Starting phenix.real_space_refine
on Wed Aug  5 14:22:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vcw_64970/08_2026/9vcw_64970.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vcw_64970/08_2026/9vcw_64970.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vcw_64970/08_2026/9vcw_64970.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vcw_64970/08_2026/9vcw_64970.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vcw_64970/08_2026/9vcw_64970.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vcw_64970/08_2026/9vcw_64970.map"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      56      5.16       5
     C    6353      2.51       5
     N    1695      2.21       5
     O    1829      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9936
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 5057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 636, 5057
          Classifications: {'peptide': 636}
          Link IDs: {'PTRANS': 37, 'TRANS': 598}
    Chain: "C"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'RNA': 3}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 2}
    Chain: "A"
      Number of atoms: 4819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4819
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 32, 'TRANS': 569}
  Time building chain proxies: 2.39, per 1000 atoms: 0.24
  Number of scatterers: 9936
  At special positions: 0
  Unit cell: (99.6, 97.94, 131.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     P       3     15.00
     O    1829      8.00
     N    1695      7.00
     C    6353      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 288.7 milliseconds
  

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2354

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 9 sheets defined
      57.5% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'B' and resid 79 through 85
    Processing helix  chain 'B' and resid 89 through 103
    Processing helix  chain 'B' and resid 103 through 113
      removed outlier: 3.576A  pdb=" N   TYR B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 133
      removed outlier: 4.262A  pdb=" N   GLN B 122 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 150
    Processing helix  chain 'B' and resid 154 through 170
      Proline residue:  B 160  - end of helix
    Processing helix  chain 'B' and resid 175 through 182
    Processing helix  chain 'B' and resid 187 through 191
    Processing helix  chain 'B' and resid 192 through 198
      removed outlier: 3.638A  pdb=" N   ARG B 196 " --> pdb=" O   TYR B 192 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   MET B 198 " --> pdb=" O   ASP B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 224
    Processing helix  chain 'B' and resid 233 through 247
    Processing helix  chain 'B' and resid 292 through 298
      removed outlier: 3.901A  pdb=" N   MET B 295 " --> pdb=" O   GLU B 292 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ARG B 297 " --> pdb=" O   GLN B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 312
      removed outlier: 4.173A  pdb=" N   TRP B 305 " --> pdb=" O   ARG B 301 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 312 " --> pdb=" O   ALA B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 336
    Processing helix  chain 'B' and resid 374 through 389
    Processing helix  chain 'B' and resid 400 through 413
      removed outlier: 3.593A  pdb=" N   ASP B 413 " --> pdb=" O   LYS B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 429
    Processing helix  chain 'B' and resid 460 through 469
    Processing helix  chain 'B' and resid 487 through 499
      removed outlier: 3.749A  pdb=" N   LYS B 499 " --> pdb=" O   LYS B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 524
      removed outlier: 3.878A  pdb=" N   ILE B 517 " --> pdb=" O   THR B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 539
      removed outlier: 3.533A  pdb=" N   LEU B 532 " --> pdb=" O   THR B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 561
    Processing helix  chain 'B' and resid 567 through 577
      removed outlier: 4.058A  pdb=" N   ARG B 571 " --> pdb=" O   SER B 567 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ALA B 577 " --> pdb=" O   VAL B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 600
      removed outlier: 3.699A  pdb=" N   CYS B 587 " --> pdb=" O   GLN B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 613
    Processing helix  chain 'B' and resid 621 through 643
    Processing helix  chain 'B' and resid 652 through 671
    Processing helix  chain 'B' and resid 672 through 683
    Processing helix  chain 'A' and resid 89 through 103
    Processing helix  chain 'A' and resid 104 through 113
    Processing helix  chain 'A' and resid 116 through 133
    Processing helix  chain 'A' and resid 138 through 150
    Processing helix  chain 'A' and resid 154 through 157
    Processing helix  chain 'A' and resid 158 through 170
    Processing helix  chain 'A' and resid 170 through 176
      removed outlier: 3.981A  pdb=" N   ASP A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 183
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 194 through 198
      removed outlier: 3.648A  pdb=" N   MET A 198 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 223
    Processing helix  chain 'A' and resid 233 through 248
    Processing helix  chain 'A' and resid 277 through 279
      No H-bonds generated for 'chain 'A' and resid 277 through 279'
    Processing helix  chain 'A' and resid 293 through 298
      removed outlier: 3.795A  pdb=" N   ARG A 297 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 312
      removed outlier: 3.931A  pdb=" N   TRP A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 325 through 337
    Processing helix  chain 'A' and resid 360 through 364
      removed outlier: 3.775A  pdb=" N   ASN A 363 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 388
    Processing helix  chain 'A' and resid 400 through 412
    Processing helix  chain 'A' and resid 425 through 429
      removed outlier: 4.100A  pdb=" N   MET A 429 " --> pdb=" O   ALA A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 470
    Processing helix  chain 'A' and resid 487 through 499
      removed outlier: 3.578A  pdb=" N   LYS A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 524
    Processing helix  chain 'A' and resid 528 through 540
    Processing helix  chain 'A' and resid 551 through 561
      removed outlier: 3.689A  pdb=" N   ILE A 561 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 564
      No H-bonds generated for 'chain 'A' and resid 562 through 564'
    Processing helix  chain 'A' and resid 567 through 577
      removed outlier: 3.572A  pdb=" N   ALA A 577 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 600
      removed outlier: 4.325A  pdb=" N   CYS A 587 " --> pdb=" O   GLN A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 613
    Processing helix  chain 'A' and resid 621 through 645
    Processing helix  chain 'A' and resid 651 through 671
    Processing helix  chain 'A' and resid 672 through 685
    Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 204
      removed outlier: 6.229A  pdb=" N   ILE B 202 " --> pdb=" O   GLU B 341 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 271 through 272
      removed outlier: 6.953A  pdb=" N   VAL B 228 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ALA B 288 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 253 through 254
      removed outlier: 3.755A  pdb=" N   LEU B 253 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 353
      removed outlier: 5.502A  pdb=" N   ILE B 438 " --> pdb=" O   THR B 484 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ASP B 368 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   ALA B 423 " --> pdb=" O   ASP B 368 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   ILE B 370 " --> pdb=" O   ALA B 423 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 444 through 448
      removed outlier: 3.938A  pdb=" N   GLU B 457 " --> pdb=" O   LYS B 445 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER B 447 " --> pdb=" O   GLU B 455 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 260
      removed outlier: 5.768A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   THR A 275 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   VAL A 254 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   GLY A 227 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   CYS A 274 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   TYR A 229 " --> pdb=" O   CYS A 274 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ASP A 291 " --> pdb=" O   CYS A 230 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   ALA A 288 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   CYS A 320 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE A 290 " --> pdb=" O   CYS A 320 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   ARG A 343 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   PHE A 204 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 353
      removed outlier: 6.138A  pdb=" N   SER A 352 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ASP A 368 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   ALA A 423 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ILE A 370 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL A 422 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE A 395 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 444 through 445
    Processing sheet with id=AA9, first strand: chain 'A' and resid 508 through 509
      removed outlier: 5.214A  pdb=" N   ALA A 508 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    482 hydrogen bonds defined for protein.
    1398 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: 1.66

  Time building geometry restraints manager: 1.26 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: 3217
        1.34 -     1.46: 1409
        1.46 -     1.58: 5451
        1.58 -     1.69: 7
        1.69 -     1.81: 84
  Bond restraints: 10168
  Sorted by residual:
  bond pdb=" CB  PRO B 189 "
       pdb=" CG  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.642 -0.150 5.00e-02 4.00e+02 8.95e+00
  bond pdb=" CG  PRO B 189 "
       pdb=" CD  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.401  0.102 3.40e-02 8.65e+02 8.95e+00
  bond pdb=" N1    U C   1 "
       pdb=" C2    U C   1 "
    ideal  model  delta    sigma   weight residual
    1.381  1.401 -0.020 9.00e-03 1.23e+04 5.10e+00
  bond pdb=" N   PRO B 189 "
       pdb=" CD  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.473  1.504 -0.031 1.40e-02 5.10e+03 4.97e+00
  bond pdb=" N1    U C   2 "
       pdb=" C2    U C   2 "
    ideal  model  delta    sigma   weight residual
    1.381  1.400 -0.019 9.00e-03 1.23e+04 4.57e+00
  ... (remaining 10163 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.87: 13698
        3.87 -     7.74: 73
        7.74 -    11.62: 13
       11.62 -    15.49: 0
       15.49 -    19.36: 1
  Bond angle restraints: 13785
  Sorted by residual:
  angle pdb=" CA  PRO B 189 "
        pdb=" N   PRO B 189 "
        pdb=" CD  PRO B 189 "
      ideal   model   delta    sigma   weight residual
     112.00   92.64   19.36 1.40e+00 5.10e-01 1.91e+02
  angle pdb=" C1'   U C   1 "
        pdb=" N1    U C   1 "
        pdb=" C2    U C   1 "
      ideal   model   delta    sigma   weight residual
     117.70  126.56   -8.86 1.20e+00 6.94e-01 5.45e+01
  angle pdb=" C1'   U C   2 "
        pdb=" N1    U C   2 "
        pdb=" C2    U C   2 "
      ideal   model   delta    sigma   weight residual
     117.70  126.07   -8.37 1.20e+00 6.94e-01 4.87e+01
  angle pdb=" N1    U C   1 "
        pdb=" C2    U C   1 "
        pdb=" O2    U C   1 "
      ideal   model   delta    sigma   weight residual
     122.80  127.47   -4.67 7.00e-01 2.04e+00 4.45e+01
  angle pdb=" N1    U C   2 "
        pdb=" C2    U C   2 "
        pdb=" O2    U C   2 "
      ideal   model   delta    sigma   weight residual
     122.80  127.41   -4.61 7.00e-01 2.04e+00 4.34e+01
  ... (remaining 13780 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 5952
       35.90 -    71.80: 236
       71.80 -   107.70: 11
      107.70 -   143.61: 0
      143.61 -   179.51: 1
  Dihedral angle restraints: 6200
    sinusoidal: 2570
      harmonic: 3630
  Sorted by residual:
  dihedral pdb=" O4'   U C   3 "
           pdb=" C1'   U C   3 "
           pdb=" N1    U C   3 "
           pdb=" C2    U C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.49  179.51     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U C   2 "
           pdb=" C1'   U C   2 "
           pdb=" N1    U C   2 "
           pdb=" C2    U C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   93.57  106.43     1      1.50e+01 4.44e-03 5.47e+01
  dihedral pdb=" O4'   U C   1 "
           pdb=" C1'   U C   1 "
           pdb=" N1    U C   1 "
           pdb=" C2    U C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00  101.29   98.71     1      1.50e+01 4.44e-03 4.91e+01
  ... (remaining 6197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1205
       0.048 -    0.095: 258
       0.095 -    0.143: 69
       0.143 -    0.190: 10
       0.190 -    0.238: 2
  Chirality restraints: 1544
  Sorted by residual:
  chirality pdb=" CA  PRO B 189 "
            pdb=" N   PRO B 189 "
            pdb=" C   PRO B 189 "
            pdb=" CB  PRO B 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CG  LEU A 560 "
            pdb=" CB  LEU A 560 "
            pdb=" CD1 LEU A 560 "
            pdb=" CD2 LEU A 560 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CG  LEU B 641 "
            pdb=" CB  LEU B 641 "
            pdb=" CD1 LEU B 641 "
            pdb=" CD2 LEU B 641 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.61e-01
  ... (remaining 1541 not shown)

  Planarity restraints: 1767
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 188 "    0.096 5.00e-02 4.00e+02   1.30e-01 2.68e+01
        pdb=" N   PRO B 189 "   -0.223 5.00e-02 4.00e+02
        pdb=" CA  PRO B 189 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO B 189 "    0.071 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 601 "   -0.062 5.00e-02 4.00e+02   9.02e-02 1.30e+01
        pdb=" N   PRO B 602 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO B 602 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B 602 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 614 "    0.051 5.00e-02 4.00e+02   7.69e-02 9.46e+00
        pdb=" N   PRO B 615 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B 615 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 615 "    0.043 5.00e-02 4.00e+02
  ... (remaining 1764 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 302
        2.69 -     3.24: 10937
        3.24 -     3.80: 17484
        3.80 -     4.35: 22197
        4.35 -     4.90: 33822
  Nonbonded interactions: 84742
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 101 "
            pdb=" O   PHE A 120 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" NE2 GLN B 122 "
            pdb=" O   ARG A 196 "
     model   vdw
     2.150 3.120
  nonbonded pdb=" O   LEU A 676 "
            pdb=" OG  SER A 680 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" NH1 ARG A 200 "
            pdb=" O   LEU A 309 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" OG1 THR A 460 "
            pdb=" NE2 GLN A 463 "
     model   vdw
     2.210 3.120
  ... (remaining 84737 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 87 through 688)
}

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:             1.750
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.250
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.010
  Internal consistency checks:             0.000
  Total:   13.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6681
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      :  0.004   0.150  10168  Z= 0.164
  Angle     :  0.788  19.362  13785  Z= 0.455
  Chirality :  0.044   0.238   1544
  Planarity :  0.006   0.130   1767
  Dihedral  : 18.107 179.508   3846
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 24.02
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.92 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 35.75 %
    Favored  : 63.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.24), residues: 1234
  helix:  0.31 (0.20), residues: 650
  sheet: -0.37 (0.54), residues: 99
  loop : -1.43 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 470 
 TYR   0.017   0.002   TYR B 572 
 PHE   0.043   0.002   PHE A 593 
 TRP   0.020   0.002   TRP A 614 
 HIS   0.009   0.001   HIS A 318 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.16 (10168)
  covalent geometry    : angle       0.78763 /  0.46 (13785)
  hydrogen bonds       : bond        0.15186 /  9.92 (  482)
  hydrogen bonds       : angle       6.55311 /  4.55 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.383 
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: symmetry clash
REVERT: A  159 PHE cc_start: 0.8703 (t80) cc_final: 0.8349 (p90)
REVERT: A  534 ASP cc_start: 0.8465 (m-30) cc_final: 0.8146 (m-30)
  outliers start: 4
  outliers final: 2
  residues processed: 138
  average time/residue: 0.0833
  time to fit residues: 17.1560
Evaluate side-chains
  129 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  488 HIS
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    8.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 580 ASN ** 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 = 0.4459 r_free = 0.4459 target = 0.130847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.109783 restraints weight = 39626.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.112351 restraints weight = 26196.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.114046 restraints weight = 19311.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.115182 restraints weight = 15467.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 66)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.115986 restraints weight = 13185.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  10168  Z= 0.289
  Angle     :  0.769   9.471  13785  Z= 0.405
  Chirality :  0.047   0.286   1544
  Planarity :  0.006   0.060   1767
  Dihedral  :  9.025 178.574   1392
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 27.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.05 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 29.70 %
    Favored  : 64.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.24), residues: 1234
  helix:  0.16 (0.19), residues: 662
  sheet: -0.97 (0.48), residues: 120
  loop : -1.82 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 470 
 TYR   0.021   0.003   TYR A 101 
 PHE   0.033   0.003   PHE A 593 
 TRP   0.019   0.003   TRP A 614 
 HIS   0.008   0.002   HIS A 671 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00637 /  0.29 (10168)
  covalent geometry    : angle       0.76870 /  0.40 (13785)
  hydrogen bonds       : bond        0.05108 /  3.45 (  482)
  hydrogen bonds       : angle       5.77592 /  3.98 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 131
  time to evaluate  : 0.379 
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: B  170 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6448 (t80)
REVERT: B  574 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7396 (m-80)
REVERT: A  159 PHE cc_start: 0.8721 (t80) cc_final: 0.8329 (p90)
REVERT: A  333 MET cc_start: 0.7420 (tpp) cc_final: 0.7090 (tpp)
  outliers start: 62
  outliers final: 32
  residues processed: 177
  average time/residue: 0.0865
  time to fit residues: 22.7329
Evaluate side-chains
  156 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  255 THR
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  533 ILE
Chi-restraints excluded: chain B residue  574 PHE
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  552 ASP
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  624 ASP
Chi-restraints excluded: chain A residue  649 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 60 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 120 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0370
   overall best weight:    0.6862

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 HIS ** 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 = 0.4438 r_free = 0.4438 target = 0.134600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.113639 restraints weight = 37070.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.116568 restraints weight = 23024.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.118542 restraints weight = 16220.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 73)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.119909 restraints weight = 12492.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.120793 restraints weight = 10290.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6612
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10168  Z= 0.137
  Angle     :  0.672  10.679  13785  Z= 0.339
  Chirality :  0.044   0.305   1544
  Planarity :  0.004   0.047   1767
  Dihedral  :  8.847 177.392   1390
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.43 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 30.89 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.24), residues: 1234
  helix:  0.42 (0.20), residues: 668
  sheet: -1.15 (0.48), residues: 109
  loop : -1.56 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 470 
 TYR   0.014   0.002   TYR A 101 
 PHE   0.037   0.002   PHE A 120 
 TRP   0.018   0.001   TRP A 640 
 HIS   0.009   0.001   HIS A 318 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.14 (10168)
  covalent geometry    : angle       0.67187 /  0.34 (13785)
  hydrogen bonds       : bond        0.04167 /  2.78 (  482)
  hydrogen bonds       : angle       5.27126 /  3.67 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 142
  time to evaluate  : 0.354 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  170 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6431 (t80)
REVERT: B  233 LEU cc_start: 0.8823 (tp) cc_final: 0.8505 (mm)
REVERT: B  486 MET cc_start: 0.6265 (tmm) cc_final: 0.5905 (tmm)
REVERT: B  599 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7515 (tpm170)
REVERT: B  613 LYS cc_start: 0.8584 (tmtt) cc_final: 0.8305 (tmtt)
REVERT: A  159 PHE cc_start: 0.8610 (t80) cc_final: 0.8314 (p90)
REVERT: A  333 MET cc_start: 0.7588 (tpp) cc_final: 0.7128 (tpp)
REVERT: A  638 TYR cc_start: 0.8000 (t80) cc_final: 0.7769 (t80)
  outliers start: 44
  outliers final: 22
  residues processed: 175
  average time/residue: 0.0925
  time to fit residues: 23.6605
Evaluate side-chains
  153 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  192 TYR
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  596 GLN
Chi-restraints excluded: chain B residue  599 ARG
Chi-restraints excluded: chain B residue  614 TRP
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain B residue  636 ASP
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  566 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 63 optimal weight:   30.0000
   chunk 62 optimal weight:    9.9990
   chunk 109 optimal weight:    0.0870
   chunk 56 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 103 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    5.6166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 667 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 = 0.4434 r_free = 0.4434 target = 0.129036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.107557 restraints weight = 40416.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.110090 restraints weight = 26839.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.111776 restraints weight = 19808.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.112952 restraints weight = 15901.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.113570 restraints weight = 13528.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068  10168  Z= 0.311
  Angle     :  0.791  10.819  13785  Z= 0.415
  Chirality :  0.049   0.308   1544
  Planarity :  0.006   0.049   1767
  Dihedral  :  9.199 178.334   1390
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 30.65
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.78 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 29.51 %
    Favored  : 63.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.24), residues: 1234
  helix:  0.11 (0.20), residues: 662
  sheet: -1.20 (0.45), residues: 135
  loop : -1.79 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 470 
 TYR   0.023   0.003   TYR B 221 
 PHE   0.037   0.003   PHE A 593 
 TRP   0.016   0.003   TRP A 614 
 HIS   0.009   0.002   HIS B 563 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00690 /  0.31 (10168)
  covalent geometry    : angle       0.79123 /  0.41 (13785)
  hydrogen bonds       : bond        0.05136 /  3.43 (  482)
  hydrogen bonds       : angle       5.85214 /  4.06 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 125
  time to evaluate  : 0.393 
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: symmetry clash
   revert: symmetry clash
REVERT: B   57 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6411 (ptpp)
REVERT: B  170 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6312 (t80)
REVERT: B  198 MET cc_start: 0.4933 (OUTLIER) cc_final: 0.4623 (ppp)
REVERT: B  297 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.4733 (ptm160)
REVERT: B  322 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6674 (mm-30)
REVERT: B  519 MET cc_start: 0.8660 (mpp) cc_final: 0.8412 (mpp)
REVERT: B  569 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7552 (ptm-80)
REVERT: A  333 MET cc_start: 0.7732 (tpp) cc_final: 0.7075 (tpp)
REVERT: A  506 ARG cc_start: 0.5962 (OUTLIER) cc_final: 0.5603 (pmt-80)
  outliers start: 71
  outliers final: 45
  residues processed: 182
  average time/residue: 0.0926
  time to fit residues: 24.5013
Evaluate side-chains
  169 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 117
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  127 PHE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  255 THR
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  297 ARG
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  488 HIS
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  533 ILE
Chi-restraints excluded: chain B residue  569 ARG
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  596 GLN
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain A residue  624 ASP
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  649 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 109 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 667 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 = 0.4451 r_free = 0.4451 target = 0.132749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.110971 restraints weight = 38970.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.113673 restraints weight = 25587.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.115491 restraints weight = 18669.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.116795 restraints weight = 14813.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 74)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.117691 restraints weight = 12488.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10168  Z= 0.146
  Angle     :  0.693  11.746  13785  Z= 0.347
  Chirality :  0.045   0.315   1544
  Planarity :  0.004   0.043   1767
  Dihedral  :  9.051 176.794   1390
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 21.10
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.24 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 30.16 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.24), residues: 1234
  helix:  0.33 (0.20), residues: 668
  sheet: -1.23 (0.49), residues: 111
  loop : -1.65 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 610 
 TYR   0.013   0.002   TYR B 334 
 PHE   0.029   0.002   PHE B 120 
 TRP   0.041   0.002   TRP A 614 
 HIS   0.008   0.001   HIS A 318 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.15 (10168)
  covalent geometry    : angle       0.69288 /  0.35 (13785)
  hydrogen bonds       : bond        0.04067 /  2.70 (  482)
  hydrogen bonds       : angle       5.36337 /  3.77 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 137
  time to evaluate  : 0.255 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  170 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6144 (t80)
REVERT: B  198 MET cc_start: 0.4785 (OUTLIER) cc_final: 0.4533 (ppp)
REVERT: B  322 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6633 (mm-30)
REVERT: B  470 ARG cc_start: 0.4814 (mmp-170) cc_final: 0.4545 (mmp-170)
REVERT: B  519 MET cc_start: 0.8630 (mpp) cc_final: 0.8360 (mpp)
REVERT: B  599 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7580 (tpm170)
REVERT: B  613 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8316 (tmtt)
REVERT: A  113 TYR cc_start: 0.6073 (m-10) cc_final: 0.5579 (m-10)
REVERT: A  175 CYS cc_start: 0.8852 (m) cc_final: 0.8295 (m)
REVERT: A  177 ASP cc_start: 0.8022 (p0) cc_final: 0.7657 (t0)
REVERT: A  333 MET cc_start: 0.7841 (tpp) cc_final: 0.7456 (tpp)
REVERT: A  506 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5518 (pmt-80)
  outliers start: 52
  outliers final: 35
  residues processed: 177
  average time/residue: 0.0879
  time to fit residues: 22.4642
Evaluate side-chains
  164 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  127 PHE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  192 TYR
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  488 HIS
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  599 ARG
Chi-restraints excluded: chain B residue  614 TRP
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  644 ARG
Chi-restraints excluded: chain A residue  655 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 78 optimal weight:    9.9990
   chunk 99 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 GLN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 667 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 = 0.4461 r_free = 0.4461 target = 0.134008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.113322 restraints weight = 38791.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.116105 restraints weight = 24417.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.118014 restraints weight = 17306.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.119328 restraints weight = 13385.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.120154 restraints weight = 11080.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10168  Z= 0.139
  Angle     :  0.673  11.263  13785  Z= 0.335
  Chirality :  0.045   0.352   1544
  Planarity :  0.004   0.040   1767
  Dihedral  :  9.111 177.743   1390
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 18.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.83 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 29.06 %
    Favored  : 64.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.24), residues: 1234
  helix:  0.42 (0.20), residues: 668
  sheet: -1.14 (0.49), residues: 111
  loop : -1.59 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 383 
 TYR   0.015   0.002   TYR B 572 
 PHE   0.041   0.002   PHE A 120 
 TRP   0.021   0.002   TRP A 614 
 HIS   0.009   0.001   HIS A 318 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 (10168)
  covalent geometry    : angle       0.67331 /  0.34 (13785)
  hydrogen bonds       : bond        0.03866 /  2.57 (  482)
  hydrogen bonds       : angle       5.19535 /  3.66 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 137
  time to evaluate  : 0.275 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  198 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.4606 (ppp)
REVERT: B  297 ARG cc_start: 0.5885 (OUTLIER) cc_final: 0.4627 (ptm160)
REVERT: B  322 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6538 (mm-30)
REVERT: B  362 ASP cc_start: 0.5141 (OUTLIER) cc_final: 0.4816 (m-30)
REVERT: B  596 GLN cc_start: 0.6082 (OUTLIER) cc_final: 0.5734 (mm-40)
REVERT: B  599 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7569 (tpm170)
REVERT: B  613 LYS cc_start: 0.8600 (tmtt) cc_final: 0.8329 (tmtt)
REVERT: A  175 CYS cc_start: 0.8930 (m) cc_final: 0.8331 (m)
REVERT: A  177 ASP cc_start: 0.7986 (p0) cc_final: 0.7629 (t0)
REVERT: A  333 MET cc_start: 0.7789 (tpp) cc_final: 0.7422 (tpp)
REVERT: A  354 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8600 (mm)
REVERT: A  506 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5426 (pmt-80)
REVERT: A  638 TYR cc_start: 0.8014 (t80) cc_final: 0.7424 (t80)
  outliers start: 66
  outliers final: 41
  residues processed: 191
  average time/residue: 0.0786
  time to fit residues: 21.8875
Evaluate side-chains
  177 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 128
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 HIS
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  192 TYR
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  297 ARG
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  362 ASP
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  488 HIS
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  596 GLN
Chi-restraints excluded: chain B residue  599 ARG
Chi-restraints excluded: chain B residue  614 TRP
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain B residue  636 ASP
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  409 LYS
Chi-restraints excluded: chain A residue  415 ASN
Chi-restraints excluded: chain A residue  449 ASN
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  644 ARG
Chi-restraints excluded: chain A residue  655 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 122 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0870
   chunk 70 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.7964

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  72 GLN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 667 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 = 0.4484 r_free = 0.4484 target = 0.135127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.113282 restraints weight = 38284.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.116012 restraints weight = 24989.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.117942 restraints weight = 18191.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.119292 restraints weight = 14322.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.120149 restraints weight = 11980.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10168  Z= 0.133
  Angle     :  0.695  12.594  13785  Z= 0.343
  Chirality :  0.044   0.324   1544
  Planarity :  0.004   0.039   1767
  Dihedral  :  9.261 177.913   1390
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 18.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.27 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 30.43 %
    Favored  : 64.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.24), residues: 1234
  helix:  0.45 (0.20), residues: 666
  sheet: -1.09 (0.50), residues: 109
  loop : -1.49 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 470 
 TYR   0.014   0.002   TYR B 572 
 PHE   0.040   0.002   PHE A 593 
 TRP   0.021   0.002   TRP A 640 
 HIS   0.010   0.001   HIS A 318 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 (10168)
  covalent geometry    : angle       0.69487 /  0.34 (13785)
  hydrogen bonds       : bond        0.03768 /  2.50 (  482)
  hydrogen bonds       : angle       5.11860 /  3.61 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 134
  time to evaluate  : 0.328 
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: B  297 ARG cc_start: 0.5931 (OUTLIER) cc_final: 0.4710 (ptm160)
REVERT: B  322 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7244 (mm-30)
REVERT: B  362 ASP cc_start: 0.5012 (OUTLIER) cc_final: 0.4674 (m-30)
REVERT: B  596 GLN cc_start: 0.6006 (OUTLIER) cc_final: 0.5728 (mm-40)
REVERT: B  613 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8361 (tmtt)
REVERT: A  175 CYS cc_start: 0.8906 (m) cc_final: 0.8337 (m)
REVERT: A  177 ASP cc_start: 0.8079 (p0) cc_final: 0.7729 (t0)
REVERT: A  258 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.4752 (mm-30)
REVERT: A  333 MET cc_start: 0.7723 (tpp) cc_final: 0.7456 (tpp)
REVERT: A  354 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8568 (mm)
REVERT: A  506 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5589 (pmt-80)
  outliers start: 52
  outliers final: 36
  residues processed: 175
  average time/residue: 0.0827
  time to fit residues: 21.1434
Evaluate side-chains
  169 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 126
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  297 ARG
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  362 ASP
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  596 GLN
Chi-restraints excluded: chain B residue  614 TRP
Chi-restraints excluded: chain B residue  636 ASP
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  409 LYS
Chi-restraints excluded: chain A residue  415 ASN
Chi-restraints excluded: chain A residue  449 ASN
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  511 HIS
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  655 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0870
   chunk 112 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 69 optimal weight:   40.0000
   chunk 40 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 667 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 = 0.4498 r_free = 0.4498 target = 0.135997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.114019 restraints weight = 37908.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.116716 restraints weight = 24974.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.118615 restraints weight = 18290.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.119928 restraints weight = 14490.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.120755 restraints weight = 12212.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10168  Z= 0.134
  Angle     :  0.714  12.902  13785  Z= 0.347
  Chirality :  0.044   0.347   1544
  Planarity :  0.004   0.038   1767
  Dihedral  :  9.388 178.091   1390
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.35 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 31.35 %
    Favored  : 63.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.24), residues: 1234
  helix:  0.46 (0.20), residues: 669
  sheet: -1.05 (0.50), residues: 109
  loop : -1.51 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 470 
 TYR   0.025   0.002   TYR B 572 
 PHE   0.041   0.002   PHE A 120 
 TRP   0.020   0.002   TRP A 640 
 HIS   0.011   0.001   HIS A 318 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 (10168)
  covalent geometry    : angle       0.71392 /  0.35 (13785)
  hydrogen bonds       : bond        0.03678 /  2.43 (  482)
  hydrogen bonds       : angle       5.05772 /  3.57 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 134
  time to evaluate  : 0.337 
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: symmetry clash
   revert: symmetry clash
REVERT: B  297 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.4719 (ptm160)
REVERT: B  322 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6275 (mm-30)
REVERT: B  362 ASP cc_start: 0.5002 (OUTLIER) cc_final: 0.4664 (m-30)
REVERT: B  599 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7627 (tpm170)
REVERT: B  613 LYS cc_start: 0.8637 (tmtt) cc_final: 0.8352 (tmtt)
REVERT: A  159 PHE cc_start: 0.8549 (t80) cc_final: 0.8247 (p90)
REVERT: A  175 CYS cc_start: 0.8953 (m) cc_final: 0.8416 (m)
REVERT: A  177 ASP cc_start: 0.7997 (p0) cc_final: 0.7675 (t0)
REVERT: A  258 GLU cc_start: 0.5067 (OUTLIER) cc_final: 0.4807 (mm-30)
REVERT: A  333 MET cc_start: 0.7710 (tpp) cc_final: 0.7483 (tpp)
REVERT: A  519 MET cc_start: 0.7898 (mpp) cc_final: 0.7071 (mtm)
  outliers start: 52
  outliers final: 43
  residues processed: 176
  average time/residue: 0.0834
  time to fit residues: 21.5588
Evaluate side-chains
  177 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 129
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  192 TYR
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  297 ARG
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  362 ASP
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  596 GLN
Chi-restraints excluded: chain B residue  599 ARG
Chi-restraints excluded: chain B residue  614 TRP
Chi-restraints excluded: chain B residue  636 ASP
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  409 LYS
Chi-restraints excluded: chain A residue  415 ASN
Chi-restraints excluded: chain A residue  449 ASN
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  511 HIS
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  655 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 14 optimal weight:    6.9990
   chunk 71 optimal weight:    9.9990
   chunk 24 optimal weight:    0.6980
   chunk 97 optimal weight:    0.0370
   chunk 17 optimal weight:    0.0870
   chunk 83 optimal weight:    9.9990
   chunk 105 optimal weight:    7.9990
   chunk 121 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.9438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 407 GLN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 667 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 = 0.4500 r_free = 0.4500 target = 0.136024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.114259 restraints weight = 38385.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.116905 restraints weight = 25329.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.118800 restraints weight = 18527.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 71)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.120113 restraints weight = 14710.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.120957 restraints weight = 12336.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6594
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10168  Z= 0.131
  Angle     :  0.715  12.162  13785  Z= 0.346
  Chirality :  0.044   0.342   1544
  Planarity :  0.004   0.038   1767
  Dihedral  :  9.433 178.278   1390
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.02 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 31.44 %
    Favored  : 63.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.24), residues: 1234
  helix:  0.52 (0.20), residues: 666
  sheet: -1.04 (0.50), residues: 109
  loop : -1.37 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 470 
 TYR   0.023   0.002   TYR B 572 
 PHE   0.016   0.001   PHE B 120 
 TRP   0.022   0.002   TRP A 640 
 HIS   0.008   0.001   HIS A 318 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 (10168)
  covalent geometry    : angle       0.71527 /  0.35 (13785)
  hydrogen bonds       : bond        0.03584 /  2.38 (  482)
  hydrogen bonds       : angle       5.01036 /  3.54 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 131
  time to evaluate  : 0.262 
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: symmetry clash
REVERT: B  297 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.4725 (ptm160)
REVERT: B  322 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7148 (mm-30)
REVERT: B  333 MET cc_start: 0.8231 (mmm) cc_final: 0.7931 (mmm)
REVERT: B  362 ASP cc_start: 0.5117 (OUTLIER) cc_final: 0.4790 (m-30)
REVERT: B  599 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7623 (tpm170)
REVERT: B  613 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8351 (tmtt)
REVERT: A  159 PHE cc_start: 0.8566 (t80) cc_final: 0.8229 (p90)
REVERT: A  175 CYS cc_start: 0.8949 (m) cc_final: 0.8439 (m)
REVERT: A  177 ASP cc_start: 0.8074 (p0) cc_final: 0.7789 (t0)
  outliers start: 53
  outliers final: 45
  residues processed: 171
  average time/residue: 0.0788
  time to fit residues: 19.8908
Evaluate side-chains
  177 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 128
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  192 TYR
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  297 ARG
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  362 ASP
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  596 GLN
Chi-restraints excluded: chain B residue  599 ARG
Chi-restraints excluded: chain B residue  614 TRP
Chi-restraints excluded: chain B residue  636 ASP
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  646 MET
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  409 LYS
Chi-restraints excluded: chain A residue  415 ASN
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  449 ASN
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  511 HIS
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  655 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 91 optimal weight:    8.9990
   chunk 110 optimal weight:    6.9990
   chunk 112 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 583 GLN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 667 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 = 0.4493 r_free = 0.4493 target = 0.135609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.114048 restraints weight = 38055.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.116763 restraints weight = 24874.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.118649 restraints weight = 18062.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.119796 restraints weight = 14266.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.120763 restraints weight = 12122.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.095  10168  Z= 0.140
  Angle     :  0.736  13.638  13785  Z= 0.357
  Chirality :  0.045   0.344   1544
  Planarity :  0.004   0.037   1767
  Dihedral  :  9.442 178.105   1390
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.11 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 31.90 %
    Favored  : 63.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.24), residues: 1234
  helix:  0.64 (0.20), residues: 654
  sheet: -1.02 (0.50), residues: 109
  loop : -1.38 (0.30), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 259 
 TYR   0.036   0.002   TYR B 334 
 PHE   0.044   0.002   PHE A 120 
 TRP   0.050   0.002   TRP A 614 
 HIS   0.007   0.001   HIS A 671 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 (10168)
  covalent geometry    : angle       0.73603 /  0.36 (13785)
  hydrogen bonds       : bond        0.03691 /  2.46 (  482)
  hydrogen bonds       : angle       5.04439 /  3.56 ( 1398)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 135
  time to evaluate  : 0.332 
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: symmetry clash
REVERT: B  297 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.4747 (ptm160)
REVERT: B  322 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7152 (mm-30)
REVERT: B  333 MET cc_start: 0.8179 (mmm) cc_final: 0.7815 (mmm)
REVERT: B  362 ASP cc_start: 0.5191 (OUTLIER) cc_final: 0.4859 (m-30)
REVERT: B  599 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7643 (tpm170)
REVERT: B  613 LYS cc_start: 0.8648 (tmtt) cc_final: 0.8370 (tmtt)
REVERT: A  159 PHE cc_start: 0.8531 (t80) cc_final: 0.8112 (p90)
REVERT: A  175 CYS cc_start: 0.8985 (m) cc_final: 0.8496 (m)
REVERT: A  177 ASP cc_start: 0.8044 (p0) cc_final: 0.7764 (t0)
REVERT: A  506 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.5557 (pmt-80)
  outliers start: 49
  outliers final: 44
  residues processed: 171
  average time/residue: 0.0854
  time to fit residues: 21.1565
Evaluate side-chains
  181 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 132
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  297 ARG
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  362 ASP
Chi-restraints excluded: chain B residue  372 CYS
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  596 GLN
Chi-restraints excluded: chain B residue  599 ARG
Chi-restraints excluded: chain B residue  614 TRP
Chi-restraints excluded: chain B residue  636 ASP
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  646 MET
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  409 LYS
Chi-restraints excluded: chain A residue  415 ASN
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  449 ASN
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  511 HIS
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  655 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 18 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 102 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 667 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 = 0.4506 r_free = 0.4506 target = 0.136419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.115136 restraints weight = 38577.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.117792 restraints weight = 25339.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.119632 restraints weight = 18509.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.120816 restraints weight = 14661.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.121791 restraints weight = 12467.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6575
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092  10168  Z= 0.134
  Angle     :  0.739  13.369  13785  Z= 0.358
  Chirality :  0.045   0.360   1544
  Planarity :  0.004   0.037   1767
  Dihedral  :  9.465 177.843   1390
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.59 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 32.72 %
    Favored  : 62.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.24), residues: 1234
  helix:  0.58 (0.20), residues: 661
  sheet: -0.95 (0.50), residues: 109
  loop : -1.38 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 470 
 TYR   0.021   0.002   TYR B 572 
 PHE   0.032   0.001   PHE A 100 
 TRP   0.064   0.002   TRP A 614 
 HIS   0.008   0.001   HIS A 318 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.13 (10168)
  covalent geometry    : angle       0.73897 /  0.36 (13785)
  hydrogen bonds       : bond        0.03558 /  2.37 (  482)
  hydrogen bonds       : angle       5.03149 /  3.55 ( 1398)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1853.11 seconds
wall clock time: 32 minutes 49.41 seconds (1969.41 seconds total)