Starting phenix.real_space_refine
on Fri Aug 22 19:49:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ozc_17304/08_2025/8ozc_17304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ozc_17304/08_2025/8ozc_17304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ozc_17304/08_2025/8ozc_17304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ozc_17304/08_2025/8ozc_17304.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ozc_17304/08_2025/8ozc_17304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ozc_17304/08_2025/8ozc_17304.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    4840      2.51       5
     N    1233      2.21       5
     O    1382      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7478
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3758
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 12, 'TRANS': 439}
    Chain: "B"
      Number of atoms: 3720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3720
          Classifications: {'peptide': 461}
          Link IDs: {'PTRANS': 24, 'TRANS': 436}
          Chain breaks: 1
  Time building chain proxies: 2.06, per 1000 atoms: 0.28
  Number of scatterers: 7478
  At special positions: 0
  Unit cell: (76.23, 85.3776, 126.034, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O    1382      8.00
     N    1233      7.00
     C    4840      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: 0.60
  Conformation dependent library (CDL) restraints added in 316.6 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1738

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 11 sheets defined
      36.1% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 28
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 4.054A  pdb=" N   ASN A  69 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 4.237A  pdb=" N   LEU A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 124 through 138
      removed outlier: 4.184A  pdb=" N   GLN A 138 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 227 through 232
      removed outlier: 4.086A  pdb=" N   GLU A 231 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   THR A 232 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 243 through 248
    Processing helix  chain 'A' and resid 257 through 281
      removed outlier: 3.651A  pdb=" N   LYS A 262 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ARG A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU A 264 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A 265 " --> pdb=" O   CYS A 261 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 266 " --> pdb=" O   LYS A 262 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLN A 267 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 302
      No H-bonds generated for 'chain 'A' and resid 300 through 302'
    Processing helix  chain 'A' and resid 354 through 366
    Processing helix  chain 'A' and resid 370 through 385
      removed outlier: 4.693A  pdb=" N   LYS A 376 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 429
      removed outlier: 3.743A  pdb=" N   GLU A 427 " --> pdb=" O   THR A 423 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU A 429 " --> pdb=" O   GLU A 425 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 423 through 429'
    Processing helix  chain 'A' and resid 442 through 448
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 22 through 30
    Processing helix  chain 'B' and resid 46 through 62
    Processing helix  chain 'B' and resid 78 through 83
    Processing helix  chain 'B' and resid 97 through 102
    Processing helix  chain 'B' and resid 109 through 124
      removed outlier: 3.585A  pdb=" N   ASP B 116 " --> pdb=" O   LYS B 112 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   SER B 119 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 151
    Processing helix  chain 'B' and resid 208 through 213
      removed outlier: 4.244A  pdb=" N   ARG B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 217
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 249 through 263
      removed outlier: 3.883A  pdb=" N   ILE B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER B 257 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   THR B 258 " --> pdb=" O   TRP B 254 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   ALA B 259 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA B 260 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   LYS B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 350
      removed outlier: 4.762A  pdb=" N   ALA B 337 " --> pdb=" O   LYS B 333 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 377
      removed outlier: 4.603A  pdb=" N   ALA B 372 " --> pdb=" O   GLN B 368 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLU B 375 " --> pdb=" O   ASP B 371 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 464
      removed outlier: 3.617A  pdb=" N   LYS B 457 " --> pdb=" O   LYS B 453 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 482
    Processing helix  chain 'B' and resid 482 through 493
      removed outlier: 3.844A  pdb=" N   SER B 493 " --> pdb=" O   ILE B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7
      removed outlier: 6.745A  pdb=" N   PHE A   6 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 8.517A  pdb=" N   VAL A  63 " --> pdb=" O   PHE A   6 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   PHE A  60 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   LEU A  97 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   LEU A  62 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 178
      removed outlier: 5.608A  pdb=" N   LYS A 167 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 414 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   VAL A 408 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   TRP A 175 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   GLU A 406 " --> pdb=" O   TRP A 175 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   SER A 177 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   VAL A 401 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.562A  pdb=" N   VAL A 208 " --> pdb=" O   CYS A 215 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A 214 " --> pdb=" O   HIS A 188 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   HIS A 188 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   THR A 216 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG A 186 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 292 through 294
    Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 305
    Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 314
      removed outlier: 3.584A  pdb=" N   ASN A 318 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 6
      removed outlier: 3.671A  pdb=" N   ILE B 443 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU B 420 " --> pdb=" O   LEU B 441 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   GLY B 385 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   VAL B 357 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   VAL B 386 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ILE B 359 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   ILE B 388 " --> pdb=" O   ILE B 359 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ALA B 361 " --> pdb=" O   ILE B 388 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   CYS B 279 " --> pdb=" O   PHE B 358 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   HIS B 360 " --> pdb=" O   CYS B 279 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 20
    Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 143
    Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 305
      removed outlier: 3.903A  pdb=" N   LYS B 314 " --> pdb=" O   GLN B 302 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 425 through 426
      removed outlier: 3.894A  pdb=" N   VAL B 426 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   THR B 431 " --> pdb=" O   VAL B 426 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    227 hydrogen bonds defined for protein.
    612 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: 1.16

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2353
        1.34 -     1.46: 1494
        1.46 -     1.58: 3780
        1.58 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 7662
  Sorted by residual:
  bond pdb=" C   LEU A 227 "
       pdb=" O   LEU A 227 "
    ideal  model  delta    sigma   weight residual
    1.249  1.238  0.011 8.50e-03 1.38e+04 1.72e+00
  bond pdb=" C   ASN B 322 "
       pdb=" N   PRO B 323 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.25e-02 6.40e+03 1.63e+00
  bond pdb=" CA  ILE B 248 "
       pdb=" CB  ILE B 248 "
    ideal  model  delta    sigma   weight residual
    1.535  1.550 -0.015 1.29e-02 6.01e+03 1.35e+00
  bond pdb=" CD  GLU A 133 "
       pdb=" OE1 GLU A 133 "
    ideal  model  delta    sigma   weight residual
    1.249  1.227  0.022 1.90e-02 2.77e+03 1.35e+00
  bond pdb=" CA  GLU B 348 "
       pdb=" C   GLU B 348 "
    ideal  model  delta    sigma   weight residual
    1.522  1.539 -0.016 1.40e-02 5.10e+03 1.35e+00
  ... (remaining 7657 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 10206
        2.21 -     4.43: 120
        4.43 -     6.64: 22
        6.64 -     8.85: 2
        8.85 -    11.07: 1
  Bond angle restraints: 10351
  Sorted by residual:
  angle pdb=" CA  GLU B 348 "
        pdb=" C   GLU B 348 "
        pdb=" N   GLN B 349 "
      ideal   model   delta    sigma   weight residual
     118.14  129.21  -11.07 1.31e+00 5.83e-01 7.14e+01
  angle pdb=" CA  GLU B 348 "
        pdb=" C   GLU B 348 "
        pdb=" O   GLU B 348 "
      ideal   model   delta    sigma   weight residual
     119.38  113.21    6.17 1.23e+00 6.61e-01 2.52e+01
  angle pdb=" C   LEU A 132 "
        pdb=" N   GLU A 133 "
        pdb=" CA  GLU A 133 "
      ideal   model   delta    sigma   weight residual
     120.72  113.42    7.30 1.67e+00 3.59e-01 1.91e+01
  angle pdb=" N   VAL A  43 "
        pdb=" CA  VAL A  43 "
        pdb=" C   VAL A  43 "
      ideal   model   delta    sigma   weight residual
     113.42  108.67    4.75 1.17e+00 7.31e-01 1.65e+01
  angle pdb=" N   GLU A 133 "
        pdb=" CA  GLU A 133 "
        pdb=" CB  GLU A 133 "
      ideal   model   delta    sigma   weight residual
     110.39  117.12   -6.73 1.66e+00 3.63e-01 1.64e+01
  ... (remaining 10346 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 4135
       17.43 -    34.85: 394
       34.85 -    52.28: 54
       52.28 -    69.70: 8
       69.70 -    87.13: 4
  Dihedral angle restraints: 4595
    sinusoidal: 1907
      harmonic: 2688
  Sorted by residual:
  dihedral pdb=" CA  LYS B  85 "
           pdb=" C   LYS B  85 "
           pdb=" N   TRP B  86 "
           pdb=" CA  TRP B  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.16   23.84     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  LYS B 324 "
           pdb=" C   LYS B 324 "
           pdb=" N   ASN B 325 "
           pdb=" CA  ASN B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.34  -20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  PHE B 313 "
           pdb=" C   PHE B 313 "
           pdb=" N   LYS B 314 "
           pdb=" CA  LYS B 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.47  -18.53     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 4592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 876
       0.048 -    0.095: 181
       0.095 -    0.143: 54
       0.143 -    0.190: 2
       0.190 -    0.238: 1
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CB  ILE B 248 "
            pdb=" CA  ILE B 248 "
            pdb=" CG1 ILE B 248 "
            pdb=" CG2 ILE B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  GLN B 349 "
            pdb=" N   GLN B 349 "
            pdb=" C   GLN B 349 "
            pdb=" CB  GLN B 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.32e-01
  chirality pdb=" CA  GLU A 133 "
            pdb=" N   GLU A 133 "
            pdb=" C   GLU A 133 "
            pdb=" CB  GLU A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 1111 not shown)

  Planarity restraints: 1311
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  86 "   -0.019 2.00e-02 2.50e+03   1.63e-02 6.62e+00
        pdb=" CG  TRP B  86 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  86 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  86 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  86 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  86 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  86 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  86 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  86 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  86 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 499 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.84e+00
        pdb=" N   PRO B 500 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 500 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 500 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 175 "    0.014 2.00e-02 2.50e+03   1.25e-02 3.90e+00
        pdb=" CG  TRP A 175 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 175 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 175 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 175 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 175 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 175 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 175 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 175 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 175 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1308 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 168
        2.68 -     3.23: 7300
        3.23 -     3.79: 11796
        3.79 -     4.34: 15451
        4.34 -     4.90: 24496
  Nonbonded interactions: 59211
  Sorted by model distance:
  nonbonded pdb=" O   TRP B 269 "
            pdb=" OH  TYR B 467 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OH  TYR A 416 "
            pdb=" O   THR B 404 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OG1 THR B 377 "
            pdb=" OG1 THR B 381 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OE1 GLU A 429 "
            pdb=" OG1 THR B 431 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" ND2 ASN B 322 "
            pdb=" O   HIS B 329 "
     model   vdw
     2.264 3.120
  ... (remaining 59206 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 group one per residue
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:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.810
  Find NCS groups from input model:        0.040
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6370
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   0.030   7662  Z= 0.117
  Angle     :  0.618  11.066  10351  Z= 0.342
  Chirality :  0.042   0.238   1114
  Planarity :  0.004   0.055   1311
  Dihedral  : 13.399  87.128   2857
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.73 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (0.28), residues: 907
  helix: -0.00 (0.34), residues: 262
  sheet: -1.09 (0.51), residues: 120
  loop : -2.14 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 481 
 TYR   0.025   0.001   TYR A 190 
 PHE   0.025   0.001   PHE A 135 
 TRP   0.044   0.002   TRP B  86 
 HIS   0.011   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7662)
  covalent geometry    : angle       0.61799 (10351)
  hydrogen bonds       : bond        0.23213 (  227)
  hydrogen bonds       : angle       7.60403 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.3722 (tmtt) cc_final: 0.3486 (tptp)
REVERT: A   94 ILE cc_start: 0.7719 (pt) cc_final: 0.7335 (pt)
REVERT: A  122 MET cc_start: 0.5792 (tpt) cc_final: 0.5465 (tpt)
REVERT: A  198 PHE cc_start: 0.7769 (m-80) cc_final: 0.7415 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0948
  time to fit residues: 17.1775
Evaluate side-chains
  96 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0070
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.4002

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 409 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.161316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.138109 restraints weight = 27170.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.140277 restraints weight = 21244.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.142049 restraints weight = 17684.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.143299 restraints weight = 15240.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.144297 restraints weight = 13568.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   7662  Z= 0.170
  Angle     :  0.675  11.639  10351  Z= 0.352
  Chirality :  0.045   0.284   1114
  Planarity :  0.005   0.055   1311
  Dihedral  :  4.580  21.569    983
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 19.22
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.94 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 10.27 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.27), residues: 907
  helix: -0.35 (0.31), residues: 288
  sheet: -0.99 (0.53), residues: 108
  loop : -2.35 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  71 
 TYR   0.016   0.002   TYR B 280 
 PHE   0.030   0.002   PHE A 305 
 TRP   0.031   0.002   TRP B  86 
 HIS   0.009   0.002   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 7662)
  covalent geometry    : angle       0.67539 (10351)
  hydrogen bonds       : bond        0.04121 (  227)
  hydrogen bonds       : angle       5.76557 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5766 (p0)
REVERT: A   51 LYS cc_start: 0.3718 (tmtt) cc_final: 0.3516 (tmtt)
REVERT: A  122 MET cc_start: 0.6231 (tpt) cc_final: 0.5854 (tpt)
REVERT: A  198 PHE cc_start: 0.7355 (m-80) cc_final: 0.7080 (m-80)
REVERT: B   74 MET cc_start: 0.5998 (ppp) cc_final: 0.5485 (ppp)
REVERT: B  247 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7274 (pttm)
  outliers start: 21
  outliers final: 12
  residues processed: 135
  average time/residue: 0.1120
  time to fit residues: 19.8132
Evaluate side-chains
  117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 39 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 44 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 138 GLN
A 191 ASN
B 344 GLN
** B 368 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 = 0.4588 r_free = 0.4588 target = 0.171635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.152138 restraints weight = 32069.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.154142 restraints weight = 24890.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.155612 restraints weight = 20580.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.156759 restraints weight = 17746.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.157620 restraints weight = 15803.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6558
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7662  Z= 0.134
  Angle     :  0.646  11.313  10351  Z= 0.333
  Chirality :  0.045   0.236   1114
  Planarity :  0.005   0.053   1311
  Dihedral  :  4.428  19.389    983
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.06 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 14.18 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.27), residues: 907
  helix: -0.34 (0.31), residues: 278
  sheet: -0.79 (0.54), residues: 109
  loop : -2.31 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  71 
 TYR   0.026   0.002   TYR B 506 
 PHE   0.022   0.002   PHE A 305 
 TRP   0.043   0.002   TRP A  46 
 HIS   0.004   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7662)
  covalent geometry    : angle       0.64586 (10351)
  hydrogen bonds       : bond        0.03809 (  227)
  hydrogen bonds       : angle       5.59871 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.3473 (tmtt) cc_final: 0.3238 (tptp)
REVERT: A  122 MET cc_start: 0.6251 (tpt) cc_final: 0.5804 (tpt)
REVERT: A  198 PHE cc_start: 0.7535 (m-80) cc_final: 0.7181 (m-80)
REVERT: A  274 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8349 (pm20)
REVERT: A  430 LEU cc_start: 0.8689 (mt) cc_final: 0.8416 (pp)
REVERT: B   74 MET cc_start: 0.5983 (ppp) cc_final: 0.5388 (ppp)
REVERT: B  344 GLN cc_start: 0.7725 (mm110) cc_final: 0.7419 (pp30)
REVERT: B  400 GLU cc_start: 0.7833 (tp30) cc_final: 0.7276 (tp30)
  outliers start: 26
  outliers final: 14
  residues processed: 133
  average time/residue: 0.1044
  time to fit residues: 18.3978
Evaluate side-chains
  114 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   65 TYR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0570
   chunk 29 optimal weight:    7.9990
   chunk 75 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 14 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   overall best weight:    5.2106

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 138 GLN
A 234 HIS
B 341 GLN
** B 368 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 = 0.4409 r_free = 0.4409 target = 0.151444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.127519 restraints weight = 26451.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.129782 restraints weight = 19810.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.131522 restraints weight = 16114.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.132851 restraints weight = 13817.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.133442 restraints weight = 12214.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.141   7662  Z= 0.305
  Angle     :  0.873  12.702  10351  Z= 0.456
  Chirality :  0.050   0.292   1114
  Planarity :  0.006   0.054   1311
  Dihedral  :  5.707  20.634    983
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 32.21
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 10.25 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 16.99 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.91 (0.26), residues: 907
  helix: -1.08 (0.29), residues: 280
  sheet: -1.46 (0.50), residues: 123
  loop : -2.65 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  72 
 TYR   0.031   0.003   TYR B 506 
 PHE   0.023   0.003   PHE B  53 
 TRP   0.073   0.003   TRP A  46 
 HIS   0.007   0.002   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00687 ( 7662)
  covalent geometry    : angle       0.87271 (10351)
  hydrogen bonds       : bond        0.05180 (  227)
  hydrogen bonds       : angle       6.52108 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 122
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.3709 (tmtt) cc_final: 0.3491 (tmtt)
REVERT: A   94 ILE cc_start: 0.8530 (pt) cc_final: 0.8209 (pt)
REVERT: A  108 ILE cc_start: 0.8402 (mp) cc_final: 0.7839 (tp)
REVERT: A  122 MET cc_start: 0.6523 (tpt) cc_final: 0.6019 (tpt)
REVERT: A  198 PHE cc_start: 0.7640 (m-80) cc_final: 0.7246 (m-80)
REVERT: A  235 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7329 (tppt)
REVERT: A  256 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6569 (tp)
REVERT: B  140 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7821 (m-80)
REVERT: B  344 GLN cc_start: 0.8252 (mm110) cc_final: 0.7270 (pp30)
  outliers start: 45
  outliers final: 32
  residues processed: 147
  average time/residue: 0.0950
  time to fit residues: 18.8822
Evaluate side-chains
  141 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   65 TYR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  328 TYR
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  425 TYR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  501 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    9.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 138 GLN
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.159163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.134640 restraints weight = 26270.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.136925 restraints weight = 20142.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.138556 restraints weight = 16628.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.139895 restraints weight = 14387.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.140802 restraints weight = 12861.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7662  Z= 0.136
  Angle     :  0.696  12.171  10351  Z= 0.353
  Chirality :  0.046   0.238   1114
  Planarity :  0.004   0.049   1311
  Dihedral  :  5.060  19.392    983
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 20.02
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.16 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.07 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.26), residues: 907
  helix: -0.61 (0.30), residues: 280
  sheet: -1.24 (0.50), residues: 121
  loop : -2.54 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  24 
 TYR   0.015   0.002   TYR B 506 
 PHE   0.026   0.002   PHE B 140 
 TRP   0.049   0.002   TRP A  46 
 HIS   0.004   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7662)
  covalent geometry    : angle       0.69584 (10351)
  hydrogen bonds       : bond        0.03740 (  227)
  hydrogen bonds       : angle       5.86369 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8432 (pt) cc_final: 0.8098 (pt)
REVERT: A  122 MET cc_start: 0.6459 (tpt) cc_final: 0.5961 (tpt)
REVERT: A  198 PHE cc_start: 0.7552 (m-80) cc_final: 0.7164 (m-80)
REVERT: A  235 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7323 (tppt)
REVERT: A  256 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7051 (tp)
REVERT: B   74 MET cc_start: 0.6013 (ppp) cc_final: 0.5378 (ppp)
REVERT: B  344 GLN cc_start: 0.8117 (mm110) cc_final: 0.7394 (pp30)
REVERT: B  506 TYR cc_start: 0.6371 (m-80) cc_final: 0.5780 (m-80)
  outliers start: 34
  outliers final: 26
  residues processed: 137
  average time/residue: 0.1077
  time to fit residues: 19.3522
Evaluate side-chains
  133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   65 TYR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  501 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 9 optimal weight:    0.3980
   chunk 19 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.160305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.137522 restraints weight = 26797.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.139789 restraints weight = 20531.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.141522 restraints weight = 16807.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.142775 restraints weight = 14447.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.143709 restraints weight = 12857.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6685
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7662  Z= 0.125
  Angle     :  0.680  11.532  10351  Z= 0.345
  Chirality :  0.045   0.236   1114
  Planarity :  0.004   0.042   1311
  Dihedral  :  4.882  21.385    983
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 18.42
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.49 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.29 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.27), residues: 907
  helix: -0.49 (0.31), residues: 275
  sheet: -1.26 (0.50), residues: 121
  loop : -2.41 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 225 
 TYR   0.011   0.001   TYR B 506 
 PHE   0.022   0.002   PHE B 140 
 TRP   0.030   0.002   TRP A 175 
 HIS   0.004   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7662)
  covalent geometry    : angle       0.67970 (10351)
  hydrogen bonds       : bond        0.03557 (  227)
  hydrogen bonds       : angle       5.74888 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.8961 (mmpt) cc_final: 0.8666 (mmmt)
REVERT: A   94 ILE cc_start: 0.8426 (pt) cc_final: 0.8013 (pt)
REVERT: A  122 MET cc_start: 0.6237 (tpt) cc_final: 0.5771 (tpt)
REVERT: A  175 TRP cc_start: 0.6286 (m100) cc_final: 0.5945 (m100)
REVERT: A  198 PHE cc_start: 0.7535 (m-80) cc_final: 0.7158 (m-80)
REVERT: A  235 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7250 (tppt)
REVERT: B   74 MET cc_start: 0.6095 (ppp) cc_final: 0.5364 (ppp)
REVERT: B  344 GLN cc_start: 0.7970 (mm110) cc_final: 0.7462 (pp30)
REVERT: B  425 TYR cc_start: 0.7300 (t80) cc_final: 0.7073 (t80)
REVERT: B  501 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7678 (pp)
REVERT: B  506 TYR cc_start: 0.6166 (m-80) cc_final: 0.5618 (m-80)
  outliers start: 32
  outliers final: 26
  residues processed: 129
  average time/residue: 0.1141
  time to fit residues: 19.1203
Evaluate side-chains
  135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  501 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 88 optimal weight:    0.0980
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.159339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.134592 restraints weight = 26511.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.136707 restraints weight = 20860.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.138332 restraints weight = 17572.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.139507 restraints weight = 15396.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.140066 restraints weight = 13948.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7662  Z= 0.117
  Angle     :  0.660  11.482  10351  Z= 0.333
  Chirality :  0.045   0.265   1114
  Planarity :  0.004   0.039   1311
  Dihedral  :  4.680  20.709    983
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.05 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.39 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.31 (0.27), residues: 907
  helix: -0.39 (0.31), residues: 278
  sheet: -1.19 (0.50), residues: 121
  loop : -2.38 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 243 
 TYR   0.011   0.001   TYR A 190 
 PHE   0.021   0.001   PHE B 140 
 TRP   0.028   0.002   TRP A 175 
 HIS   0.004   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7662)
  covalent geometry    : angle       0.65968 (10351)
  hydrogen bonds       : bond        0.03371 (  227)
  hydrogen bonds       : angle       5.44723 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.9007 (mmpt) cc_final: 0.8709 (mmmt)
REVERT: A  122 MET cc_start: 0.6263 (tpt) cc_final: 0.5786 (tpt)
REVERT: A  198 PHE cc_start: 0.7776 (m-80) cc_final: 0.7305 (m-80)
REVERT: A  235 LYS cc_start: 0.8276 (tmtt) cc_final: 0.7335 (tppt)
REVERT: A  277 MET cc_start: 0.8791 (ppp) cc_final: 0.8207 (ppp)
REVERT: A  287 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.5928 (ppp)
REVERT: A  293 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6541 (m-80)
REVERT: B   74 MET cc_start: 0.6010 (ppp) cc_final: 0.5335 (ppp)
REVERT: B  242 ILE cc_start: 0.7694 (pt) cc_final: 0.7042 (mm)
REVERT: B  245 PHE cc_start: 0.6556 (m-80) cc_final: 0.6322 (m-10)
REVERT: B  344 GLN cc_start: 0.7932 (mm110) cc_final: 0.7438 (pp30)
REVERT: B  506 TYR cc_start: 0.5821 (m-80) cc_final: 0.5555 (m-80)
  outliers start: 29
  outliers final: 22
  residues processed: 124
  average time/residue: 0.1143
  time to fit residues: 18.5093
Evaluate side-chains
  128 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 89 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
B  61 GLN
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.147264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.122627 restraints weight = 27294.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.124791 restraints weight = 20914.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.126307 restraints weight = 17330.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.127545 restraints weight = 15122.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.128340 restraints weight = 13589.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.5386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.137   7662  Z= 0.261
  Angle     :  0.824  11.221  10351  Z= 0.429
  Chirality :  0.049   0.357   1114
  Planarity :  0.005   0.046   1311
  Dihedral  :  5.739  26.388    983
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 29.46
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 11.91 %
    Favored  : 87.87 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.27 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.76 (0.26), residues: 907
  helix: -0.83 (0.29), residues: 278
  sheet: -1.50 (0.50), residues: 120
  loop : -2.59 (0.25), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  72 
 TYR   0.025   0.003   TYR B 328 
 PHE   0.027   0.003   PHE B 503 
 TRP   0.023   0.003   TRP A  46 
 HIS   0.007   0.002   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 7662)
  covalent geometry    : angle       0.82392 (10351)
  hydrogen bonds       : bond        0.04748 (  227)
  hydrogen bonds       : angle       6.12367 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8893 (pt) cc_final: 0.8550 (pt)
REVERT: A  122 MET cc_start: 0.6282 (tpt) cc_final: 0.5816 (tpt)
REVERT: A  196 LYS cc_start: 0.7205 (tmtt) cc_final: 0.6339 (mmtt)
REVERT: A  198 PHE cc_start: 0.7815 (m-80) cc_final: 0.7328 (m-80)
REVERT: A  235 LYS cc_start: 0.8397 (tmtt) cc_final: 0.7473 (tppt)
REVERT: A  287 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6463 (ppp)
REVERT: A  336 MET cc_start: 0.7235 (mmm) cc_final: 0.6301 (tmm)
REVERT: A  384 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8621 (mm)
REVERT: B   74 MET cc_start: 0.6469 (ppp) cc_final: 0.5769 (ppp)
REVERT: B   86 TRP cc_start: 0.7579 (m-10) cc_final: 0.7003 (m-90)
REVERT: B  279 CYS cc_start: 0.8734 (t) cc_final: 0.8317 (t)
REVERT: B  338 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7295 (mp)
REVERT: B  344 GLN cc_start: 0.8336 (mm110) cc_final: 0.7447 (pp30)
REVERT: B  506 TYR cc_start: 0.6514 (m-80) cc_final: 0.5600 (m-80)
  outliers start: 39
  outliers final: 28
  residues processed: 139
  average time/residue: 0.1162
  time to fit residues: 20.8026
Evaluate side-chains
  143 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  328 TYR
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  365 PHE
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 90 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 81 optimal weight:    9.9990
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.149402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.125126 restraints weight = 26908.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.127493 restraints weight = 20324.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.129154 restraints weight = 16607.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.130333 restraints weight = 14291.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.131243 restraints weight = 12775.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.5558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.109   7662  Z= 0.201
  Angle     :  0.774  11.352  10351  Z= 0.396
  Chirality :  0.049   0.371   1114
  Planarity :  0.005   0.039   1311
  Dihedral  :  5.632  28.822    983
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 26.05
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 10.47 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 23.47 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.26), residues: 907
  helix: -0.79 (0.30), residues: 276
  sheet: -1.60 (0.49), residues: 123
  loop : -2.63 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 225 
 TYR   0.030   0.002   TYR B 425 
 PHE   0.023   0.003   PHE B 140 
 TRP   0.023   0.002   TRP B 269 
 HIS   0.005   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 7662)
  covalent geometry    : angle       0.77406 (10351)
  hydrogen bonds       : bond        0.04202 (  227)
  hydrogen bonds       : angle       6.04170 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.3421 (tptt) cc_final: 0.3211 (tptp)
REVERT: A   59 LYS cc_start: 0.9126 (mmpt) cc_final: 0.8852 (mmmt)
REVERT: A  122 MET cc_start: 0.6146 (tpt) cc_final: 0.5682 (tpt)
REVERT: A  198 PHE cc_start: 0.7770 (m-80) cc_final: 0.7326 (m-80)
REVERT: A  274 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8163 (pm20)
REVERT: A  285 TYR cc_start: 0.5663 (t80) cc_final: 0.5202 (t80)
REVERT: A  309 MET cc_start: 0.5576 (tmm) cc_final: 0.5376 (tmm)
REVERT: A  336 MET cc_start: 0.6957 (mmm) cc_final: 0.6407 (tmm)
REVERT: A  384 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8535 (mm)
REVERT: B   74 MET cc_start: 0.6334 (ppp) cc_final: 0.5692 (ppp)
REVERT: B   86 TRP cc_start: 0.7606 (m-10) cc_final: 0.7078 (m-90)
REVERT: B  279 CYS cc_start: 0.8751 (t) cc_final: 0.8310 (t)
REVERT: B  344 GLN cc_start: 0.8198 (mm110) cc_final: 0.7347 (pp30)
REVERT: B  506 TYR cc_start: 0.6522 (m-80) cc_final: 0.5669 (m-80)
  outliers start: 33
  outliers final: 26
  residues processed: 134
  average time/residue: 0.0967
  time to fit residues: 17.2320
Evaluate side-chains
  136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  328 TYR
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  365 PHE
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0040
   chunk 77 optimal weight:    0.1980
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0000
   chunk 70 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0670
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.1934

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

Flipped N/Q/H residues before XYZ refinement:
B 276 ASN
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.159816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.134991 restraints weight = 26771.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.137185 restraints weight = 20902.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.138851 restraints weight = 17530.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.140136 restraints weight = 15286.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.140981 restraints weight = 13784.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6628
moved from start:          0.5262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7662  Z= 0.137
  Angle     :  0.754  11.196  10351  Z= 0.379
  Chirality :  0.048   0.334   1114
  Planarity :  0.004   0.040   1311
  Dihedral  :  5.256  30.646    983
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.38 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 24.69 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.27), residues: 907
  helix: -0.69 (0.30), residues: 281
  sheet: -1.20 (0.52), residues: 116
  loop : -2.28 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 186 
 TYR   0.022   0.002   TYR B 425 
 PHE   0.022   0.002   PHE B  14 
 TRP   0.035   0.002   TRP A 175 
 HIS   0.005   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7662)
  covalent geometry    : angle       0.75395 (10351)
  hydrogen bonds       : bond        0.03561 (  227)
  hydrogen bonds       : angle       5.72876 (  612)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.9012 (mmpt) cc_final: 0.8761 (mmmt)
REVERT: A  122 MET cc_start: 0.5942 (tpt) cc_final: 0.5496 (tpt)
REVERT: A  198 PHE cc_start: 0.7840 (m-80) cc_final: 0.7416 (m-80)
REVERT: A  382 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8620 (tppt)
REVERT: B   74 MET cc_start: 0.5795 (ppp) cc_final: 0.5272 (ppp)
REVERT: B   86 TRP cc_start: 0.7434 (m-10) cc_final: 0.7081 (m-90)
REVERT: B  242 ILE cc_start: 0.6814 (pt) cc_final: 0.6501 (mt)
REVERT: B  339 LEU cc_start: 0.6628 (tp) cc_final: 0.6384 (tp)
REVERT: B  344 GLN cc_start: 0.7932 (mm110) cc_final: 0.7327 (pp30)
  outliers start: 21
  outliers final: 15
  residues processed: 131
  average time/residue: 0.1031
  time to fit residues: 17.6621
Evaluate side-chains
  122 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0770
   chunk 18 optimal weight:    8.9990
   chunk 78 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0270
   overall best weight:    0.9998

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

Flipped N/Q/H residues before XYZ refinement:
** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.157208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.132781 restraints weight = 26524.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.135060 restraints weight = 20717.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.136721 restraints weight = 17148.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.137925 restraints weight = 14959.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.138775 restraints weight = 13493.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6710
moved from start:          0.5357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7662  Z= 0.137
  Angle     :  0.753  11.579  10351  Z= 0.380
  Chirality :  0.048   0.472   1114
  Planarity :  0.005   0.043   1311
  Dihedral  :  5.120  29.124    983
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 19.29
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.49 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 25.92 %
    Favored  : 72.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.26), residues: 907
  helix: -0.72 (0.29), residues: 287
  sheet: -1.32 (0.50), residues: 121
  loop : -2.27 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  54 
 TYR   0.026   0.002   TYR B 425 
 PHE   0.039   0.002   PHE B 313 
 TRP   0.040   0.002   TRP A  20 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7662)
  covalent geometry    : angle       0.75333 (10351)
  hydrogen bonds       : bond        0.03620 (  227)
  hydrogen bonds       : angle       5.71935 (  612)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1544.96 seconds
wall clock time: 27 minutes 38.75 seconds (1658.75 seconds total)