Starting phenix.real_space_refine
on Thu Nov 14 21:17:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/11_2024/8ozc_17304.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/11_2024/8ozc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/11_2024/8ozc_17304.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/11_2024/8ozc_17304.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/11_2024/8ozc_17304.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/11_2024/8ozc_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-5513/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: 4.97, per 1000 atoms: 0.66
  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: 1.73
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 11 sheets defined
      36.1% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  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: 2.06

  Time building geometry restraints manager: 2.06 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:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.710
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.450
-------------------------------------------------------------------------------
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  : 0.915 
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: 0.2110
  time to fit residues: 37.6647
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  : 0.963 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
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  : 0.928 
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: 0.6020 (tpt) cc_final: 0.5666 (tpt)
REVERT: A  198 PHE cc_start: 0.7408 (m-80) cc_final: 0.7076 (m-80)
REVERT: B   74 MET cc_start: 0.5973 (ppp) cc_final: 0.5498 (ppp)
REVERT: B  344 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7306 (pp30)
REVERT: B  409 ASN cc_start: 0.6694 (OUTLIER) cc_final: 0.6490 (p0)
  outliers start: 17
  outliers final: 12
  residues processed: 131
  average time/residue: 0.2371
  time to fit residues: 40.5963
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  : 0.911 
-------------------------------------------------------------------------------
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 45 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 82 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 234 HIS
A 364 GLN
B 341 GLN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6593
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7662  Z= 0.213
  Angle     :  0.640  10.627  10351  Z= 0.330
  Chirality :  0.044   0.224   1114
  Planarity :  0.004   0.048   1311
  Dihedral  :  4.375  19.400    983
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.50 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 13.20 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.27), residues: 907
  helix: -0.26 (0.31), residues: 278
  sheet: -0.96 (0.53), residues: 109
  loop : -2.32 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  86 
 HIS   0.006   0.001   HIS A 358 
 PHE   0.020   0.002   PHE A 305 
 TYR   0.014   0.002   TYR A 190 
 ARG   0.003   0.000   ARG B 481 

*********************** 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
  148 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.6040 (tpt) cc_final: 0.5648 (tpt)
REVERT: A  198 PHE cc_start: 0.7567 (m-80) cc_final: 0.7176 (m-80)
REVERT: A  309 MET cc_start: 0.5395 (tmm) cc_final: 0.5109 (tmm)
REVERT: A  364 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8400 (tp-100)
REVERT: A  424 LEU cc_start: 0.8816 (mt) cc_final: 0.8484 (pp)
REVERT: A  430 LEU cc_start: 0.8951 (mt) cc_final: 0.8660 (pp)
REVERT: B   74 MET cc_start: 0.5838 (ppp) cc_final: 0.5322 (ppp)
REVERT: B  344 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7497 (pp30)
REVERT: B  400 GLU cc_start: 0.7958 (tp30) cc_final: 0.7358 (tp30)
  outliers start: 29
  outliers final: 16
  residues processed: 131
  average time/residue: 0.2277
  time to fit residues: 39.1083
Evaluate side-chains
  124 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  364 GLN
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 55 optimal weight:    0.0770
   chunk 83 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 78 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    2.2146

-------------------------------------------------------------------------------
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
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   7662  Z= 0.239
  Angle     :  0.658  11.589  10351  Z= 0.339
  Chirality :  0.044   0.226   1114
  Planarity :  0.005   0.045   1311
  Dihedral  :  4.530  19.320    983
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.50 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 16.01 %
    Favored  : 80.07 %
  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: -2.26 (0.27), residues: 907
  helix: -0.38 (0.31), residues: 282
  sheet: -0.86 (0.54), residues: 107
  loop : -2.40 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  33 
 HIS   0.006   0.001   HIS A 234 
 PHE   0.016   0.002   PHE A 305 
 TYR   0.025   0.002   TYR B 506 
 ARG   0.003   0.001   ARG B 481 

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

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 ARG cc_start: 0.4793 (OUTLIER) cc_final: 0.4399 (ptt-90)
REVERT: A  122 MET cc_start: 0.6243 (tpt) cc_final: 0.5790 (tpt)
REVERT: A  198 PHE cc_start: 0.7606 (m-80) cc_final: 0.7186 (m-80)
REVERT: A  235 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7322 (tppt)
REVERT: A  424 LEU cc_start: 0.8773 (mt) cc_final: 0.8481 (pp)
REVERT: B   74 MET cc_start: 0.6094 (ppp) cc_final: 0.5492 (ppp)
REVERT: B  344 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7522 (pp30)
REVERT: B  425 TYR cc_start: 0.6882 (t80) cc_final: 0.6649 (t80)
  outliers start: 32
  outliers final: 20
  residues processed: 134
  average time/residue: 0.2461
  time to fit residues: 43.0782
Evaluate side-chains
  132 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  405 ILE
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 49 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 60 optimal weight:   20.0000
   chunk 0 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7662  Z= 0.262
  Angle     :  0.693  12.342  10351  Z= 0.356
  Chirality :  0.045   0.186   1114
  Planarity :  0.005   0.043   1311
  Dihedral  :  4.873  18.472    983
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 22.77
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.60 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 17.97 %
    Favored  : 77.38 %
  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: -2.42 (0.26), residues: 907
  helix: -0.45 (0.30), residues: 278
  sheet: -1.14 (0.51), residues: 117
  loop : -2.49 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  86 
 HIS   0.007   0.002   HIS A 234 
 PHE   0.014   0.002   PHE B  14 
 TYR   0.019   0.002   TYR B 506 
 ARG   0.003   0.001   ARG B 225 

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

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 123
  time to evaluate  : 0.927 
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: 0.8403 (pt) cc_final: 0.8006 (pt)
REVERT: A  122 MET cc_start: 0.6143 (tpt) cc_final: 0.5672 (tpt)
REVERT: A  130 ASP cc_start: 0.9158 (m-30) cc_final: 0.8884 (m-30)
REVERT: A  198 PHE cc_start: 0.7738 (m-80) cc_final: 0.7290 (m-80)
REVERT: A  235 LYS cc_start: 0.8175 (tmtt) cc_final: 0.7333 (tppt)
REVERT: B   65 TYR cc_start: 0.4909 (OUTLIER) cc_final: 0.4579 (m-80)
REVERT: B   74 MET cc_start: 0.6122 (ppp) cc_final: 0.5487 (ppp)
REVERT: B  344 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7180 (pp30)
REVERT: B  381 THR cc_start: 0.7602 (t) cc_final: 0.7382 (t)
REVERT: B  506 TYR cc_start: 0.6372 (m-80) cc_final: 0.6100 (m-80)
  outliers start: 38
  outliers final: 29
  residues processed: 145
  average time/residue: 0.2186
  time to fit residues: 41.6753
Evaluate side-chains
  144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  370 ASN
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   65 TYR
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  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  394 LEU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   chunk 51 optimal weight:    0.2980
   chunk 21 optimal weight:    9.9990
   chunk 88 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7662  Z= 0.181
  Angle     :  0.668  11.530  10351  Z= 0.337
  Chirality :  0.044   0.172   1114
  Planarity :  0.004   0.039   1311
  Dihedral  :  4.621  20.437    983
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.60 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 20.17 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.27), residues: 907
  helix: -0.36 (0.31), residues: 279
  sheet: -1.10 (0.51), residues: 117
  loop : -2.38 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 175 
 HIS   0.015   0.001   HIS A 234 
 PHE   0.023   0.002   PHE B 245 
 TYR   0.013   0.001   TYR B 425 
 ARG   0.004   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
  146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8211 (pt) cc_final: 0.7792 (pt)
REVERT: A  122 MET cc_start: 0.6160 (tpt) cc_final: 0.5716 (tpt)
REVERT: A  130 ASP cc_start: 0.9109 (m-30) cc_final: 0.8801 (m-30)
REVERT: A  198 PHE cc_start: 0.7667 (m-80) cc_final: 0.7215 (m-80)
REVERT: A  235 LYS cc_start: 0.8135 (tmtt) cc_final: 0.7226 (tppt)
REVERT: B   74 MET cc_start: 0.6088 (ppp) cc_final: 0.5428 (ppp)
REVERT: B  344 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7148 (pp30)
REVERT: B  381 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7292 (t)
  outliers start: 30
  outliers final: 23
  residues processed: 130
  average time/residue: 0.2311
  time to fit residues: 39.1261
Evaluate side-chains
  130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    0.0370
   chunk 50 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0070
   chunk 49 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.5476

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 234 HIS
A 367 ASN
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 GLN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7662  Z= 0.179
  Angle     :  0.665  11.703  10351  Z= 0.335
  Chirality :  0.045   0.282   1114
  Planarity :  0.004   0.035   1311
  Dihedral  :  4.499  23.894    983
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.50 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.54 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.27), residues: 907
  helix: -0.28 (0.31), residues: 278
  sheet: -1.00 (0.53), residues: 107
  loop : -2.31 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 175 
 HIS   0.006   0.001   HIS A 234 
 PHE   0.018   0.001   PHE B  14 
 TYR   0.013   0.001   TYR B 506 
 ARG   0.003   0.000   ARG B 481 

*********************** 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
  148 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.8844 (mmpt) cc_final: 0.8555 (mmmt)
REVERT: A   94 ILE cc_start: 0.8172 (pt) cc_final: 0.7767 (pt)
REVERT: A  122 MET cc_start: 0.6163 (tpt) cc_final: 0.5697 (tpt)
REVERT: A  130 ASP cc_start: 0.9144 (m-30) cc_final: 0.8817 (m-30)
REVERT: A  198 PHE cc_start: 0.7660 (m-80) cc_final: 0.7212 (m-80)
REVERT: A  235 LYS cc_start: 0.8173 (tmtt) cc_final: 0.7280 (tppt)
REVERT: A  293 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6612 (m-80)
REVERT: B   74 MET cc_start: 0.6055 (ppp) cc_final: 0.5389 (ppp)
REVERT: B  242 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7091 (mm)
REVERT: B  344 GLN cc_start: 0.7837 (mm110) cc_final: 0.7155 (pp30)
REVERT: B  395 LYS cc_start: 0.7593 (mttt) cc_final: 0.7311 (mmtt)
  outliers start: 31
  outliers final: 25
  residues processed: 131
  average time/residue: 0.2187
  time to fit residues: 37.8080
Evaluate side-chains
  133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:   10.0000
   chunk 59 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   chunk 79 optimal weight:    0.1980
   chunk 84 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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**
A 234 HIS
** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   7662  Z= 0.250
  Angle     :  0.708  11.638  10351  Z= 0.362
  Chirality :  0.045   0.221   1114
  Planarity :  0.004   0.035   1311
  Dihedral  :  4.741  22.450    983
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 21.56
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.15 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 21.15 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.27), residues: 907
  helix: -0.27 (0.31), residues: 282
  sheet: -1.17 (0.51), residues: 117
  loop : -2.38 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP B  86 
 HIS   0.026   0.002   HIS A 234 
 PHE   0.013   0.002   PHE B  14 
 TYR   0.021   0.002   TYR B 506 
 ARG   0.004   0.000   ARG B 481 

*********************** 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
  146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 0.967 
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: 0.8476 (pt) cc_final: 0.8240 (pt)
REVERT: A  122 MET cc_start: 0.6153 (tpt) cc_final: 0.5700 (tpt)
REVERT: A  130 ASP cc_start: 0.9195 (m-30) cc_final: 0.8872 (m-30)
REVERT: A  198 PHE cc_start: 0.7797 (m-80) cc_final: 0.7347 (m-80)
REVERT: A  235 LYS cc_start: 0.8119 (tmtt) cc_final: 0.7194 (tppt)
REVERT: A  293 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6564 (m-80)
REVERT: B   74 MET cc_start: 0.6311 (ppp) cc_final: 0.5525 (ppp)
REVERT: B  314 LYS cc_start: 0.7744 (tmtt) cc_final: 0.7413 (tmtt)
REVERT: B  344 GLN cc_start: 0.8053 (mm110) cc_final: 0.7201 (pp30)
  outliers start: 35
  outliers final: 28
  residues processed: 130
  average time/residue: 0.2337
  time to fit residues: 39.8009
Evaluate side-chains
  134 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  328 TYR
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 84 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 86 optimal weight:    0.1980
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 234 HIS
** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6632
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7662  Z= 0.206
  Angle     :  0.707  11.475  10351  Z= 0.357
  Chirality :  0.046   0.332   1114
  Planarity :  0.004   0.037   1311
  Dihedral  :  4.708  22.558    983
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.71 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.49 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.27), residues: 907
  helix: -0.29 (0.31), residues: 276
  sheet: -0.94 (0.54), residues: 107
  loop : -2.31 (0.25), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP B  86 
 HIS   0.019   0.002   HIS A 234 
 PHE   0.029   0.002   PHE A  60 
 TYR   0.017   0.001   TYR B 506 
 ARG   0.005   0.000   ARG B 481 

*********************** 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
  134 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.8584 (pt) cc_final: 0.8192 (pt)
REVERT: A  122 MET cc_start: 0.6231 (tpt) cc_final: 0.5777 (tpt)
REVERT: A  130 ASP cc_start: 0.9186 (m-30) cc_final: 0.8877 (m-30)
REVERT: A  198 PHE cc_start: 0.7696 (m-80) cc_final: 0.7219 (m-80)
REVERT: A  277 MET cc_start: 0.8803 (ppp) cc_final: 0.8172 (ppp)
REVERT: A  293 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6688 (m-80)
REVERT: B   74 MET cc_start: 0.6145 (ppp) cc_final: 0.5430 (ppp)
REVERT: B  242 ILE cc_start: 0.7780 (pt) cc_final: 0.7014 (mm)
REVERT: B  344 GLN cc_start: 0.7958 (mm110) cc_final: 0.7147 (pp30)
REVERT: B  395 LYS cc_start: 0.7674 (mttt) cc_final: 0.7386 (mmtt)
REVERT: B  425 TYR cc_start: 0.6412 (t80) cc_final: 0.6142 (t80)
  outliers start: 29
  outliers final: 25
  residues processed: 120
  average time/residue: 0.2213
  time to fit residues: 35.4086
Evaluate side-chains
  130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0170
   chunk 55 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 76 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.5424

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 234 HIS
** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7662  Z= 0.215
  Angle     :  0.711  11.398  10351  Z= 0.361
  Chirality :  0.045   0.161   1114
  Planarity :  0.004   0.038   1311
  Dihedral  :  4.712  21.874    983
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.60 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.86 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.24 (0.27), residues: 907
  helix: -0.35 (0.31), residues: 275
  sheet: -1.04 (0.52), residues: 117
  loop : -2.34 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP B  86 
 HIS   0.017   0.002   HIS A 234 
 PHE   0.026   0.002   PHE A  60 
 TYR   0.019   0.002   TYR B 506 
 ARG   0.006   0.000   ARG B 481 

********************** 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: 28
    poor density    : 108
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.8944 (mmpt) cc_final: 0.8662 (mmmt)
REVERT: A   94 ILE cc_start: 0.8628 (pt) cc_final: 0.8233 (pt)
REVERT: A  122 MET cc_start: 0.6263 (tpt) cc_final: 0.5810 (tpt)
REVERT: A  130 ASP cc_start: 0.9188 (m-30) cc_final: 0.8877 (m-30)
REVERT: A  198 PHE cc_start: 0.7716 (m-80) cc_final: 0.7255 (m-80)
REVERT: A  293 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6612 (m-80)
REVERT: B   74 MET cc_start: 0.6359 (ppp) cc_final: 0.5567 (ppp)
REVERT: B  344 GLN cc_start: 0.7993 (mm110) cc_final: 0.7149 (pp30)
REVERT: B  395 LYS cc_start: 0.7649 (mttt) cc_final: 0.7365 (mmtt)
REVERT: B  425 TYR cc_start: 0.6453 (t80) cc_final: 0.6160 (t80)
  outliers start: 28
  outliers final: 25
  residues processed: 122
  average time/residue: 0.2192
  time to fit residues: 35.6920
Evaluate side-chains
  133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  358 HIS
Chi-restraints excluded: chain A residue  368 TRP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  217 HIS
Chi-restraints excluded: chain B residue  303 MET
Chi-restraints excluded: chain B residue  320 TRP
Chi-restraints excluded: chain B residue  324 LYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 20 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0870
   chunk 30 optimal weight:    8.9990
   chunk 74 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0470
   chunk 4 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 367 ASN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.163615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.138827 restraints weight = 25202.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.141259 restraints weight = 19421.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.143160 restraints weight = 15854.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.4487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7662  Z= 0.190
  Angle     :  0.719  11.121  10351  Z= 0.358
  Chirality :  0.045   0.162   1114
  Planarity :  0.004   0.037   1311
  Dihedral  :  4.602  23.423    983
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.72 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 23.11 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.31 (0.31), residues: 278
  sheet: -0.99 (0.51), residues: 121
  loop : -2.27 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP B  86 
 HIS   0.023   0.002   HIS A 234 
 PHE   0.023   0.001   PHE A  60 
 TYR   0.025   0.001   TYR A 233 
 ARG   0.004   0.000   ARG B 481 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1787.05 seconds
wall clock time: 33 minutes 31.79 seconds (2011.79 seconds total)