Starting phenix.real_space_refine
on Wed Feb 12 06:39:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ozc_17304/02_2025/8ozc_17304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ozc_17304/02_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_17304/02_2025/8ozc_17304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ozc_17304/02_2025/8ozc_17304.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ozc_17304/02_2025/8ozc_17304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ozc_17304/02_2025/8ozc_17304.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.60, per 1000 atoms: 0.62
  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: 1.81
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.91
  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: 1.93

  Time building geometry restraints manager: 2.10 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.870
  Find NCS groups from input model:        0.100
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.950
-------------------------------------------------------------------------------
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= 0.154
  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 : 14.20
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (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
 TRP   0.044   0.002   TRP B  86 
 HIS   0.011   0.001   HIS A 358 
 PHE   0.025   0.001   PHE A 135 
 TYR   0.025   0.001   TYR A 190 
 ARG   0.005   0.000   ARG B 481 

*********************** 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  : 0.794 
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: 0.7434 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2108
  time to fit residues: 37.3371
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  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0370
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    1.7864

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 HIS ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.164403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.141675 restraints weight = 27088.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.143972 restraints weight = 21038.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.145790 restraints weight = 17372.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7662  Z= 0.214
  Angle     :  0.640  10.642  10351  Z= 0.333
  Chirality :  0.044   0.252   1114
  Planarity :  0.005   0.055   1311
  Dihedral  :  4.349  21.243    983
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.06 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  9.90 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.27), residues: 907
  helix: -0.22 (0.31), residues: 288
  sheet: -1.07 (0.52), residues: 109
  loop : -2.33 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  86 
 HIS   0.009   0.001   HIS A 358 
 PHE   0.030   0.002   PHE A 305 
 TYR   0.018   0.002   TYR A 171 
 ARG   0.004   0.001   ARG A  71 

*********************** 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
  142 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.6071 (tpt) cc_final: 0.5709 (tpt)
REVERT: A  198 PHE cc_start: 0.7359 (m-80) cc_final: 0.7047 (m-80)
REVERT: B   74 MET cc_start: 0.6017 (ppp) cc_final: 0.5512 (ppp)
REVERT: B  344 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7246 (pp30)
REVERT: B  409 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6586 (p0)
  outliers start: 17
  outliers final: 12
  residues processed: 131
  average time/residue: 0.2307
  time to fit residues: 39.5372
Evaluate side-chains
  117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
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  190 TYR
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  274 GLU
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  321 TYR
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  409 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 234 HIS
A 364 GLN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.163669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.140132 restraints weight = 26995.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.142413 restraints weight = 20764.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.144217 restraints weight = 17174.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6596
moved from start:          0.2422

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= 0.197
  Angle     :  0.629  10.389  10351  Z= 0.323
  Chirality :  0.044   0.220   1114
  Planarity :  0.004   0.048   1311
  Dihedral  :  4.298  19.426    983
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.06 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 12.96 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.27), residues: 907
  helix: -0.21 (0.31), residues: 278
  sheet: -0.93 (0.53), residues: 109
  loop : -2.29 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  86 
 HIS   0.006   0.001   HIS A 234 
 PHE   0.020   0.002   PHE A 305 
 TYR   0.015   0.002   TYR A 190 
 ARG   0.003   0.000   ARG A  71 

*********************** 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
  145 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.6034 (tpt) cc_final: 0.5635 (tpt)
REVERT: A  198 PHE cc_start: 0.7474 (m-80) cc_final: 0.7117 (m-80)
REVERT: A  309 MET cc_start: 0.5414 (tmm) cc_final: 0.5165 (tmm)
REVERT: A  364 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7959 (tp-100)
REVERT: A  424 LEU cc_start: 0.8785 (mt) cc_final: 0.8501 (pp)
REVERT: A  430 LEU cc_start: 0.8830 (mt) cc_final: 0.8460 (pp)
REVERT: B   74 MET cc_start: 0.5815 (ppp) cc_final: 0.5300 (ppp)
REVERT: B  344 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7261 (pp30)
REVERT: B  400 GLU cc_start: 0.7898 (tp30) cc_final: 0.7347 (tp30)
  outliers start: 28
  outliers final: 18
  residues processed: 130
  average time/residue: 0.2222
  time to fit residues: 37.9654
Evaluate side-chains
  127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
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  155 GLN
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  364 GLN
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
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  321 TYR
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  426 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 50 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0170
   chunk 32 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.3222

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 191 ASN
A 234 HIS
A 314 GLN
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 GLN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.164106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.140255 restraints weight = 26788.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.142768 restraints weight = 20305.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.144600 restraints weight = 16566.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.4290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7662  Z= 0.184
  Angle     :  0.611  10.866  10351  Z= 0.315
  Chirality :  0.044   0.221   1114
  Planarity :  0.004   0.045   1311
  Dihedral  :  4.328  18.641    983
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.95 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.77 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.27), residues: 907
  helix: -0.28 (0.31), residues: 279
  sheet: -1.01 (0.53), residues: 109
  loop : -2.27 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  33 
 HIS   0.008   0.001   HIS A 234 
 PHE   0.016   0.001   PHE B 245 
 TYR   0.025   0.001   TYR B 506 
 ARG   0.003   0.000   ARG B 481 

*********************** 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
  141 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.6318 (tpt) cc_final: 0.5845 (tpt)
REVERT: A  198 PHE cc_start: 0.7593 (m-80) cc_final: 0.7174 (m-80)
REVERT: A  235 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7408 (tppt)
REVERT: A  424 LEU cc_start: 0.8734 (mt) cc_final: 0.8466 (pp)
REVERT: A  430 LEU cc_start: 0.8956 (mt) cc_final: 0.8695 (pp)
REVERT: B   74 MET cc_start: 0.5921 (ppp) cc_final: 0.5378 (ppp)
REVERT: B  344 GLN cc_start: 0.7945 (mm110) cc_final: 0.7571 (pp30)
REVERT: B  400 GLU cc_start: 0.7930 (tp30) cc_final: 0.7499 (tp30)
  outliers start: 27
  outliers final: 21
  residues processed: 125
  average time/residue: 0.2366
  time to fit residues: 38.6798
Evaluate side-chains
  126 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
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  155 GLN
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 A residue  377 LEU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  111 HIS
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 42 optimal weight:    0.3980
   chunk 22 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 20 optimal weight:   30.0000
   chunk 52 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    3.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 GLN
** 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 = 0.4487 r_free = 0.4487 target = 0.158918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.135002 restraints weight = 25891.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.137325 restraints weight = 19586.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.139190 restraints weight = 16002.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.093   7662  Z= 0.302
  Angle     :  0.732  12.466  10351  Z= 0.377
  Chirality :  0.045   0.205   1114
  Planarity :  0.005   0.045   1311
  Dihedral  :  4.897  18.439    983
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 23.37
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.48 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 17.36 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.26), residues: 907
  helix: -0.54 (0.30), residues: 281
  sheet: -1.23 (0.49), residues: 120
  loop : -2.57 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  86 
 HIS   0.007   0.002   HIS A 234 
 PHE   0.016   0.002   PHE B  30 
 TYR   0.021   0.002   TYR B 506 
 ARG   0.004   0.001   ARG B 225 

*********************** 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
  163 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 124
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8362 (pt) cc_final: 0.8064 (pt)
REVERT: A  122 MET cc_start: 0.6497 (tpt) cc_final: 0.5999 (tpt)
REVERT: A  198 PHE cc_start: 0.7594 (m-80) cc_final: 0.7202 (m-80)
REVERT: A  235 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7373 (tppt)
REVERT: B   74 MET cc_start: 0.6277 (ppp) cc_final: 0.5591 (ppp)
REVERT: B  344 GLN cc_start: 0.8122 (mm110) cc_final: 0.7524 (pp30)
REVERT: B  381 THR cc_start: 0.7837 (t) cc_final: 0.7300 (t)
  outliers start: 39
  outliers final: 28
  residues processed: 145
  average time/residue: 0.2321
  time to fit residues: 43.8518
Evaluate side-chains
  143 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
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   45 PHE
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  190 TYR
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  424 LEU
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  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  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 68 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 85 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 234 HIS
** 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 = 0.4509 r_free = 0.4509 target = 0.159488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.135170 restraints weight = 25791.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.137499 restraints weight = 19642.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.139230 restraints weight = 16140.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6791
moved from start:          0.3951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7662  Z= 0.227
  Angle     :  0.692  11.722  10351  Z= 0.355
  Chirality :  0.045   0.184   1114
  Planarity :  0.004   0.041   1311
  Dihedral  :  4.785  19.738    983
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 20.16
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.49 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 19.07 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.26), residues: 907
  helix: -0.45 (0.30), residues: 282
  sheet: -1.11 (0.50), residues: 117
  loop : -2.47 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  86 
 HIS   0.012   0.001   HIS A 234 
 PHE   0.022   0.002   PHE B 245 
 TYR   0.018   0.002   TYR B 506 
 ARG   0.003   0.000   ARG B 225 

*********************** 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
  153 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8392 (pt) cc_final: 0.8059 (pt)
REVERT: A  102 GLN cc_start: 0.8809 (pm20) cc_final: 0.8590 (pm20)
REVERT: A  122 MET cc_start: 0.6519 (tpt) cc_final: 0.5998 (tpt)
REVERT: A  198 PHE cc_start: 0.7646 (m-80) cc_final: 0.7208 (m-80)
REVERT: A  235 LYS cc_start: 0.8149 (tmtt) cc_final: 0.7223 (tppt)
REVERT: B   65 TYR cc_start: 0.5623 (OUTLIER) cc_final: 0.5297 (m-80)
REVERT: B   74 MET cc_start: 0.6236 (ppp) cc_final: 0.5514 (ppp)
REVERT: B  344 GLN cc_start: 0.8170 (mm110) cc_final: 0.7482 (pp30)
REVERT: B  425 TYR cc_start: 0.7101 (t80) cc_final: 0.6707 (t80)
REVERT: B  506 TYR cc_start: 0.6242 (m-80) cc_final: 0.5941 (m-80)
  outliers start: 35
  outliers final: 24
  residues processed: 137
  average time/residue: 0.2223
  time to fit residues: 39.7478
Evaluate side-chains
  137 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
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   18 THR
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  274 GLU
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  382 LYS
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  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  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  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.159323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.135393 restraints weight = 25365.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.137746 restraints weight = 19212.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.139555 restraints weight = 15582.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7662  Z= 0.254
  Angle     :  0.710  11.780  10351  Z= 0.365
  Chirality :  0.046   0.260   1114
  Planarity :  0.004   0.040   1311
  Dihedral  :  4.959  21.655    983
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.59 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.90 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.26), residues: 907
  helix: -0.49 (0.31), residues: 278
  sheet: -1.13 (0.51), residues: 113
  loop : -2.43 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  86 
 HIS   0.004   0.001   HIS A 358 
 PHE   0.016   0.002   PHE B 140 
 TYR   0.022   0.002   TYR B 506 
 ARG   0.003   0.001   ARG B 225 

*********************** 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
  152 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8443 (pt) cc_final: 0.8074 (pt)
REVERT: A  122 MET cc_start: 0.6502 (tpt) cc_final: 0.5981 (tpt)
REVERT: A  198 PHE cc_start: 0.7651 (m-80) cc_final: 0.7244 (m-80)
REVERT: A  235 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7227 (tppt)
REVERT: B   74 MET cc_start: 0.6274 (ppp) cc_final: 0.5550 (ppp)
REVERT: B  344 GLN cc_start: 0.8156 (mm110) cc_final: 0.7342 (pp30)
REVERT: B  506 TYR cc_start: 0.6399 (m-80) cc_final: 0.5734 (m-80)
  outliers start: 34
  outliers final: 30
  residues processed: 132
  average time/residue: 0.2287
  time to fit residues: 39.3364
Evaluate side-chains
  140 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
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   45 PHE
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  172 ASP
Chi-restraints excluded: chain A residue  274 GLU
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  382 LYS
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  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  349 GLN
Chi-restraints excluded: chain B residue  425 TYR
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 16 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 64 optimal weight:    0.2980
   chunk 19 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   chunk 45 optimal weight:    0.6980
   chunk 68 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 138 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.154282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.130164 restraints weight = 25839.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.132372 restraints weight = 19480.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.134132 restraints weight = 15947.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.5062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.104   7662  Z= 0.316
  Angle     :  0.771  11.708  10351  Z= 0.399
  Chirality :  0.047   0.241   1114
  Planarity :  0.005   0.043   1311
  Dihedral  :  5.368  25.176    983
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 24.38
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 10.36 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.90 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.26), residues: 907
  helix: -0.74 (0.30), residues: 278
  sheet: -1.38 (0.50), residues: 117
  loop : -2.53 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  86 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.015   0.002   PHE B  14 
 TYR   0.032   0.002   TYR A 190 
 ARG   0.008   0.001   ARG A  54 

*********************** 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
  157 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8630 (pt) cc_final: 0.8240 (pt)
REVERT: A  122 MET cc_start: 0.6486 (tpt) cc_final: 0.5972 (tpt)
REVERT: A  198 PHE cc_start: 0.7579 (m-80) cc_final: 0.7168 (m-80)
REVERT: A  235 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7228 (tppt)
REVERT: A  274 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8111 (pm20)
REVERT: A  336 MET cc_start: 0.7197 (mmm) cc_final: 0.6761 (mmm)
REVERT: B   74 MET cc_start: 0.6507 (ppp) cc_final: 0.5791 (ppp)
  outliers start: 37
  outliers final: 28
  residues processed: 138
  average time/residue: 0.2198
  time to fit residues: 39.8188
Evaluate side-chains
  135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   45 PHE
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  172 ASP
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  274 GLU
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  382 LYS
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  138 VAL
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  349 GLN
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 87 optimal weight:    0.0270
   chunk 34 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 364 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 = 0.4536 r_free = 0.4536 target = 0.162214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.137785 restraints weight = 25642.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.140220 restraints weight = 19475.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.142025 restraints weight = 15880.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.4842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7662  Z= 0.198
  Angle     :  0.726  11.445  10351  Z= 0.367
  Chirality :  0.046   0.268   1114
  Planarity :  0.004   0.034   1311
  Dihedral  :  4.981  23.898    983
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.61 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.47 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.27), residues: 907
  helix: -0.37 (0.31), residues: 274
  sheet: -1.11 (0.50), residues: 116
  loop : -2.22 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  86 
 HIS   0.005   0.001   HIS A 358 
 PHE   0.020   0.002   PHE B  14 
 TYR   0.023   0.002   TYR A 190 
 ARG   0.004   0.000   ARG A  54 

*********************** 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
  158 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.8976 (mmpt) cc_final: 0.8650 (mmmt)
REVERT: A  122 MET cc_start: 0.6425 (tpt) cc_final: 0.5885 (tpt)
REVERT: A  198 PHE cc_start: 0.7635 (m-80) cc_final: 0.7284 (m-80)
REVERT: A  277 MET cc_start: 0.8777 (ppp) cc_final: 0.8217 (ppp)
REVERT: A  293 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6458 (m-80)
REVERT: A  382 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8281 (tppt)
REVERT: B   11 LYS cc_start: 0.6112 (mmmm) cc_final: 0.5603 (mmmm)
REVERT: B   74 MET cc_start: 0.5879 (ppp) cc_final: 0.5358 (ppp)
REVERT: B  245 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.5511 (m-80)
REVERT: B  248 ILE cc_start: 0.8557 (tp) cc_final: 0.8278 (tp)
REVERT: B  344 GLN cc_start: 0.8008 (mm110) cc_final: 0.7171 (pp30)
  outliers start: 27
  outliers final: 21
  residues processed: 141
  average time/residue: 0.2313
  time to fit residues: 42.7504
Evaluate side-chains
  139 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  274 GLU
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  382 LYS
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  111 HIS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  245 PHE
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  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 52 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.4510 r_free = 0.4510 target = 0.158841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.134280 restraints weight = 25506.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.135962 restraints weight = 19565.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.138125 restraints weight = 16605.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   7662  Z= 0.228
  Angle     :  0.763  11.488  10351  Z= 0.383
  Chirality :  0.047   0.264   1114
  Planarity :  0.004   0.040   1311
  Dihedral  :  5.009  24.355    983
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 19.55
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.81 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 24.69 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.27), residues: 907
  helix: -0.49 (0.30), residues: 281
  sheet: -1.00 (0.51), residues: 113
  loop : -2.32 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A  20 
 HIS   0.004   0.001   HIS A 358 
 PHE   0.019   0.002   PHE B  14 
 TYR   0.028   0.002   TYR A 190 
 ARG   0.014   0.001   ARG A  54 

********************** 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
  143 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.842 
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: 0.9027 (mmpt) cc_final: 0.8649 (mmmt)
REVERT: A  108 ILE cc_start: 0.8332 (mp) cc_final: 0.8023 (mt)
REVERT: A  122 MET cc_start: 0.6562 (tpt) cc_final: 0.6043 (tpt)
REVERT: A  274 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8122 (pm20)
REVERT: A  293 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6469 (m-80)
REVERT: B   74 MET cc_start: 0.6320 (ppp) cc_final: 0.5674 (ppp)
REVERT: B  344 GLN cc_start: 0.8043 (mm110) cc_final: 0.7161 (pp30)
REVERT: B  481 ARG cc_start: 0.6864 (tpt90) cc_final: 0.6511 (tpt90)
REVERT: B  506 TYR cc_start: 0.6215 (m-80) cc_final: 0.5639 (m-80)
  outliers start: 25
  outliers final: 22
  residues processed: 128
  average time/residue: 0.2260
  time to fit residues: 37.9681
Evaluate side-chains
  136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  274 GLU
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  382 LYS
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  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  330 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
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 79 optimal weight:    6.9990
   chunk 90 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4489 r_free = 0.4489 target = 0.156899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.132573 restraints weight = 25497.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.134909 restraints weight = 19470.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.136638 restraints weight = 16010.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.5196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   7662  Z= 0.246
  Angle     :  0.761  11.273  10351  Z= 0.385
  Chirality :  0.047   0.296   1114
  Planarity :  0.004   0.053   1311
  Dihedral  :  5.179  30.331    983
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 21.09
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.37 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.45 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.27), residues: 907
  helix: -0.50 (0.30), residues: 284
  sheet: -1.15 (0.50), residues: 115
  loop : -2.38 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A  20 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.017   0.002   PHE B  14 
 TYR   0.030   0.002   TYR A 190 
 ARG   0.014   0.001   ARG A  54 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2493.00 seconds
wall clock time: 45 minutes 51.84 seconds (2751.84 seconds total)