb=" O   LEU R 261 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 4.194A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ASP R 287 " --> pdb=" O   PRO R 283 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 319
    Processing helix  chain 'Y' and resid 7 through 24
    Processing helix  chain 'Y' and resid 29 through 44
    Processing helix  chain 'Y' and resid 45 through 48
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 4.212A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.544A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 3.813A  pdb=" N   ASP A 200 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 9.600A  pdb=" N   ALA A 220 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.533A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.726A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.692A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.710A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.607A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.442A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.913A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.680A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60
      removed outlier: 3.829A  pdb=" N   VAL S  48 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147
    Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195
      removed outlier: 3.585A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    429 hydrogen bonds defined for protein.
    1236 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1428
        1.31 -     1.44: 2583
        1.44 -     1.56: 5024
        1.56 -     1.69: 0
        1.69 -     1.81: 101
  Bond restraints: 9136
  Sorted by residual:
  bond pdb=" CA  THR R 194 "
       pdb=" C   THR R 194 "
    ideal  model  delta    sigma   weight residual
    1.523  1.440  0.083 1.35e-02 5.49e+03 3.76e+01
  bond pdb=" C   THR R 194 "
       pdb=" O   THR R 194 "
    ideal  model  delta    sigma   weight residual
    1.236  1.187  0.049 1.26e-02 6.30e+03 1.51e+01
  bond pdb=" N   TRP B 332 "
       pdb=" CA  TRP B 332 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.32e-02 5.74e+03 5.54e+00
  bond pdb=" N   ASP R 103 "
       pdb=" CA  ASP R 103 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.17e-02 7.31e+03 5.47e+00
  bond pdb=" N   ASP B 333 "
       pdb=" CA  ASP B 333 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.40e-02 5.10e+03 5.18e+00
  ... (remaining 9131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 12064
        1.67 -     3.33: 257
        3.33 -     5.00: 38
        5.00 -     6.67: 15
        6.67 -     8.34: 3
  Bond angle restraints: 12377
  Sorted by residual:
  angle pdb=" N   ASP B 333 "
        pdb=" CA  ASP B 333 "
        pdb=" C   ASP B 333 "
      ideal   model   delta    sigma   weight residual
     113.15  108.97    4.18 1.19e+00 7.06e-01 1.24e+01
  angle pdb=" N   SER S 193 "
        pdb=" CA  SER S 193 "
        pdb=" C   SER S 193 "
      ideal   model   delta    sigma   weight residual
     114.56  110.81    3.75 1.27e+00 6.20e-01 8.71e+00
  angle pdb=" N   TRP B 332 "
        pdb=" CA  TRP B 332 "
        pdb=" C   TRP B 332 "
      ideal   model   delta    sigma   weight residual
     113.16  109.69    3.47 1.24e+00 6.50e-01 7.85e+00
  angle pdb=" CB  MET R 273 "
        pdb=" CG  MET R 273 "
        pdb=" SD  MET R 273 "
      ideal   model   delta    sigma   weight residual
     112.70  121.04   -8.34 3.00e+00 1.11e-01 7.72e+00
  angle pdb=" N   ILE R 201 "
        pdb=" CA  ILE R 201 "
        pdb=" C   ILE R 201 "
      ideal   model   delta    sigma   weight residual
     112.35  109.18    3.17 1.20e+00 6.94e-01 6.96e+00
  ... (remaining 12372 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.19: 4803
       16.19 -    32.39: 484
       32.39 -    48.58: 137
       48.58 -    64.78: 16
       64.78 -    80.97: 11
  Dihedral angle restraints: 5451
    sinusoidal: 2165
      harmonic: 3286
  Sorted by residual:
  dihedral pdb=" CB  CYS R  96 "
           pdb=" SG  CYS R  96 "
           pdb=" SG  CYS R 182 "
           pdb=" CB  CYS R 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.05   75.05     1      1.00e+01 1.00e-02 7.12e+01
  dihedral pdb=" CA  TYR S 235 "
           pdb=" C   TYR S 235 "
           pdb=" N   PRO S 236 "
           pdb=" CA  PRO S 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.77   22.23     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  PHE S  32 "
           pdb=" C   PHE S  32 "
           pdb=" N   GLY S  33 "
           pdb=" CA  GLY S  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.12   19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5448 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1281
       0.082 -    0.164: 102
       0.164 -    0.246: 1
       0.246 -    0.329: 0
       0.329 -    0.411: 1
  Chirality restraints: 1385
  Sorted by residual:
  chirality pdb=" C3  VRK R 401 "
            pdb=" C14 VRK R 401 "
            pdb=" C4  VRK R 401 "
            pdb=" O1  VRK R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.00    0.41 2.00e-01 2.50e+01 4.22e+00
  chirality pdb=" C2  VRK R 401 "
            pdb=" C1  VRK R 401 "
            pdb=" C16 VRK R 401 "
            pdb=" O1  VRK R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.20    0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  ILE A 255 "
            pdb=" N   ILE A 255 "
            pdb=" C   ILE A 255 "
            pdb=" CB  ILE A 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.29e-01
  ... (remaining 1382 not shown)

  Planarity restraints: 1561
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 298 "   -0.046 5.00e-02 4.00e+02   6.90e-02 7.61e+00
        pdb=" N   PRO A 299 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 299 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 299 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 292 "   -0.043 5.00e-02 4.00e+02   6.58e-02 6.93e+00
        pdb=" N   PRO A 293 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 293 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 293 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 308 "   -0.042 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO R 309 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO R 309 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO R 309 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1558 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 710
        2.74 -     3.28: 9244
        3.28 -     3.82: 15591
        3.82 -     4.36: 18651
        4.36 -     4.90: 32163
  Nonbonded interactions: 76359
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   ARG A 250 "
            pdb=" OG1 THR A 251 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP Y  48 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   PHE R 186 "
            pdb=" OH  TYR R 279 "
     model   vdw
     2.261 3.040
  ... (remaining 76354 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:             0.650
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.960
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   9139  Z= 0.165
  Angle     :  0.613   8.335  12383  Z= 0.333
  Chirality :  0.044   0.411   1385
  Planarity :  0.005   0.069   1561
  Dihedral  : 14.183  80.969   3322
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.31 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.25), residues: 1112
  helix:  1.60 (0.26), residues: 385
  sheet: -0.84 (0.30), residues: 265
  loop : -1.15 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  23 
 TYR   0.016   0.001   TYR S 228 
 PHE   0.012   0.001   PHE S  29 
 TRP   0.029   0.002   TRP B 339 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9136)
  covalent geometry    : angle       0.61261 (12377)
  SS BOND              : bond        0.00087 (    3)
  SS BOND              : angle       0.38851 (    6)
  hydrogen bonds       : bond        0.14255 (  429)
  hydrogen bonds       : angle       6.38229 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 212
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 TYR cc_start: 0.7378 (m-80) cc_final: 0.7044 (m-10)
REVERT: A  274 LYS cc_start: 0.7765 (mmpt) cc_final: 0.7504 (mmtt)
REVERT: R  123 TYR cc_start: 0.7732 (m-80) cc_final: 0.7403 (m-80)
REVERT: R  211 TYR cc_start: 0.7978 (t80) cc_final: 0.7480 (t80)
REVERT: S  228 TYR cc_start: 0.7710 (m-80) cc_final: 0.7034 (m-80)
REVERT: S  237 LEU cc_start: 0.5182 (mp) cc_final: 0.4930 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 213
  average time/residue: 0.4249
  time to fit residues: 99.0577
Evaluate side-chains
  165 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  194 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.2980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
B 266 HIS
B 268 ASN
R  63 HIS
S 142 GLN
S 183 GLN
S 231 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.209942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.163639 restraints weight = 10251.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.27
r_work: 0.3736 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3580 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9139  Z= 0.129
  Angle     :  0.584   7.240  12383  Z= 0.307
  Chirality :  0.043   0.223   1385
  Planarity :  0.005   0.056   1561
  Dihedral  :  5.350  41.909   1279
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 10.27 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.25), residues: 1112
  helix:  1.57 (0.25), residues: 394
  sheet: -0.70 (0.31), residues: 258
  loop : -1.08 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 134 
 TYR   0.018   0.002   TYR S  95 
 PHE   0.015   0.001   PHE R 299 
 TRP   0.019   0.002   TRP B 211 
 HIS   0.003   0.001   HIS R  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9136)
  covalent geometry    : angle       0.58413 (12377)
  SS BOND              : bond        0.00302 (    3)
  SS BOND              : angle       0.78572 (    6)
  hydrogen bonds       : bond        0.04094 (  429)
  hydrogen bonds       : angle       5.32161 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 179
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 TYR cc_start: 0.7657 (m-80) cc_final: 0.7381 (m-10)
REVERT: A  274 LYS cc_start: 0.7235 (mmpt) cc_final: 0.6885 (mmtt)
REVERT: B   76 ASP cc_start: 0.8612 (p0) cc_final: 0.8384 (p0)
REVERT: B  163 ASP cc_start: 0.7217 (t0) cc_final: 0.6916 (t0)
REVERT: B  254 ASP cc_start: 0.7368 (t70) cc_final: 0.6970 (m-30)
REVERT: R  123 TYR cc_start: 0.8565 (m-80) cc_final: 0.8229 (m-80)
REVERT: R  248 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7835 (ttmt)
REVERT: S   79 LEU cc_start: 0.4692 (mt) cc_final: 0.4422 (pp)
REVERT: S  228 TYR cc_start: 0.7509 (m-80) cc_final: 0.6527 (m-80)
REVERT: S  231 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7125 (pp30)
  outliers start: 23
  outliers final: 7
  residues processed: 189
  average time/residue: 0.3974
  time to fit residues: 82.5772
Evaluate side-chains
  176 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 168
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  231 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 108 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** R  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 142 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.208067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.161342 restraints weight = 10318.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 2.44
r_work: 0.3668 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3510 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9139  Z= 0.148
  Angle     :  0.575   7.328  12383  Z= 0.301
  Chirality :  0.043   0.179   1385
  Planarity :  0.005   0.054   1561
  Dihedral  :  5.136  36.357   1279
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.30 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.25), residues: 1112
  helix:  1.56 (0.25), residues: 394
  sheet: -0.75 (0.31), residues: 258
  loop : -1.10 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 214 
 TYR   0.016   0.002   TYR S 190 
 PHE   0.013   0.001   PHE A 189 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9136)
  covalent geometry    : angle       0.57500 (12377)
  SS BOND              : bond        0.00297 (    3)
  SS BOND              : angle       0.59688 (    6)
  hydrogen bonds       : bond        0.03763 (  429)
  hydrogen bonds       : angle       5.11143 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 TYR cc_start: 0.7715 (m-80) cc_final: 0.7396 (m-10)
REVERT: A  274 LYS cc_start: 0.7015 (mmpt) cc_final: 0.6660 (mmtt)
REVERT: B   76 ASP cc_start: 0.8777 (p0) cc_final: 0.8500 (p0)
REVERT: B  163 ASP cc_start: 0.7280 (t0) cc_final: 0.6992 (t0)
REVERT: B  184 THR cc_start: 0.8262 (m) cc_final: 0.8051 (p)
REVERT: B  211 TRP cc_start: 0.8460 (m100) cc_final: 0.8110 (m100)
REVERT: B  254 ASP cc_start: 0.7393 (t70) cc_final: 0.6851 (m-30)
REVERT: R   97 LYS cc_start: 0.8132 (tppt) cc_final: 0.7927 (mttm)
REVERT: R  123 TYR cc_start: 0.8605 (m-80) cc_final: 0.8279 (m-80)
REVERT: R  194 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8161 (p)
REVERT: R  211 TYR cc_start: 0.8048 (t80) cc_final: 0.7695 (t80)
REVERT: R  248 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7742 (ttmt)
REVERT: S  188 LEU cc_start: 0.7215 (mt) cc_final: 0.6836 (mt)
REVERT: S  228 TYR cc_start: 0.7527 (m-80) cc_final: 0.6690 (m-80)
  outliers start: 19
  outliers final: 9
  residues processed: 193
  average time/residue: 0.4065
  time to fit residues: 86.0475
Evaluate side-chains
  185 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 175
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0870
   chunk 3 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0980
   chunk 104 optimal weight:    0.4980
   chunk 53 optimal weight:   10.0000
   chunk 100 optimal weight:    0.0270
   chunk 93 optimal weight:    8.9990
   overall best weight:    0.2816

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 GLN
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
S  82 GLN
S 231 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.211812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.164757 restraints weight = 10466.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 2.33
r_work: 0.3738 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3578 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9139  Z= 0.105
  Angle     :  0.549  13.383  12383  Z= 0.284
  Chirality :  0.042   0.183   1385
  Planarity :  0.004   0.053   1561
  Dihedral  :  4.856  34.889   1279
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.14 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.02 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.25), residues: 1112
  helix:  1.64 (0.25), residues: 394
  sheet: -0.78 (0.31), residues: 262
  loop : -1.00 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 129 
 TYR   0.017   0.001   TYR S  95 
 PHE   0.014   0.001   PHE A 189 
 TRP   0.015   0.002   TRP B 211 
 HIS   0.002   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 9136)
  covalent geometry    : angle       0.54897 (12377)
  SS BOND              : bond        0.00255 (    3)
  SS BOND              : angle       0.46546 (    6)
  hydrogen bonds       : bond        0.03465 (  429)
  hydrogen bonds       : angle       4.79910 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  230 TYR cc_start: 0.7580 (m-80) cc_final: 0.7271 (m-10)
REVERT: A  274 LYS cc_start: 0.7038 (mmpt) cc_final: 0.6724 (mmtt)
REVERT: A  290 ASP cc_start: 0.7009 (p0) cc_final: 0.6445 (t0)
REVERT: B   76 ASP cc_start: 0.8704 (p0) cc_final: 0.8464 (p0)
REVERT: B  163 ASP cc_start: 0.7344 (t0) cc_final: 0.7123 (t0)
REVERT: B  211 TRP cc_start: 0.8393 (m100) cc_final: 0.8156 (m100)
REVERT: B  239 ASN cc_start: 0.7322 (m-40) cc_final: 0.6887 (m110)
REVERT: R   91 PHE cc_start: 0.7258 (m-80) cc_final: 0.7017 (m-80)
REVERT: R  123 TYR cc_start: 0.8582 (m-80) cc_final: 0.8167 (m-80)
REVERT: R  158 MET cc_start: 0.7121 (tmm) cc_final: 0.6891 (ttm)
REVERT: R  194 THR cc_start: 0.8411 (m) cc_final: 0.8072 (p)
REVERT: R  212 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7666 (mmm-85)
REVERT: R  248 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7860 (ttmt)
REVERT: S  188 LEU cc_start: 0.7554 (mt) cc_final: 0.7202 (mt)
REVERT: S  228 TYR cc_start: 0.7541 (m-80) cc_final: 0.6883 (m-80)
REVERT: S  231 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7279 (pp30)
  outliers start: 18
  outliers final: 7
  residues processed: 199
  average time/residue: 0.4315
  time to fit residues: 93.7100
Evaluate side-chains
  184 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 176
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  231 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 108 optimal weight:    9.9990
   chunk 85 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0770
   chunk 98 optimal weight:    8.9990
   chunk 35 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
R  41 ASN
** R  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.210107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.162324 restraints weight = 10329.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.53
r_work: 0.3710 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9139  Z= 0.130
  Angle     :  0.562   8.676  12383  Z= 0.293
  Chirality :  0.043   0.187   1385
  Planarity :  0.004   0.052   1561
  Dihedral  :  4.751  32.484   1278
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.66 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.25), residues: 1112
  helix:  1.65 (0.25), residues: 395
  sheet: -0.76 (0.31), residues: 269
  loop : -0.98 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 214 
 TYR   0.019   0.002   TYR S  95 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9136)
  covalent geometry    : angle       0.56203 (12377)
  SS BOND              : bond        0.00359 (    3)
  SS BOND              : angle       0.76437 (    6)
  hydrogen bonds       : bond        0.03478 (  429)
  hydrogen bonds       : angle       4.74339 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 186
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7495 (mm-30)
REVERT: A  274 LYS cc_start: 0.7053 (mmpt) cc_final: 0.6712 (mmtt)
REVERT: A  290 ASP cc_start: 0.7078 (p0) cc_final: 0.6513 (t0)
REVERT: B  163 ASP cc_start: 0.7344 (t0) cc_final: 0.7032 (t0)
REVERT: B  239 ASN cc_start: 0.7512 (m-40) cc_final: 0.7066 (m110)
REVERT: R  123 TYR cc_start: 0.8589 (m-80) cc_final: 0.8233 (m-80)
REVERT: R  158 MET cc_start: 0.7026 (tmm) cc_final: 0.6768 (ttm)
REVERT: R  194 THR cc_start: 0.8450 (m) cc_final: 0.8095 (p)
REVERT: R  248 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7868 (ttmt)
REVERT: S  140 MET cc_start: 0.5618 (ptm) cc_final: 0.4980 (pp-130)
REVERT: S  188 LEU cc_start: 0.7488 (mt) cc_final: 0.7138 (mt)
REVERT: S  228 TYR cc_start: 0.7615 (m-80) cc_final: 0.6989 (m-80)
  outliers start: 26
  outliers final: 11
  residues processed: 201
  average time/residue: 0.4386
  time to fit residues: 96.0796
Evaluate side-chains
  179 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  325 TYR
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 99 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 108 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** R  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.209621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.161690 restraints weight = 10392.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 2.48
r_work: 0.3707 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9139  Z= 0.127
  Angle     :  0.578  10.906  12383  Z= 0.299
  Chirality :  0.042   0.194   1385
  Planarity :  0.005   0.057   1561
  Dihedral  :  4.708  31.133   1278
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.92 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.25), residues: 1112
  helix:  1.65 (0.25), residues: 396
  sheet: -0.75 (0.31), residues: 269
  loop : -0.98 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 129 
 TYR   0.019   0.002   TYR S 103 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.016   0.001   TRP B 211 
 HIS   0.003   0.001   HIS S 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9136)
  covalent geometry    : angle       0.57809 (12377)
  SS BOND              : bond        0.00272 (    3)
  SS BOND              : angle       0.66975 (    6)
  hydrogen bonds       : bond        0.03450 (  429)
  hydrogen bonds       : angle       4.71580 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  197 HIS cc_start: 0.8215 (m170) cc_final: 0.7890 (m-70)
REVERT: A  274 LYS cc_start: 0.7003 (mmpt) cc_final: 0.6660 (mmtt)
REVERT: A  290 ASP cc_start: 0.7054 (p0) cc_final: 0.6413 (t0)
REVERT: A  310 ASP cc_start: 0.7569 (m-30) cc_final: 0.7302 (m-30)
REVERT: B   59 TYR cc_start: 0.8343 (m-80) cc_final: 0.8037 (m-80)
REVERT: B  163 ASP cc_start: 0.7397 (t0) cc_final: 0.7078 (t0)
REVERT: B  197 ARG cc_start: 0.7775 (mmm160) cc_final: 0.7555 (tpt-90)
REVERT: B  239 ASN cc_start: 0.7548 (m-40) cc_final: 0.7059 (m110)
REVERT: R   91 PHE cc_start: 0.7177 (m-80) cc_final: 0.6899 (m-80)
REVERT: R  123 TYR cc_start: 0.8603 (m-80) cc_final: 0.8269 (m-80)
REVERT: R  194 THR cc_start: 0.8430 (m) cc_final: 0.8048 (p)
REVERT: R  248 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7820 (ttmt)
REVERT: S  188 LEU cc_start: 0.7530 (mt) cc_final: 0.7200 (mt)
REVERT: S  228 TYR cc_start: 0.7514 (m-80) cc_final: 0.6983 (m-80)
REVERT: S  231 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7344 (pp30)
  outliers start: 23
  outliers final: 11
  residues processed: 188
  average time/residue: 0.4299
  time to fit residues: 88.0986
Evaluate side-chains
  180 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 168
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  325 TYR
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  231 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** R  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 296 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.206874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.158084 restraints weight = 10346.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 2.62
r_work: 0.3658 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9139  Z= 0.168
  Angle     :  0.612  10.658  12383  Z= 0.315
  Chirality :  0.043   0.192   1385
  Planarity :  0.005   0.058   1561
  Dihedral  :  4.795  28.874   1278
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.43 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.25), residues: 1112
  helix:  1.61 (0.25), residues: 394
  sheet: -0.81 (0.31), residues: 271
  loop : -0.95 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 129 
 TYR   0.016   0.002   TYR S  95 
 PHE   0.018   0.001   PHE A 189 
 TRP   0.016   0.002   TRP B 211 
 HIS   0.004   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9136)
  covalent geometry    : angle       0.61191 (12377)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.60720 (    6)
  hydrogen bonds       : bond        0.03560 (  429)
  hydrogen bonds       : angle       4.80594 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7114 (mmpt) cc_final: 0.6773 (mmtt)
REVERT: A  290 ASP cc_start: 0.7014 (p0) cc_final: 0.6409 (t0)
REVERT: A  310 ASP cc_start: 0.7461 (m-30) cc_final: 0.7132 (m-30)
REVERT: B  163 ASP cc_start: 0.7220 (t0) cc_final: 0.7017 (t0)
REVERT: R  123 TYR cc_start: 0.8511 (m-80) cc_final: 0.8164 (m-80)
REVERT: R  194 THR cc_start: 0.8490 (m) cc_final: 0.8100 (p)
REVERT: R  211 TYR cc_start: 0.8033 (t80) cc_final: 0.7612 (t80)
REVERT: R  285 LEU cc_start: 0.8419 (mt) cc_final: 0.8202 (mp)
REVERT: S  188 LEU cc_start: 0.7555 (mt) cc_final: 0.7248 (mt)
REVERT: S  228 TYR cc_start: 0.7573 (m-80) cc_final: 0.7031 (m-80)
  outliers start: 24
  outliers final: 17
  residues processed: 191
  average time/residue: 0.3870
  time to fit residues: 81.4890
Evaluate side-chains
  179 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  325 TYR
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  199 VAL
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 87 optimal weight:    6.9990
   chunk 104 optimal weight:    8.9990
   chunk 96 optimal weight:    4.9990
   chunk 81 optimal weight:    0.0770
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0970
   overall best weight:    1.9740

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** R  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.200948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.152564 restraints weight = 10271.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.51
r_work: 0.3563 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   9139  Z= 0.239
  Angle     :  0.667  10.705  12383  Z= 0.344
  Chirality :  0.046   0.200   1385
  Planarity :  0.005   0.058   1561
  Dihedral  :  5.074  36.815   1278
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.56 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.25), residues: 1112
  helix:  1.48 (0.25), residues: 395
  sheet: -0.78 (0.31), residues: 269
  loop : -0.99 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 129 
 TYR   0.021   0.002   TYR B  85 
 PHE   0.017   0.002   PHE A 189 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS R  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 ( 9136)
  covalent geometry    : angle       0.66699 (12377)
  SS BOND              : bond        0.00272 (    3)
  SS BOND              : angle       0.69844 (    6)
  hydrogen bonds       : bond        0.03792 (  429)
  hydrogen bonds       : angle       4.96384 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  290 ASP cc_start: 0.7066 (p0) cc_final: 0.6402 (t0)
REVERT: B   59 TYR cc_start: 0.8247 (m-80) cc_final: 0.7942 (m-80)
REVERT: B  163 ASP cc_start: 0.7441 (t0) cc_final: 0.7142 (t0)
REVERT: B  197 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7575 (tpt-90)
REVERT: B  254 ASP cc_start: 0.7454 (t70) cc_final: 0.7061 (m-30)
REVERT: R  194 THR cc_start: 0.8535 (m) cc_final: 0.8079 (p)
REVERT: R  211 TYR cc_start: 0.8148 (t80) cc_final: 0.7833 (t80)
REVERT: R  285 LEU cc_start: 0.8505 (mt) cc_final: 0.8278 (mp)
REVERT: S  140 MET cc_start: 0.5617 (ptm) cc_final: 0.5335 (ppp)
REVERT: S  188 LEU cc_start: 0.7484 (mt) cc_final: 0.7181 (mt)
REVERT: S  228 TYR cc_start: 0.7635 (m-80) cc_final: 0.7181 (m-80)
REVERT: S  231 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7401 (pp30)
  outliers start: 25
  outliers final: 14
  residues processed: 178
  average time/residue: 0.3986
  time to fit residues: 78.0604
Evaluate side-chains
  176 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  199 VAL
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  230 MET
Chi-restraints excluded: chain S residue  231 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 106 optimal weight:    9.9990
   chunk 58 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** R  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  35 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.205993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.157886 restraints weight = 10313.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 2.35
r_work: 0.3655 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3492 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9139  Z= 0.149
  Angle     :  0.626  10.446  12383  Z= 0.320
  Chirality :  0.044   0.197   1385
  Planarity :  0.005   0.060   1561
  Dihedral  :  4.939  30.837   1278
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 22.18 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.25), residues: 1112
  helix:  1.61 (0.26), residues: 393
  sheet: -0.76 (0.30), residues: 267
  loop : -0.97 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 129 
 TYR   0.014   0.002   TYR S  95 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS S 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9136)
  covalent geometry    : angle       0.62617 (12377)
  SS BOND              : bond        0.00241 (    3)
  SS BOND              : angle       0.74093 (    6)
  hydrogen bonds       : bond        0.03547 (  429)
  hydrogen bonds       : angle       4.84619 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.7903 (tp30) cc_final: 0.7662 (mp0)
REVERT: A  274 LYS cc_start: 0.6785 (mmmt) cc_final: 0.6346 (mmtt)
REVERT: A  290 ASP cc_start: 0.7279 (p0) cc_final: 0.6564 (t0)
REVERT: B  118 ASP cc_start: 0.7123 (p0) cc_final: 0.6836 (p0)
REVERT: B  163 ASP cc_start: 0.7579 (t0) cc_final: 0.7302 (t0)
REVERT: R   91 PHE cc_start: 0.7125 (m-80) cc_final: 0.6852 (m-80)
REVERT: R  123 TYR cc_start: 0.8635 (m-80) cc_final: 0.8294 (m-80)
REVERT: R  186 PHE cc_start: 0.7564 (m-80) cc_final: 0.7277 (m-80)
REVERT: R  194 THR cc_start: 0.8467 (m) cc_final: 0.8040 (p)
REVERT: R  211 TYR cc_start: 0.8073 (t80) cc_final: 0.7728 (t80)
REVERT: R  285 LEU cc_start: 0.8480 (mt) cc_final: 0.8247 (mp)
REVERT: S  188 LEU cc_start: 0.7472 (mt) cc_final: 0.7187 (mt)
REVERT: S  228 TYR cc_start: 0.7516 (m-80) cc_final: 0.7163 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 180
  average time/residue: 0.4015
  time to fit residues: 79.1626
Evaluate side-chains
  176 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  199 VAL
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0970
   chunk 15 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 231 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.206928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.159145 restraints weight = 10315.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 2.35
r_work: 0.3663 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9139  Z= 0.138
  Angle     :  0.630  11.200  12383  Z= 0.319
  Chirality :  0.044   0.225   1385
  Planarity :  0.005   0.060   1561
  Dihedral  :  4.841  29.216   1278
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 22.79 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.25), residues: 1112
  helix:  1.66 (0.25), residues: 394
  sheet: -0.66 (0.31), residues: 265
  loop : -1.02 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 129 
 TYR   0.022   0.002   TYR B  59 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9136)
  covalent geometry    : angle       0.63012 (12377)
  SS BOND              : bond        0.00198 (    3)
  SS BOND              : angle       0.65903 (    6)
  hydrogen bonds       : bond        0.03521 (  429)
  hydrogen bonds       : angle       4.80591 ( 1236)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 LYS cc_start: 0.7012 (mmmt) cc_final: 0.6651 (mmtt)
REVERT: A  290 ASP cc_start: 0.7079 (p0) cc_final: 0.6396 (t0)
REVERT: B  163 ASP cc_start: 0.7377 (t0) cc_final: 0.7089 (t0)
REVERT: R  123 TYR cc_start: 0.8513 (m-80) cc_final: 0.8177 (m-80)
REVERT: R  194 THR cc_start: 0.8473 (m) cc_final: 0.8068 (p)
REVERT: R  211 TYR cc_start: 0.8012 (t80) cc_final: 0.7591 (t80)
REVERT: R  285 LEU cc_start: 0.8493 (mt) cc_final: 0.8274 (mp)
REVERT: S  188 LEU cc_start: 0.7430 (mt) cc_final: 0.7152 (mt)
REVERT: S  228 TYR cc_start: 0.7515 (m-80) cc_final: 0.7159 (m-80)
REVERT: S  231 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7428 (pp30)
  outliers start: 20
  outliers final: 13
  residues processed: 179
  average time/residue: 0.4177
  time to fit residues: 81.9948
Evaluate side-chains
  177 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  199 VAL
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  231 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:    0.0030
   chunk 57 optimal weight:    0.5980
   chunk 89 optimal weight:    9.9990
   chunk 105 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 97 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.206034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.159064 restraints weight = 10205.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 2.45
r_work: 0.3654 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.138   9139  Z= 0.191
  Angle     :  0.952  59.190  12383  Z= 0.544
  Chirality :  0.047   0.664   1385
  Planarity :  0.005   0.060   1561
  Dihedral  :  4.860  29.219   1278
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 23.31 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.25), residues: 1112
  helix:  1.66 (0.25), residues: 394
  sheet: -0.67 (0.31), residues: 265
  loop : -1.02 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 129 
 TYR   0.017   0.002   TYR B  59 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9136)
  covalent geometry    : angle       0.95252 (12377)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       0.64119 (    6)
  hydrogen bonds       : bond        0.03524 (  429)
  hydrogen bonds       : angle       4.81308 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3552.35 seconds
wall clock time: 61 minutes 33.27 seconds (3693.27 seconds total)