Starting phenix.real_space_refine
on Wed Feb  4 09:24:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9skq_54971/02_2026/9skq_54971.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9skq_54971/02_2026/9skq_54971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9skq_54971/02_2026/9skq_54971.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9skq_54971/02_2026/9skq_54971.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9skq_54971/02_2026/9skq_54971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9skq_54971/02_2026/9skq_54971.map"
  }
  resolution = 3.4
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     Mg      1      5.21       5
     S      57      5.16       5
     C    6259      2.51       5
     N    1656      2.21       5
     O    1770      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9750
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2247
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 275, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 260}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 2444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2444
          Classifications: {'peptide': 306}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 287}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2316
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2316
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 270}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2168
          Classifications: {'peptide': 269}
          Link IDs: {'PTRANS': 12, 'TRANS': 256}
    Chain: "J"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.39, per 1000 atoms: 0.25
  Number of scatterers: 9750
  At special positions: 0
  Unit cell: (85.4, 99.4, 137.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      57     16.00
     P       7     15.00
     Mg      1     11.99
     O    1770      8.00
     N    1656      7.00
     C    6259      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.82
  Conformation dependent library (CDL) restraints added in 288.2 milliseconds
  

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2280

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 6 sheets defined
      58.0% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'H' and resid 263 through 267
      removed outlier: 4.426A  pdb=" N   GLY H 267 " --> pdb=" O   GLU H 264 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 271 through 275
    Processing helix  chain 'H' and resid 279 through 286
    Processing helix  chain 'H' and resid 288 through 301
      removed outlier: 3.936A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 38
      removed outlier: 3.712A  pdb=" N   LEU I  19 " --> pdb=" O   SER I  15 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 49 through 69
    Processing helix  chain 'I' and resid 76 through 93
      removed outlier: 4.033A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 116
    Processing helix  chain 'I' and resid 121 through 129
      removed outlier: 4.007A  pdb=" N   LEU I 129 " --> pdb=" O   PHE I 125 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 133 through 154
      removed outlier: 4.515A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 178
    Processing helix  chain 'I' and resid 183 through 186
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.709A  pdb=" N   ALA I 191 " --> pdb=" O   LEU I 187 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
      removed outlier: 3.607A  pdb=" N   LEU I 205 " --> pdb=" O   ASP I 202 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 228 through 234
    Processing helix  chain 'I' and resid 241 through 262
    Processing helix  chain 'I' and resid 266 through 282
    Processing helix  chain 'J' and resid 56 through 67
    Processing helix  chain 'J' and resid 98 through 104
      removed outlier: 3.510A  pdb=" N   ASP J 104 " --> pdb=" O   VAL J 100 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 110 through 131
      removed outlier: 3.628A  pdb=" N   HIS J 131 " --> pdb=" O   TYR J 127 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 139 through 141
      No H-bonds generated for 'chain 'J' and resid 139 through 141'
    Processing helix  chain 'J' and resid 155 through 159
      removed outlier: 4.300A  pdb=" N   LEU J 158 " --> pdb=" O   ASP J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 175 through 179
      removed outlier: 3.694A  pdb=" N   ARG J 179 " --> pdb=" O   ARG J 176 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 180 through 186
    Processing helix  chain 'J' and resid 192 through 209
      removed outlier: 3.859A  pdb=" N   ALA J 198 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 233 through 237
    Processing helix  chain 'J' and resid 239 through 243
    Processing helix  chain 'J' and resid 256 through 261
      removed outlier: 3.589A  pdb=" N   ILE J 260 " --> pdb=" O   PRO J 256 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE J 261 " --> pdb=" O   LEU J 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 256 through 261'
    Processing helix  chain 'J' and resid 265 through 276
    Processing helix  chain 'J' and resid 285 through 291
    Processing helix  chain 'J' and resid 292 through 297
      removed outlier: 3.840A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 87 through 94
    Processing helix  chain 'A' and resid 101 through 122
    Processing helix  chain 'A' and resid 171 through 176
    Processing helix  chain 'A' and resid 184 through 200
      removed outlier: 3.555A  pdb=" N   TRP A 188 " --> pdb=" O   PRO A 184 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   SER A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ILE A 190 " --> pdb=" O   ASP A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 221
    Processing helix  chain 'A' and resid 249 through 254
      removed outlier: 3.539A  pdb=" N   VAL A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LYS A 254 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 254'
    Processing helix  chain 'A' and resid 257 through 268
      removed outlier: 3.568A  pdb=" N   LEU A 263 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.634A  pdb=" N   LEU A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 288
      removed outlier: 5.887A  pdb=" N   TYR A 286 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 185
      removed outlier: 4.098A  pdb=" N   ARG B 179 " --> pdb=" O   TYR B 175 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   GLN B 180 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU B 183 " --> pdb=" O   ARG B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 216
      removed outlier: 3.882A  pdb=" N   ILE B 204 " --> pdb=" O   ASN B 200 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU B 205 " --> pdb=" O   MET B 201 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   MET B 214 " --> pdb=" O   VAL B 210 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS B 215 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE B 216 " --> pdb=" O   VAL B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 235
      removed outlier: 4.375A  pdb=" N   MET B 223 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   TYR B 224 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 242
      No H-bonds generated for 'chain 'B' and resid 240 through 242'
    Processing helix  chain 'B' and resid 243 through 260
      removed outlier: 3.748A  pdb=" N   TYR B 258 " --> pdb=" O   ILE B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 272
      removed outlier: 3.631A  pdb=" N   PHE B 269 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL B 272 " --> pdb=" O   ASP B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 294
    Processing helix  chain 'B' and resid 301 through 313
      removed outlier: 3.972A  pdb=" N   PHE B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 331
    Processing helix  chain 'B' and resid 340 through 356
    Processing helix  chain 'B' and resid 362 through 364
      No H-bonds generated for 'chain 'B' and resid 362 through 364'
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 376 through 392
    Processing helix  chain 'B' and resid 397 through 402
      removed outlier: 4.410A  pdb=" N   LYS B 401 " --> pdb=" O   HIS B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 419
      Proline residue:  B 416  - end of helix
    Processing helix  chain 'B' and resid 420 through 429
      removed outlier: 3.562A  pdb=" N   GLN B 424 " --> pdb=" O   SER B 420 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B 426 " --> pdb=" O   LEU B 422 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA B 429 " --> pdb=" O   ASP B 425 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'J' and resid 19 through 20
      removed outlier: 3.533A  pdb=" N   ALA J  29 " --> pdb=" O   VAL J  38 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU J  89 " --> pdb=" O   LYS J  41 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASP J  79 " --> pdb=" O   VAL J  90 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   LEU J  77 " --> pdb=" O   ASP J  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134
    Processing sheet with id=AA4, first strand: chain 'A' and resid 6 through 11
      removed outlier: 5.903A  pdb=" N   LYS A   6 " --> pdb=" O   ARG A  22 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ARG A  22 " --> pdb=" O   LYS A   6 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL A  18 " --> pdb=" O   ILE A  10 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR A  19 " --> pdb=" O   MET A  32 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86
      removed outlier: 4.020A  pdb=" N   MET A  85 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 124 through 125

    454 hydrogen bonds defined for protein.
    1293 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: 1.50

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3123
        1.35 -     1.47: 2277
        1.47 -     1.59: 4468
        1.59 -     1.71: 8
        1.71 -     1.83: 100
  Bond restraints: 9976
  Sorted by residual:
  bond pdb=" C   ACE I   0 "
       pdb=" O   ACE I   0 "
    ideal  model  delta    sigma   weight residual
    1.199  1.230 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" CG  LEU I 249 "
       pdb=" CD2 LEU I 249 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.22e+00
  bond pdb=" CB  ASP I  44 "
       pdb=" CG  ASP I  44 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.09e+00
  bond pdb=" CA  ASP I  44 "
       pdb=" C   ASP I  44 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.10e-02 2.27e+03 9.53e-01
  bond pdb=" CB  MET B 243 "
       pdb=" CG  MET B 243 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.36e-01
  ... (remaining 9971 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 13436
        2.95 -     5.90: 68
        5.90 -     8.85: 5
        8.85 -    11.79: 4
       11.79 -    14.74: 1
  Bond angle restraints: 13514
  Sorted by residual:
  angle pdb=" CA  MET B 243 "
        pdb=" CB  MET B 243 "
        pdb=" CG  MET B 243 "
      ideal   model   delta    sigma   weight residual
     114.10  122.62   -8.52 2.00e+00 2.50e-01 1.81e+01
  angle pdb=" CA  LEU J 344 "
        pdb=" CB  LEU J 344 "
        pdb=" CG  LEU J 344 "
      ideal   model   delta    sigma   weight residual
     116.30  131.04  -14.74 3.50e+00 8.16e-02 1.77e+01
  angle pdb=" CA  LEU B 329 "
        pdb=" CB  LEU B 329 "
        pdb=" CG  LEU B 329 "
      ideal   model   delta    sigma   weight residual
     116.30  128.06  -11.76 3.50e+00 8.16e-02 1.13e+01
  angle pdb=" CB  MET B 243 "
        pdb=" CG  MET B 243 "
        pdb=" SD  MET B 243 "
      ideal   model   delta    sigma   weight residual
     112.70  122.48   -9.78 3.00e+00 1.11e-01 1.06e+01
  angle pdb=" CA  LEU I 245 "
        pdb=" CB  LEU I 245 "
        pdb=" CG  LEU I 245 "
      ideal   model   delta    sigma   weight residual
     116.30  127.15  -10.85 3.50e+00 8.16e-02 9.61e+00
  ... (remaining 13509 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5146
       17.97 -    35.94: 707
       35.94 -    53.90: 167
       53.90 -    71.87: 36
       71.87 -    89.84: 21
  Dihedral angle restraints: 6077
    sinusoidal: 2550
      harmonic: 3527
  Sorted by residual:
  dihedral pdb=" CA  MET J  94 "
           pdb=" C   MET J  94 "
           pdb=" N   GLU J  95 "
           pdb=" CA  GLU J  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.20  -17.80     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  ASP J 239 "
           pdb=" CB  ASP J 239 "
           pdb=" CG  ASP J 239 "
           pdb=" OD1 ASP J 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.76   57.76     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  LEU A  70 "
           pdb=" C   LEU A  70 "
           pdb=" N   MET A  71 "
           pdb=" CA  MET A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.59   16.41     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 6074 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 930
       0.031 -    0.061: 372
       0.061 -    0.091: 125
       0.091 -    0.122: 65
       0.122 -    0.152: 8
  Chirality restraints: 1500
  Sorted by residual:
  chirality pdb=" CA  ASP I  44 "
            pdb=" N   ASP I  44 "
            pdb=" C   ASP I  44 "
            pdb=" CB  ASP I  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.81e-01
  chirality pdb=" CG  LEU I  22 "
            pdb=" CB  LEU I  22 "
            pdb=" CD1 LEU I  22 "
            pdb=" CD2 LEU I  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  MET J  94 "
            pdb=" N   MET J  94 "
            pdb=" C   MET J  94 "
            pdb=" CB  MET J  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.70e-01
  ... (remaining 1497 not shown)

  Planarity restraints: 1706
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP J 137 "    0.013 2.00e-02 2.50e+03   2.68e-02 7.17e+00
        pdb=" CG  ASP J 137 "   -0.046 2.00e-02 2.50e+03
        pdb=" OD1 ASP J 137 "    0.017 2.00e-02 2.50e+03
        pdb=" OD2 ASP J 137 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP J 137 "   -0.011 2.00e-02 2.50e+03   2.11e-02 4.47e+00
        pdb=" C   ASP J 137 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASP J 137 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU J 138 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU I 185 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.10e+00
        pdb=" CD  GLU I 185 "    0.035 2.00e-02 2.50e+03
        pdb=" OE1 GLU I 185 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU I 185 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1703 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 102
        2.62 -     3.19: 8584
        3.19 -     3.76: 15019
        3.76 -     4.33: 20513
        4.33 -     4.90: 34099
  Nonbonded interactions: 78317
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN J 142 "
            pdb="MG    MG J 402 "
     model   vdw
     2.055 2.170
  nonbonded pdb=" OG1 THR A  14 "
            pdb=" O2G ANP A 301 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   GLN B 417 "
            pdb=" OG  SER B 420 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OH  TYR I 178 "
            pdb=" OG  SER I 230 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ALA A 198 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.255 3.120
  ... (remaining 78312 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:             0.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.140
  Find NCS groups from input model:        0.070
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
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      :  0.002   0.036   9976  Z= 0.114
  Angle     :  0.598  14.743  13514  Z= 0.300
  Chirality :  0.041   0.152   1500
  Planarity :  0.004   0.046   1706
  Dihedral  : 17.835  89.837   3797
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  3.72 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 26.65 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.17 (0.25), residues: 1182
  helix:  1.44 (0.22), residues: 580
  sheet: -2.66 (0.58), residues: 65
  loop : -1.01 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 299 
 TYR   0.010   0.001   TYR I  60 
 PHE   0.014   0.001   PHE B 339 
 TRP   0.006   0.001   TRP A 188 
 HIS   0.003   0.000   HIS B 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9976)
  covalent geometry    : angle       0.59759 (13514)
  hydrogen bonds       : bond        0.16143 (  454)
  hydrogen bonds       : angle       6.35423 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 174
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  137 ASP cc_start: 0.8413 (t0) cc_final: 0.8132 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 176
  average time/residue: 0.1012
  time to fit residues: 24.8518
Evaluate side-chains
  167 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  177 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.0040
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    2.5598

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

Flipped N/Q/H residues before XYZ refinement:
I 124 GLN
I 128 ASN
I 152 GLN
I 196 ASN
I 247 GLN
J 221 GLN
J 306 GLN
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 386 ASN
B 391 ASN
B 419 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.141734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.115409 restraints weight = 14860.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.05
r_work: 0.3192 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.0960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9976  Z= 0.190
  Angle     :  0.605  12.416  13514  Z= 0.306
  Chirality :  0.043   0.149   1500
  Planarity :  0.005   0.053   1706
  Dihedral  :  7.743  86.029   1381
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.16 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.67 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.30 (0.25), residues: 1182
  helix:  1.66 (0.22), residues: 592
  sheet: -2.53 (0.60), residues: 61
  loop : -1.18 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  75 
 TYR   0.012   0.001   TYR I  60 
 PHE   0.024   0.002   PHE B 253 
 TRP   0.007   0.001   TRP A 188 
 HIS   0.004   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 9976)
  covalent geometry    : angle       0.60516 (13514)
  hydrogen bonds       : bond        0.04950 (  454)
  hydrogen bonds       : angle       4.74419 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 168
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  128 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.8016 (t0)
REVERT: I  231 TYR cc_start: 0.8484 (t80) cc_final: 0.8173 (t80)
REVERT: J   52 LYS cc_start: 0.8668 (tptt) cc_final: 0.7535 (ptpp)
REVERT: J   94 MET cc_start: 0.8098 (mmm) cc_final: 0.7881 (mmp)
REVERT: J  137 ASP cc_start: 0.8807 (t0) cc_final: 0.8232 (t0)
  outliers start: 35
  outliers final: 19
  residues processed: 194
  average time/residue: 0.0989
  time to fit residues: 27.1408
Evaluate side-chains
  181 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  116 ASP
Chi-restraints excluded: chain I residue  128 ASN
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   43 ILE
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
I 124 GLN
I 128 ASN
I 152 GLN
A 162 HIS
A 224 ASN
B 281 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.116015 restraints weight = 14701.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.03
r_work: 0.3211 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9976  Z= 0.144
  Angle     :  0.567  13.003  13514  Z= 0.285
  Chirality :  0.042   0.141   1500
  Planarity :  0.004   0.054   1706
  Dihedral  :  7.310  86.675   1377
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.31 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 23.92 %
    Favored  : 72.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.43 (0.25), residues: 1182
  helix:  1.86 (0.22), residues: 587
  sheet: -2.53 (0.59), residues: 61
  loop : -1.21 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 209 
 TYR   0.012   0.001   TYR I  60 
 PHE   0.020   0.001   PHE B 253 
 TRP   0.005   0.001   TRP J 132 
 HIS   0.004   0.001   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9976)
  covalent geometry    : angle       0.56716 (13514)
  hydrogen bonds       : bond        0.04212 (  454)
  hydrogen bonds       : angle       4.49041 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 166
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: I  198 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7567 (mt)
REVERT: J   11 ARG cc_start: 0.7522 (ptm160) cc_final: 0.7210 (ptm-80)
REVERT: J   52 LYS cc_start: 0.8686 (tptt) cc_final: 0.7575 (ptpp)
REVERT: J  137 ASP cc_start: 0.8961 (t0) cc_final: 0.8278 (t0)
REVERT: A  157 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8231 (mm)
REVERT: B  281 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8015 (pm20)
  outliers start: 37
  outliers final: 23
  residues processed: 191
  average time/residue: 0.1006
  time to fit residues: 26.9543
Evaluate side-chains
  180 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue  116 ASP
Chi-restraints excluded: chain I residue  142 GLN
Chi-restraints excluded: chain I residue  149 LEU
Chi-restraints excluded: chain I residue  180 ILE
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  281 GLN
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
I 124 GLN
** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 152 GLN
A 162 HIS
A 224 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.139738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.113793 restraints weight = 14980.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.04
r_work: 0.3178 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9976  Z= 0.197
  Angle     :  0.622  13.991  13514  Z= 0.309
  Chirality :  0.045   0.361   1500
  Planarity :  0.005   0.055   1706
  Dihedral  :  7.319  87.331   1377
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.33 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 23.63 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.29 (0.25), residues: 1182
  helix:  1.65 (0.22), residues: 597
  sheet: -2.61 (0.62), residues: 53
  loop : -1.23 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I 177 
 TYR   0.013   0.001   TYR I  60 
 PHE   0.017   0.002   PHE B 253 
 TRP   0.008   0.001   TRP J 132 
 HIS   0.004   0.001   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 9976)
  covalent geometry    : angle       0.62211 (13514)
  hydrogen bonds       : bond        0.04570 (  454)
  hydrogen bonds       : angle       4.50786 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 160
  time to evaluate  : 0.337 
Fit side-chains
REVERT: I   54 MET cc_start: 0.7948 (mmm) cc_final: 0.7602 (mmt)
REVERT: I   88 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8897 (mtmt)
REVERT: I  105 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7897 (ttm)
REVERT: I  185 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: I  198 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7839 (mt)
REVERT: J   52 LYS cc_start: 0.8726 (tptt) cc_final: 0.7607 (ptpp)
REVERT: A  157 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8275 (mm)
REVERT: B  261 MET cc_start: 0.7661 (mtp) cc_final: 0.7423 (mtp)
REVERT: B  279 LYS cc_start: 0.6686 (ttpt) cc_final: 0.6446 (ttpp)
REVERT: B  281 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8131 (pm20)
  outliers start: 45
  outliers final: 32
  residues processed: 190
  average time/residue: 0.0989
  time to fit residues: 25.8644
Evaluate side-chains
  193 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 156
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   22 LEU
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   88 LYS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  116 ASP
Chi-restraints excluded: chain I residue  149 LEU
Chi-restraints excluded: chain I residue  180 ILE
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  269 PHE
Chi-restraints excluded: chain B residue  281 GLN
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 113 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0570
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.7904

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

Flipped N/Q/H residues before XYZ refinement:
** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 152 GLN
A 162 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115211 restraints weight = 14916.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.03
r_work: 0.3201 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9976  Z= 0.146
  Angle     :  0.593  14.438  13514  Z= 0.293
  Chirality :  0.043   0.290   1500
  Planarity :  0.004   0.054   1706
  Dihedral  :  7.143  88.557   1377
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.40 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 24.86 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.46 (0.25), residues: 1182
  helix:  1.81 (0.22), residues: 591
  sheet: -2.53 (0.65), residues: 51
  loop : -1.15 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 268 
 TYR   0.014   0.001   TYR B 334 
 PHE   0.016   0.001   PHE B 253 
 TRP   0.005   0.001   TRP J 132 
 HIS   0.005   0.001   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9976)
  covalent geometry    : angle       0.59272 (13514)
  hydrogen bonds       : bond        0.04088 (  454)
  hydrogen bonds       : angle       4.37568 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 170
  time to evaluate  : 0.265 
Fit side-chains
REVERT: I   88 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8892 (mtmt)
REVERT: I  105 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7886 (ttm)
REVERT: I  185 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8023 (tm-30)
REVERT: I  198 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7735 (mt)
REVERT: A  157 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8236 (mm)
REVERT: B  185 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7908 (mt0)
REVERT: B  299 ARG cc_start: 0.7437 (mtt180) cc_final: 0.7059 (mtp85)
  outliers start: 45
  outliers final: 33
  residues processed: 198
  average time/residue: 0.0875
  time to fit residues: 24.7211
Evaluate side-chains
  198 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   88 LYS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  116 ASP
Chi-restraints excluded: chain I residue  149 LEU
Chi-restraints excluded: chain I residue  180 ILE
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  269 PHE
Chi-restraints excluded: chain B residue  277 TYR
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  415 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   chunk 91 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 109 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
I 124 GLN
** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
A 224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.137999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112354 restraints weight = 15142.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.03
r_work: 0.3138 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   9976  Z= 0.269
  Angle     :  0.698  15.288  13514  Z= 0.346
  Chirality :  0.047   0.245   1500
  Planarity :  0.005   0.056   1706
  Dihedral  :  7.333  91.257   1377
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.67 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 24.11 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole: -0.09 (0.24), residues: 1182
  helix:  1.34 (0.21), residues: 594
  sheet: -2.66 (0.62), residues: 54
  loop : -1.42 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG J 209 
 TYR   0.014   0.002   TYR B 334 
 PHE   0.022   0.002   PHE B 253 
 TRP   0.011   0.002   TRP J 132 
 HIS   0.007   0.001   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 ( 9976)
  covalent geometry    : angle       0.69755 (13514)
  hydrogen bonds       : bond        0.05248 (  454)
  hydrogen bonds       : angle       4.64895 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 156
  time to evaluate  : 0.405 
Fit side-chains
REVERT: I   54 MET cc_start: 0.7998 (mmm) cc_final: 0.7693 (mmt)
REVERT: I   88 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8914 (mtmt)
REVERT: I  105 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7911 (ttm)
REVERT: I  185 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8189 (tm-30)
REVERT: I  198 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8027 (mt)
REVERT: J   27 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.7162 (p90)
REVERT: J   94 MET cc_start: 0.8379 (mmm) cc_final: 0.8175 (mmp)
REVERT: A  157 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8324 (mm)
REVERT: A  256 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8171 (mt)
  outliers start: 56
  outliers final: 37
  residues processed: 196
  average time/residue: 0.0966
  time to fit residues: 26.5954
Evaluate side-chains
  192 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue   88 LYS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  116 ASP
Chi-restraints excluded: chain I residue  140 LEU
Chi-restraints excluded: chain I residue  149 LEU
Chi-restraints excluded: chain I residue  180 ILE
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   27 TYR
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   43 ILE
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  415 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0060
   chunk 34 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 63 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.4198

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

Flipped N/Q/H residues before XYZ refinement:
I 128 ASN
A 162 HIS
A 224 ASN
** B 281 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 = 0.3675 r_free = 0.3675 target = 0.141119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115336 restraints weight = 14895.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.04
r_work: 0.3195 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9976  Z= 0.135
  Angle     :  0.594  14.248  13514  Z= 0.298
  Chirality :  0.044   0.426   1500
  Planarity :  0.005   0.073   1706
  Dihedral  :  6.935  96.441   1377
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.23 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 24.86 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.28 (0.25), residues: 1182
  helix:  1.71 (0.22), residues: 588
  sheet: -2.73 (0.62), residues: 53
  loop : -1.27 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I 177 
 TYR   0.012   0.001   TYR I  60 
 PHE   0.022   0.001   PHE B 253 
 TRP   0.007   0.001   TRP B 208 
 HIS   0.004   0.001   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9976)
  covalent geometry    : angle       0.59399 (13514)
  hydrogen bonds       : bond        0.03968 (  454)
  hydrogen bonds       : angle       4.37955 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 162
  time to evaluate  : 0.376 
Fit side-chains
REVERT: H  307 GLN cc_start: 0.6586 (pm20) cc_final: 0.6384 (pm20)
REVERT: I   54 MET cc_start: 0.8063 (mmm) cc_final: 0.7691 (mmt)
REVERT: I   88 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8892 (mtmt)
REVERT: I  105 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7894 (ttm)
REVERT: I  128 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7871 (t0)
REVERT: I  185 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: J   52 LYS cc_start: 0.8787 (tppt) cc_final: 0.7560 (ptpp)
REVERT: B  185 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8038 (mt0)
REVERT: B  299 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7403 (mtp85)
  outliers start: 52
  outliers final: 38
  residues processed: 195
  average time/residue: 0.1030
  time to fit residues: 27.9967
Evaluate side-chains
  202 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 160
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   88 LYS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  116 ASP
Chi-restraints excluded: chain I residue  128 ASN
Chi-restraints excluded: chain I residue  149 LEU
Chi-restraints excluded: chain I residue  180 ILE
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  234 MET
Chi-restraints excluded: chain B residue  269 PHE
Chi-restraints excluded: chain B residue  277 TYR
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
I 124 GLN
** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
A 224 ASN
** B 281 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 = 0.3661 r_free = 0.3661 target = 0.140009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.114226 restraints weight = 15016.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.04
r_work: 0.3174 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9976  Z= 0.179
  Angle     :  0.626  14.330  13514  Z= 0.311
  Chirality :  0.045   0.401   1500
  Planarity :  0.005   0.099   1706
  Dihedral  :  6.868  96.806   1377
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.08 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.29 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.22 (0.25), residues: 1182
  helix:  1.67 (0.22), residues: 587
  sheet: -2.72 (0.62), residues: 53
  loop : -1.30 (0.25), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG I 177 
 TYR   0.013   0.001   TYR I  60 
 PHE   0.020   0.002   PHE B 253 
 TRP   0.006   0.001   TRP J 132 
 HIS   0.004   0.001   HIS B 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 9976)
  covalent geometry    : angle       0.62570 (13514)
  hydrogen bonds       : bond        0.04265 (  454)
  hydrogen bonds       : angle       4.45743 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 165
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  307 GLN cc_start: 0.6594 (pm20) cc_final: 0.6384 (pm20)
REVERT: I   54 MET cc_start: 0.7943 (mmm) cc_final: 0.7621 (mmt)
REVERT: I   88 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8893 (mtmt)
REVERT: I  105 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7902 (ttm)
REVERT: I  185 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: B  185 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8066 (mt0)
REVERT: B  299 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7416 (mtp85)
  outliers start: 51
  outliers final: 40
  residues processed: 199
  average time/residue: 0.0945
  time to fit residues: 26.4663
Evaluate side-chains
  205 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 162
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   88 LYS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  116 ASP
Chi-restraints excluded: chain I residue  149 LEU
Chi-restraints excluded: chain I residue  180 ILE
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   43 ILE
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  234 MET
Chi-restraints excluded: chain B residue  269 PHE
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  415 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 80 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
H 274 HIS
I 128 ASN
A  72 GLN
A 224 ASN
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.142568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.116988 restraints weight = 14796.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.02
r_work: 0.3212 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9976  Z= 0.121
  Angle     :  0.592  14.332  13514  Z= 0.295
  Chirality :  0.044   0.392   1500
  Planarity :  0.005   0.066   1706
  Dihedral  :  6.663  99.830   1377
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.06 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 25.80 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.45 (0.25), residues: 1182
  helix:  1.84 (0.22), residues: 588
  sheet: -2.60 (0.64), residues: 53
  loop : -1.18 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG I 177 
 TYR   0.012   0.001   TYR I  60 
 PHE   0.019   0.001   PHE B 253 
 TRP   0.007   0.001   TRP A 188 
 HIS   0.004   0.001   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9976)
  covalent geometry    : angle       0.59179 (13514)
  hydrogen bonds       : bond        0.03630 (  454)
  hydrogen bonds       : angle       4.32334 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 164
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: H  307 GLN cc_start: 0.6911 (pm20) cc_final: 0.6611 (pm20)
REVERT: I   54 MET cc_start: 0.8073 (mmm) cc_final: 0.7713 (mmt)
REVERT: I  105 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7676 (ttm)
REVERT: I  185 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8170 (tm-30)
REVERT: I  187 LEU cc_start: 0.8867 (mp) cc_final: 0.8614 (mp)
REVERT: J   42 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7971 (tmmt)
REVERT: B  185 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7946 (mt0)
REVERT: B  299 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7417 (mtp85)
  outliers start: 39
  outliers final: 34
  residues processed: 188
  average time/residue: 0.0843
  time to fit residues: 22.6784
Evaluate side-chains
  197 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 160
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  149 LEU
Chi-restraints excluded: chain I residue  180 ILE
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   43 ILE
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  234 MET
Chi-restraints excluded: chain B residue  269 PHE
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  415 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 99 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 69 optimal weight:    0.0470
   chunk 30 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
I 124 GLN
** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  72 GLN
A 224 ASN
** B 281 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 = 0.3702 r_free = 0.3702 target = 0.143379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.117886 restraints weight = 14833.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.04
r_work: 0.3221 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9976  Z= 0.111
  Angle     :  0.582  13.750  13514  Z= 0.290
  Chirality :  0.043   0.371   1500
  Planarity :  0.005   0.055   1706
  Dihedral  :  6.545 100.575   1377
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.23 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 25.71 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.56 (0.25), residues: 1182
  helix:  1.92 (0.22), residues: 588
  sheet: -2.44 (0.65), residues: 53
  loop : -1.12 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I 177 
 TYR   0.012   0.001   TYR I  60 
 PHE   0.018   0.001   PHE B 253 
 TRP   0.007   0.001   TRP A 188 
 HIS   0.004   0.001   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9976)
  covalent geometry    : angle       0.58185 (13514)
  hydrogen bonds       : bond        0.03441 (  454)
  hydrogen bonds       : angle       4.26380 ( 1293)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: H  307 GLN cc_start: 0.6912 (pm20) cc_final: 0.6580 (pm20)
REVERT: I   54 MET cc_start: 0.8032 (mmm) cc_final: 0.7630 (mmt)
REVERT: I  105 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7571 (ttm)
REVERT: I  185 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8017 (tm-30)
REVERT: I  187 LEU cc_start: 0.8784 (mp) cc_final: 0.8544 (mp)
REVERT: J   25 THR cc_start: 0.8792 (m) cc_final: 0.8564 (p)
REVERT: J   42 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7784 (tmmt)
REVERT: J   52 LYS cc_start: 0.8783 (tppt) cc_final: 0.7533 (ptpp)
REVERT: J   94 MET cc_start: 0.8127 (mmp) cc_final: 0.7863 (mmp)
REVERT: J  106 SER cc_start: 0.8802 (m) cc_final: 0.8527 (p)
REVERT: B  185 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7913 (mt0)
REVERT: B  299 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7430 (mtp85)
  outliers start: 36
  outliers final: 30
  residues processed: 191
  average time/residue: 0.0920
  time to fit residues: 24.9294
Evaluate side-chains
  200 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 167
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  149 LEU
Chi-restraints excluded: chain I residue  180 ILE
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   43 ILE
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain J residue  107 LEU
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  234 MET
Chi-restraints excluded: chain B residue  269 PHE
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  383 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0570
   chunk 115 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 112 optimal weight:    8.9990
   chunk 93 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.118699 restraints weight = 14785.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.03
r_work: 0.3235 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9976  Z= 0.107
  Angle     :  0.572  13.660  13514  Z= 0.284
  Chirality :  0.043   0.380   1500
  Planarity :  0.005   0.053   1706
  Dihedral  :  6.418 101.065   1377
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.98 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 25.71 %
    Favored  : 71.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.69 %
    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 are not related in a simple way.
  whole:  0.63 (0.25), residues: 1182
  helix:  1.98 (0.22), residues: 588
  sheet: -2.34 (0.65), residues: 53
  loop : -1.10 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I 177 
 TYR   0.011   0.001   TYR I  60 
 PHE   0.018   0.001   PHE B 253 
 TRP   0.006   0.001   TRP A 188 
 HIS   0.004   0.000   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9976)
  covalent geometry    : angle       0.57195 (13514)
  hydrogen bonds       : bond        0.03300 (  454)
  hydrogen bonds       : angle       4.19863 ( 1293)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2264.66 seconds
wall clock time: 39 minutes 34.44 seconds (2374.44 seconds total)