Starting phenix.real_space_refine
on Wed Mar 12 06:39:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ozc_17304/03_2025/8ozc_17304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ozc_17304/03_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_17304/03_2025/8ozc_17304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ozc_17304/03_2025/8ozc_17304.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ozc_17304/03_2025/8ozc_17304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ozc_17304/03_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-5624/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: 4.28, per 1000 atoms: 0.57
  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: 1.54
  Conformation dependent library (CDL) restraints added in 901.3 milliseconds
  

  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: 0.77
  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: 1.90

  Time building geometry restraints manager: 1.88 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 168
        2.68 -     3.23: 7300
        3.23 -     3.79: 11796
        3.79 -     4.34: 15451
        4.34 -     4.90: 24496
  Nonbonded interactions: 59211
  Sorted by model distance:
  nonbonded pdb=" O   TRP B 269 "
            pdb=" OH  TYR B 467 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OH  TYR A 416 "
            pdb=" O   THR B 404 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OG1 THR B 377 "
            pdb=" OG1 THR B 381 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OE1 GLU A 429 "
            pdb=" OG1 THR B 431 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" ND2 ASN B 322 "
            pdb=" O   HIS B 329 "
     model   vdw
     2.264 3.120
  ... (remaining 59206 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.750
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.520
-------------------------------------------------------------------------------
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  : 0.781 
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: 0.1953
  time to fit residues: 34.9530
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  : 0.789 
-------------------------------------------------------------------------------
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 = 48)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.141678 restraints weight = 27088.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.143890 restraints weight = 21033.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.145779 restraints weight = 17379.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
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  : 0.919 
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: 0.6072 (tpt) cc_final: 0.5710 (tpt)
REVERT: A  198 PHE cc_start: 0.7355 (m-80) cc_final: 0.7044 (m-80)
REVERT: B   74 MET cc_start: 0.6016 (ppp) cc_final: 0.5511 (ppp)
REVERT: B  344 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7250 (pp30)
REVERT: B  409 ASN cc_start: 0.6815 (OUTLIER) cc_final: 0.6602 (p0)
  outliers start: 17
  outliers final: 12
  residues processed: 131
  average time/residue: 0.2285
  time to fit residues: 39.2153
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  : 0.895 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 87 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.7760

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.167458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.143529 restraints weight = 26348.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.146072 restraints weight = 19944.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.147944 restraints weight = 16251.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7662  Z= 0.164
  Angle     :  0.614   9.938  10351  Z= 0.314
  Chirality :  0.044   0.217   1114
  Planarity :  0.004   0.050   1311
  Dihedral  :  4.172  19.112    983
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.95 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.84 %
    Favored  : 84.47 %
  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: -0.27 (0.31), residues: 280
  sheet: -0.84 (0.55), residues: 101
  loop : -2.27 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  86 
 HIS   0.006   0.001   HIS A 234 
 PHE   0.020   0.001   PHE A 305 
 TYR   0.016   0.001   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
  143 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.795 
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: 0.6026 (tpt) cc_final: 0.5670 (tpt)
REVERT: A  198 PHE cc_start: 0.7443 (m-80) cc_final: 0.7078 (m-80)
REVERT: A  309 MET cc_start: 0.5188 (tmm) cc_final: 0.4960 (tmm)
REVERT: A  424 LEU cc_start: 0.8810 (mt) cc_final: 0.8467 (pp)
REVERT: A  430 LEU cc_start: 0.8951 (mt) cc_final: 0.8587 (pp)
REVERT: B   74 MET cc_start: 0.5804 (ppp) cc_final: 0.5332 (ppp)
REVERT: B  344 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7388 (pp30)
REVERT: B  400 GLU cc_start: 0.7910 (tp30) cc_final: 0.7460 (tp30)
  outliers start: 22
  outliers final: 15
  residues processed: 132
  average time/residue: 0.2233
  time to fit residues: 38.8377
Evaluate side-chains
  120 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  155 GLN
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 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  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  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:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0040
   chunk 62 optimal weight:    8.9990
   chunk 30 optimal weight:    0.2980
   chunk 32 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.5792

-------------------------------------------------------------------------------
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 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 302 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 = 0.4600 r_free = 0.4600 target = 0.168619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.145218 restraints weight = 26095.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.147530 restraints weight = 20199.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.149271 restraints weight = 16721.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7662  Z= 0.161
  Angle     :  0.610  11.100  10351  Z= 0.310
  Chirality :  0.044   0.200   1114
  Planarity :  0.004   0.044   1311
  Dihedral  :  4.153  17.842    983
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.28 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.16 %
    Favored  : 82.03 %
  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: -2.09 (0.27), residues: 907
  helix: -0.26 (0.31), residues: 280
  sheet: -1.02 (0.52), residues: 112
  loop : -2.21 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP A  46 
 HIS   0.008   0.001   HIS A 234 
 PHE   0.020   0.001   PHE A  38 
 TYR   0.018   0.001   TYR A 190 
 ARG   0.003   0.000   ARG A  71 

*********************** 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
  132 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.813 
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: 0.6033 (tpt) cc_final: 0.5636 (tpt)
REVERT: A  198 PHE cc_start: 0.7422 (m-80) cc_final: 0.7051 (m-80)
REVERT: A  430 LEU cc_start: 0.8825 (mt) cc_final: 0.8539 (pp)
REVERT: B   74 MET cc_start: 0.5645 (ppp) cc_final: 0.5188 (ppp)
  outliers start: 23
  outliers final: 17
  residues processed: 119
  average time/residue: 0.2149
  time to fit residues: 33.9128
Evaluate side-chains
  117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  155 GLN
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   13 LEU
Chi-restraints excluded: chain B residue  111 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:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 52 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 364 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.160927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.137356 restraints weight = 26890.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.139653 restraints weight = 20847.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.141222 restraints weight = 17269.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7662  Z= 0.218
  Angle     :  0.650  11.432  10351  Z= 0.331
  Chirality :  0.044   0.143   1114
  Planarity :  0.004   0.038   1311
  Dihedral  :  4.354  18.579    983
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.27 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 16.01 %
    Favored  : 79.95 %
  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: -2.22 (0.26), residues: 907
  helix: -0.37 (0.30), residues: 282
  sheet: -1.00 (0.53), residues: 107
  loop : -2.31 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP A  46 
 HIS   0.007   0.001   HIS A 234 
 PHE   0.014   0.002   PHE A  38 
 TYR   0.015   0.002   TYR B 506 
 ARG   0.004   0.001   ARG A  71 

*********************** 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
  147 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 114
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 ARG cc_start: 0.5071 (OUTLIER) cc_final: 0.4696 (ptt-90)
REVERT: A  122 MET cc_start: 0.6361 (tpt) cc_final: 0.5859 (tpt)
REVERT: A  130 ASP cc_start: 0.9301 (m-30) cc_final: 0.9033 (m-30)
REVERT: A  198 PHE cc_start: 0.7562 (m-80) cc_final: 0.7126 (m-80)
REVERT: A  364 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8387 (tp-100)
REVERT: B   11 LYS cc_start: 0.6043 (mmmm) cc_final: 0.5614 (mmmm)
REVERT: B   74 MET cc_start: 0.6186 (ppp) cc_final: 0.5432 (ppp)
REVERT: B   86 TRP cc_start: 0.7107 (m-10) cc_final: 0.6807 (m-90)
REVERT: B  242 ILE cc_start: 0.7486 (pt) cc_final: 0.6792 (mm)
REVERT: B  283 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8485 (pp)
REVERT: B  289 GLU cc_start: 0.8156 (mp0) cc_final: 0.7590 (tm-30)
  outliers start: 33
  outliers final: 22
  residues processed: 132
  average time/residue: 0.2194
  time to fit residues: 38.5440
Evaluate side-chains
  131 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  155 GLN
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  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  111 HIS
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  283 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  426 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 367 ASN ** 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 = 0.4545 r_free = 0.4545 target = 0.162879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.138482 restraints weight = 25264.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.140948 restraints weight = 19141.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.142842 restraints weight = 15562.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   7662  Z= 0.219
  Angle     :  0.659  11.301  10351  Z= 0.335
  Chirality :  0.045   0.242   1114
  Planarity :  0.004   0.038   1311
  Dihedral  :  4.472  17.717    983
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 18.42
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.50 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.83 %
    Favored  : 77.63 %
  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: -2.23 (0.26), residues: 907
  helix: -0.39 (0.30), residues: 282
  sheet: -0.85 (0.54), residues: 106
  loop : -2.35 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A  46 
 HIS   0.016   0.002   HIS A 234 
 PHE   0.022   0.002   PHE A  45 
 TYR   0.020   0.002   TYR B 506 
 ARG   0.003   0.000   ARG A  71 

*********************** 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
  138 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 ARG cc_start: 0.4985 (OUTLIER) cc_final: 0.4343 (ptt-90)
REVERT: A  122 MET cc_start: 0.6548 (tpt) cc_final: 0.6019 (tpt)
REVERT: A  130 ASP cc_start: 0.9302 (m-30) cc_final: 0.9000 (m-30)
REVERT: A  198 PHE cc_start: 0.7504 (m-80) cc_final: 0.7069 (m-80)
REVERT: A  235 LYS cc_start: 0.8080 (tmtt) cc_final: 0.7179 (tppt)
REVERT: B   74 MET cc_start: 0.6166 (ppp) cc_final: 0.5402 (ppp)
REVERT: B   86 TRP cc_start: 0.7184 (m-10) cc_final: 0.6758 (m-90)
REVERT: B  283 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8479 (pp)
  outliers start: 29
  outliers final: 22
  residues processed: 125
  average time/residue: 0.2258
  time to fit residues: 37.0832
Evaluate side-chains
  125 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   21 LEU
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  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  217 HIS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  283 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0270
   chunk 28 optimal weight:    0.7980
   overall best weight:    2.1442

-------------------------------------------------------------------------------
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 341 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.157906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.133806 restraints weight = 26188.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.136219 restraints weight = 20102.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.137868 restraints weight = 16496.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6747
moved from start:          0.3868

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= 0.241
  Angle     :  0.683  11.651  10351  Z= 0.351
  Chirality :  0.045   0.264   1114
  Planarity :  0.004   0.039   1311
  Dihedral  :  4.677  20.697    983
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 20.29
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.15 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.44 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.34 (0.26), residues: 907
  helix: -0.46 (0.30), residues: 278
  sheet: -0.92 (0.53), residues: 108
  loop : -2.42 (0.25), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A  46 
 HIS   0.005   0.001   HIS A 358 
 PHE   0.016   0.002   PHE A  45 
 TYR   0.019   0.002   TYR B 506 
 ARG   0.003   0.000   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
  143 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.775 
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: 0.8217 (pt) cc_final: 0.7836 (pt)
REVERT: A  122 MET cc_start: 0.6530 (tpt) cc_final: 0.6037 (tpt)
REVERT: A  130 ASP cc_start: 0.9268 (m-30) cc_final: 0.8943 (m-30)
REVERT: A  198 PHE cc_start: 0.7561 (m-80) cc_final: 0.7141 (m-80)
REVERT: A  235 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7274 (tppt)
REVERT: B   74 MET cc_start: 0.6335 (ppp) cc_final: 0.5539 (ppp)
REVERT: B   86 TRP cc_start: 0.7060 (m-10) cc_final: 0.6774 (m-90)
REVERT: B  242 ILE cc_start: 0.7636 (pt) cc_final: 0.7086 (mm)
REVERT: B  245 PHE cc_start: 0.6648 (m-80) cc_final: 0.6318 (m-10)
REVERT: B  425 TYR cc_start: 0.7077 (t80) cc_final: 0.6805 (t80)
  outliers start: 31
  outliers final: 21
  residues processed: 129
  average time/residue: 0.2174
  time to fit residues: 36.8963
Evaluate side-chains
  129 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  274 GLU
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  217 HIS
Chi-restraints excluded: chain B residue  252 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  426 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 344 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 = 0.4484 r_free = 0.4484 target = 0.156079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.131987 restraints weight = 25803.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.134212 restraints weight = 19855.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.135876 restraints weight = 16380.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   7662  Z= 0.256
  Angle     :  0.720  12.849  10351  Z= 0.367
  Chirality :  0.045   0.188   1114
  Planarity :  0.004   0.040   1311
  Dihedral  :  4.907  22.709    983
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 21.70
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.48 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 19.07 %
    Favored  : 76.89 %
  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: -2.34 (0.26), residues: 907
  helix: -0.47 (0.31), residues: 276
  sheet: -1.01 (0.53), residues: 107
  loop : -2.39 (0.25), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A  46 
 HIS   0.005   0.001   HIS A 358 
 PHE   0.013   0.002   PHE B  30 
 TYR   0.022   0.002   TYR B 506 
 ARG   0.003   0.000   ARG B 225 

*********************** 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
  149 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.782 
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   94 ILE cc_start: 0.8330 (pt) cc_final: 0.8087 (pt)
REVERT: A  122 MET cc_start: 0.6600 (tpt) cc_final: 0.6092 (tpt)
REVERT: A  130 ASP cc_start: 0.9295 (m-30) cc_final: 0.8976 (m-30)
REVERT: A  198 PHE cc_start: 0.7727 (m-80) cc_final: 0.7285 (m-80)
REVERT: A  235 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7268 (tppt)
REVERT: A  293 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6603 (m-80)
REVERT: B   74 MET cc_start: 0.6216 (ppp) cc_final: 0.5442 (ppp)
REVERT: B   86 TRP cc_start: 0.7270 (m-10) cc_final: 0.6865 (m-90)
REVERT: B  242 ILE cc_start: 0.7635 (pt) cc_final: 0.7206 (mm)
REVERT: B  381 THR cc_start: 0.7693 (t) cc_final: 0.7104 (t)
REVERT: B  425 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.7097 (t80)
  outliers start: 33
  outliers final: 24
  residues processed: 132
  average time/residue: 0.2140
  time to fit residues: 37.4898
Evaluate side-chains
  136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
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   21 LEU
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  135 PHE
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  217 HIS
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  252 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 31 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 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 = 0.4445 r_free = 0.4445 target = 0.150705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.127212 restraints weight = 26861.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.129420 restraints weight = 20471.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.130985 restraints weight = 16891.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.4979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.108   7662  Z= 0.313
  Angle     :  0.777  12.729  10351  Z= 0.402
  Chirality :  0.046   0.222   1114
  Planarity :  0.005   0.041   1311
  Dihedral  :  5.329  31.604    983
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 25.11
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 10.36 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.15 %
    Favored  : 74.94 %
  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: -2.57 (0.27), residues: 907
  helix: -0.74 (0.30), residues: 278
  sheet: -1.25 (0.51), residues: 113
  loop : -2.46 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  46 
 HIS   0.006   0.002   HIS A 188 
 PHE   0.019   0.002   PHE B  53 
 TYR   0.034   0.002   TYR A 190 
 ARG   0.007   0.001   ARG A  71 

*********************** 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
  150 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8553 (pt) cc_final: 0.8137 (pt)
REVERT: A  122 MET cc_start: 0.6317 (tpt) cc_final: 0.5813 (tpt)
REVERT: A  130 ASP cc_start: 0.9293 (m-30) cc_final: 0.8956 (m-30)
REVERT: A  198 PHE cc_start: 0.7629 (m-80) cc_final: 0.7194 (m-80)
REVERT: A  235 LYS cc_start: 0.8269 (tmtt) cc_final: 0.7316 (tppt)
REVERT: B   74 MET cc_start: 0.6212 (ppp) cc_final: 0.5485 (ppp)
  outliers start: 32
  outliers final: 25
  residues processed: 129
  average time/residue: 0.2090
  time to fit residues: 36.2378
Evaluate side-chains
  136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  135 PHE
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 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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 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 = 0.4495 r_free = 0.4495 target = 0.155650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.131696 restraints weight = 26387.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.133946 restraints weight = 20356.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.135550 restraints weight = 16816.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.4955

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= 0.216
  Angle     :  0.744  13.103  10351  Z= 0.373
  Chirality :  0.046   0.288   1114
  Planarity :  0.004   0.034   1311
  Dihedral  :  5.104  28.963    983
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.49 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 23.23 %
    Favored  : 74.21 %
  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: -2.29 (0.27), residues: 907
  helix: -0.52 (0.31), residues: 273
  sheet: -1.06 (0.51), residues: 113
  loop : -2.26 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A  20 
 HIS   0.004   0.001   HIS A 358 
 PHE   0.021   0.002   PHE A 187 
 TYR   0.032   0.002   TYR B 425 
 ARG   0.004   0.000   ARG A  71 

********************** 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
  136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8443 (mp) cc_final: 0.7743 (tp)
REVERT: A  122 MET cc_start: 0.6478 (tpt) cc_final: 0.5980 (tpt)
REVERT: A  130 ASP cc_start: 0.9276 (m-30) cc_final: 0.8969 (m-30)
REVERT: A  198 PHE cc_start: 0.7728 (m-80) cc_final: 0.7286 (m-80)
REVERT: A  235 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7280 (tppt)
REVERT: A  293 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6444 (m-80)
REVERT: B   74 MET cc_start: 0.6017 (ppp) cc_final: 0.5435 (ppp)
REVERT: B  242 ILE cc_start: 0.7631 (pt) cc_final: 0.7265 (mm)
  outliers start: 21
  outliers final: 17
  residues processed: 124
  average time/residue: 0.2003
  time to fit residues: 33.5044
Evaluate side-chains
  128 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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  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  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:    0.8980
   chunk 90 optimal weight:    0.4980
   chunk 57 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0670
   chunk 76 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0670
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 155 GLN
** B 344 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 = 0.4544 r_free = 0.4544 target = 0.161023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.137224 restraints weight = 26601.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.139490 restraints weight = 20499.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.141149 restraints weight = 16952.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.4282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.4829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7662  Z= 0.188
  Angle     :  0.740  12.550  10351  Z= 0.369
  Chirality :  0.046   0.233   1114
  Planarity :  0.004   0.033   1311
  Dihedral  :  4.839  27.630    983
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.83 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 23.23 %
    Favored  : 74.69 %
  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: -0.52 (0.31), residues: 273
  sheet: -1.14 (0.49), residues: 115
  loop : -2.03 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A  20 
 HIS   0.005   0.001   HIS A 358 
 PHE   0.025   0.002   PHE B 245 
 TYR   0.018   0.001   TYR A 190 
 ARG   0.005   0.000   ARG B 481 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2563.70 seconds
wall clock time: 45 minutes 33.68 seconds (2733.68 seconds total)