Starting phenix.real_space_refine
on Thu Jul  2 10:21:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jew_36201/07_2026/8jew_36201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jew_36201/07_2026/8jew_36201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jew_36201/07_2026/8jew_36201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jew_36201/07_2026/8jew_36201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jew_36201/07_2026/8jew_36201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jew_36201/07_2026/8jew_36201.cif"
  }
  resolution = 2.49
  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
-------------------------------------------------------------------------------
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=   0.001 sd=   0.014
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      58      5.16       5
     Na      4      4.78       5
     C    5504      2.51       5
     N    1246      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8284
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 3881
          Classifications: {'peptide': 512}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 478}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 259
          Ad-hoc single atom residues: {' NA': 2}
          Unusual residues: {'ASC': 1, 'AV0': 2, 'CLR': 2, 'LBN': 1, 'NAG': 1, 'PLM': 1}
          Classifications: {'undetermined': 8, 'water': 3}
          Link IDs: {None: 9}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'LBN:plan-3': 1, 'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.77, per 1000 atoms: 0.33
  Number of scatterers: 8284
  At special positions: 0
  Unit cell: (94.62, 108.564, 77.688, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      58     16.00
     P       2     15.00
     Na      4     11.00
     O    1470      8.00
     N    1246      7.00
     C    5504      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 298.2 milliseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1852

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 2 sheets defined
      74.4% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 60
      removed outlier: 3.720A  pdb=" N   LEU A  46 " --> pdb=" O   TYR A  42 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLY A  58 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
      removed outlier: 3.775A  pdb=" N   PHE A  64 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 101
    Processing helix  chain 'A' and resid 111 through 123
      removed outlier: 3.860A  pdb=" N   LEU A 115 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A 116 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
      Proline residue:  A 117  - end of helix
    Processing helix  chain 'A' and resid 124 through 128
    Processing helix  chain 'A' and resid 131 through 136
      removed outlier: 3.559A  pdb=" N   ILE A 135 " --> pdb=" O   PRO A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 173
      Proline residue:  A 151  - end of helix
      removed outlier: 3.562A  pdb=" N   GLU A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 180
      removed outlier: 3.894A  pdb=" N   LEU A 180 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 198
      Proline residue:  A 190  - end of helix
    Processing helix  chain 'A' and resid 199 through 208
    Processing helix  chain 'A' and resid 210 through 227
    Processing helix  chain 'A' and resid 255 through 274
    Processing helix  chain 'A' and resid 285 through 289
    Processing helix  chain 'A' and resid 317 through 346
      removed outlier: 3.895A  pdb=" N   SER A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA A 327 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 374
    Processing helix  chain 'A' and resid 382 through 393
      removed outlier: 3.682A  pdb=" N   ILE A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 413
      removed outlier: 3.715A  pdb=" N   VAL A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 421
    Processing helix  chain 'A' and resid 424 through 445
      removed outlier: 3.540A  pdb=" N   THR A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 454 through 478
      Proline residue:  A 472  - end of helix
    Processing helix  chain 'A' and resid 479 through 482
      removed outlier: 4.509A  pdb=" N   ILE A 482 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 479 through 482'
    Processing helix  chain 'A' and resid 486 through 498
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 541 through 545
    Processing helix  chain 'A' and resid 549 through 554
    Processing helix  chain 'A' and resid 556 through 561
    Processing helix  chain 'B' and resid 40 through 60
      removed outlier: 3.720A  pdb=" N   LEU B  46 " --> pdb=" O   TYR B  42 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLY B  58 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.775A  pdb=" N   PHE B  64 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 101
    Processing helix  chain 'B' and resid 111 through 123
      removed outlier: 3.860A  pdb=" N   LEU B 115 " --> pdb=" O   ALA B 111 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL B 116 " --> pdb=" O   PHE B 112 " (cutoff:3.500A)
      Proline residue:  B 117  - end of helix
    Processing helix  chain 'B' and resid 124 through 128
    Processing helix  chain 'B' and resid 131 through 136
      removed outlier: 3.559A  pdb=" N   ILE B 135 " --> pdb=" O   PRO B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 173
      Proline residue:  B 151  - end of helix
      removed outlier: 3.562A  pdb=" N   GLU B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL B 166 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU B 167 " --> pdb=" O   SER B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 180
      removed outlier: 3.894A  pdb=" N   LEU B 180 " --> pdb=" O   PRO B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 198
      Proline residue:  B 190  - end of helix
    Processing helix  chain 'B' and resid 199 through 208
    Processing helix  chain 'B' and resid 210 through 227
    Processing helix  chain 'B' and resid 255 through 274
    Processing helix  chain 'B' and resid 285 through 289
    Processing helix  chain 'B' and resid 317 through 346
      removed outlier: 3.895A  pdb=" N   SER B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA B 327 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 374
    Processing helix  chain 'B' and resid 382 through 393
      removed outlier: 3.682A  pdb=" N   ILE B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 413
      removed outlier: 3.715A  pdb=" N   VAL B 400 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 421
    Processing helix  chain 'B' and resid 424 through 445
      removed outlier: 3.540A  pdb=" N   THR B 434 " --> pdb=" O   GLY B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 450
    Processing helix  chain 'B' and resid 454 through 478
      Proline residue:  B 472  - end of helix
    Processing helix  chain 'B' and resid 479 through 482
      removed outlier: 4.509A  pdb=" N   ILE B 482 " --> pdb=" O   PRO B 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 479 through 482'
    Processing helix  chain 'B' and resid 486 through 498
    Processing helix  chain 'B' and resid 499 through 515
    Processing helix  chain 'B' and resid 541 through 545
    Processing helix  chain 'B' and resid 549 through 554
    Processing helix  chain 'B' and resid 556 through 561
    Processing sheet with id=1, first strand: chain 'A' and resid 108 through 110
    Processing sheet with id=2, first strand: chain 'B' and resid 108 through 110

    506 hydrogen bonds defined for protein.
    1452 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: 0.80

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1206
        1.31 -     1.44: 2212
        1.44 -     1.58: 4978
        1.58 -     1.71: 4
        1.71 -     1.84: 88
  Bond restraints: 8488
  Sorted by residual:
  bond pdb=" C   TYR B 474 "
       pdb=" O   TYR B 474 "
    ideal  model  delta    sigma   weight residual
    1.236  1.293 -0.057 1.15e-02 7.56e+03 2.45e+01
  bond pdb=" C   TYR A 474 "
       pdb=" O   TYR A 474 "
    ideal  model  delta    sigma   weight residual
    1.236  1.293 -0.057 1.15e-02 7.56e+03 2.45e+01
  bond pdb=" C   PRO A 301 "
       pdb=" O   PRO A 301 "
    ideal  model  delta    sigma   weight residual
    1.233  1.179  0.054 1.19e-02 7.06e+03 2.06e+01
  bond pdb=" C   PRO B 301 "
       pdb=" O   PRO B 301 "
    ideal  model  delta    sigma   weight residual
    1.233  1.179  0.054 1.19e-02 7.06e+03 2.06e+01
  bond pdb=" C   GLN B 287 "
       pdb=" O   GLN B 287 "
    ideal  model  delta    sigma   weight residual
    1.236  1.176  0.060 1.35e-02 5.49e+03 1.98e+01
  ... (remaining 8483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 8676
        2.07 -     4.14: 2672
        4.14 -     6.21: 224
        6.21 -     8.29: 12
        8.29 -    10.36: 4
  Bond angle restraints: 11588
  Sorted by residual:
  angle pdb=" N   TYR A  42 "
        pdb=" CA  TYR A  42 "
        pdb=" C   TYR A  42 "
      ideal   model   delta    sigma   weight residual
     111.71  106.27    5.44 1.15e+00 7.56e-01 2.24e+01
  angle pdb=" N   TYR B  42 "
        pdb=" CA  TYR B  42 "
        pdb=" C   TYR B  42 "
      ideal   model   delta    sigma   weight residual
     111.71  106.27    5.44 1.15e+00 7.56e-01 2.24e+01
  angle pdb=" CA  ILE A 218 "
        pdb=" C   ILE A 218 "
        pdb=" O   ILE A 218 "
      ideal   model   delta    sigma   weight residual
     121.17  116.22    4.95 1.06e+00 8.90e-01 2.18e+01
  angle pdb=" CA  ILE B 218 "
        pdb=" C   ILE B 218 "
        pdb=" O   ILE B 218 "
      ideal   model   delta    sigma   weight residual
     121.17  116.22    4.95 1.06e+00 8.90e-01 2.18e+01
  angle pdb=" O   ILE A 218 "
        pdb=" C   ILE A 218 "
        pdb=" N   LEU A 219 "
      ideal   model   delta    sigma   weight residual
     121.91  126.38   -4.47 9.80e-01 1.04e+00 2.08e+01
  ... (remaining 11583 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.32: 5262
       28.32 -    56.64: 200
       56.64 -    84.95: 32
       84.95 -   113.27: 0
      113.27 -   141.59: 8
  Dihedral angle restraints: 5502
    sinusoidal: 2602
      harmonic: 2900
  Sorted by residual:
  dihedral pdb=" C1  LBN B 605 "
           pdb=" O1  LBN B 605 "
           pdb=" P1  LBN B 605 "
           pdb=" O3  LBN B 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.60   56.99 -141.59     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" C1  LBN A 605 "
           pdb=" O1  LBN A 605 "
           pdb=" P1  LBN A 605 "
           pdb=" O3  LBN A 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.60   56.99 -141.59     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" O5  LBN A 605 "
           pdb=" C2  LBN A 605 "
           pdb=" C3  LBN A 605 "
           pdb=" O7  LBN A 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67  -60.77  123.44     1      3.00e+01 1.11e-03 1.65e+01
  ... (remaining 5499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 630
       0.049 -    0.098: 436
       0.098 -    0.147: 232
       0.147 -    0.196: 100
       0.196 -    0.244: 24
  Chirality restraints: 1422
  Sorted by residual:
  chirality pdb=" CA  PRO B 563 "
            pdb=" N   PRO B 563 "
            pdb=" C   PRO B 563 "
            pdb=" CB  PRO B 563 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  PRO A 563 "
            pdb=" N   PRO A 563 "
            pdb=" C   PRO A 563 "
            pdb=" CB  PRO A 563 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  TRP B 149 "
            pdb=" N   TRP B 149 "
            pdb=" C   TRP B 149 "
            pdb=" CB  TRP B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1419 not shown)

  Planarity restraints: 1352
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 609 "   -0.056 2.00e-02 2.50e+03   4.63e-02 2.67e+01
        pdb=" C7  NAG A 609 "    0.006 2.00e-02 2.50e+03
        pdb=" C8  NAG A 609 "   -0.040 2.00e-02 2.50e+03
        pdb=" N2  NAG A 609 "    0.076 2.00e-02 2.50e+03
        pdb=" O7  NAG A 609 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 609 "   -0.056 2.00e-02 2.50e+03   4.63e-02 2.67e+01
        pdb=" C7  NAG B 609 "    0.006 2.00e-02 2.50e+03
        pdb=" C8  NAG B 609 "   -0.040 2.00e-02 2.50e+03
        pdb=" N2  NAG B 609 "    0.076 2.00e-02 2.50e+03
        pdb=" O7  NAG B 609 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 311 "   -0.027 2.00e-02 2.50e+03   2.91e-02 2.11e+01
        pdb=" CG  TRP A 311 "    0.000 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 311 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 311 "    0.058 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 311 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 311 "    0.031 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 311 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 311 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 311 "   -0.039 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 311 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1349 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 32
        2.53 -     3.12: 6304
        3.12 -     3.71: 13560
        3.71 -     4.31: 19920
        4.31 -     4.90: 32382
  Nonbonded interactions: 72198
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 338 "
            pdb="NA    NA A 602 "
     model   vdw
     1.932 3.210
  nonbonded pdb=" OD2 ASP B 338 "
            pdb="NA    NA B 602 "
     model   vdw
     1.932 3.210
  nonbonded pdb=" ND2 ASN B 144 "
            pdb=" C1  NAG B 609 "
     model   vdw
     2.059 3.550
  nonbonded pdb=" ND2 ASN A 144 "
            pdb=" C1  NAG A 609 "
     model   vdw
     2.059 3.550
  nonbonded pdb=" OAI AV0 A 604 "
            pdb=" OH  TYR B 474 "
     model   vdw
     2.228 3.040
  ... (remaining 72193 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.380
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:5.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
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      :  0.015   0.069   8490  Z= 1.059
  Angle     :  1.791  10.357  11588  Z= 1.295
  Chirality :  0.085   0.244   1422
  Planarity :  0.014   0.117   1352
  Dihedral  : 15.566 141.589   3650
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 12.38 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.48 (0.24), residues: 1012
  helix: -0.06 (0.18), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.56 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG B 555 
 TYR   0.043   0.009   TYR B 474 
 PHE   0.050   0.010   PHE A 459 
 TRP   0.058   0.012   TRP A 311 
 HIS   0.014   0.005   HIS A 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01479 /  1.06 ( 8488)
  covalent geometry    : angle       1.79076 /  1.29 (11588)
  hydrogen bonds       : bond        0.18082 / 12.17 (  506)
  hydrogen bonds       : angle       7.15593 /  4.96 ( 1452)
  Misc. bond           : bond        0.01839 /  0.92 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   78 MET cc_start: 0.8861 (tmt) cc_final: 0.8390 (tmt)
REVERT: A   99 THR cc_start: 0.8314 (t) cc_final: 0.8100 (p)
REVERT: A  119 LYS cc_start: 0.7518 (pttp) cc_final: 0.7301 (mtmm)
REVERT: A  161 MET cc_start: 0.8740 (mtp) cc_final: 0.8324 (mtm)
REVERT: A  172 LEU cc_start: 0.8139 (tp) cc_final: 0.7673 (mt)
REVERT: A  201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7092 (mt0)
REVERT: A  251 ILE cc_start: 0.7110 (tt) cc_final: 0.6770 (pt)
REVERT: A  334 GLU cc_start: 0.8383 (tt0) cc_final: 0.8141 (tt0)
REVERT: A  381 SER cc_start: 0.8036 (m) cc_final: 0.7664 (p)
REVERT: A  476 GLU cc_start: 0.7849 (tp30) cc_final: 0.7310 (mm-30)
REVERT: A  500 GLU cc_start: 0.7758 (mp0) cc_final: 0.7470 (mp0)
REVERT: A  550 MET cc_start: 0.3349 (tpt) cc_final: 0.3060 (tpt)
REVERT: B   78 MET cc_start: 0.8857 (tmt) cc_final: 0.8387 (tmt)
REVERT: B   99 THR cc_start: 0.8316 (t) cc_final: 0.8101 (p)
REVERT: B  119 LYS cc_start: 0.7520 (pttp) cc_final: 0.7302 (mtmm)
REVERT: B  161 MET cc_start: 0.8740 (mtp) cc_final: 0.8323 (mtm)
REVERT: B  172 LEU cc_start: 0.8133 (tp) cc_final: 0.7668 (mt)
REVERT: B  201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7093 (mt0)
REVERT: B  251 ILE cc_start: 0.7110 (tt) cc_final: 0.6772 (pt)
REVERT: B  334 GLU cc_start: 0.8380 (tt0) cc_final: 0.8139 (tt0)
REVERT: B  381 SER cc_start: 0.8037 (m) cc_final: 0.7664 (p)
REVERT: B  476 GLU cc_start: 0.7850 (tp30) cc_final: 0.7312 (mm-30)
REVERT: B  500 GLU cc_start: 0.7761 (mp0) cc_final: 0.7473 (mp0)
REVERT: B  550 MET cc_start: 0.3351 (tpt) cc_final: 0.3063 (tpt)
  outliers start: 4
  outliers final: 0
  residues processed: 148
  average time/residue: 0.4334
  time to fit residues: 68.5086
Evaluate side-chains
  120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0270
   overall best weight:    2.6046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 HIS
B 108 GLN
B 147 HIS
B 483 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.151693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.116818 restraints weight = 7904.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.17
r_work: 0.3096 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.105   8490  Z= 0.246
  Angle     :  1.255  39.279  11588  Z= 0.577
  Chirality :  0.067   0.506   1422
  Planarity :  0.013   0.188   1352
  Dihedral  : 13.130 127.667   1940
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  2.17 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 13.10 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.52 %
    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: -0.43 (0.25), residues: 1012
  helix:  0.10 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -0.84 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.071   0.005   ARG B 456 
 TYR   0.187   0.008   TYR B 402 
 PHE   0.101   0.006   PHE B 255 
 TRP   0.076   0.004   TRP B 265 
 HIS   0.061   0.007   HIS B 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00583 /  0.25 ( 8488)
  covalent geometry    : angle       1.25465 /  0.58 (11588)
  hydrogen bonds       : bond        0.06764 /  4.86 (  506)
  hydrogen bonds       : angle       5.62938 /  4.02 ( 1452)
  Misc. bond           : bond        0.00007 /  0.00 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 135
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   46 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6820 (tm)
REVERT: A   78 MET cc_start: 0.8796 (tmt) cc_final: 0.8341 (tmt)
REVERT: A  161 MET cc_start: 0.9015 (mtp) cc_final: 0.8575 (mtm)
REVERT: A  172 LEU cc_start: 0.8612 (tp) cc_final: 0.8179 (mt)
REVERT: A  251 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7213 (pt)
REVERT: A  550 MET cc_start: 0.4915 (tpt) cc_final: 0.4404 (tpt)
REVERT: B   78 MET cc_start: 0.8715 (tmt) cc_final: 0.8181 (tmt)
REVERT: B  172 LEU cc_start: 0.8557 (tp) cc_final: 0.8124 (OUTLIER)
REVERT: B  249 ILE cc_start: 0.5833 (OUTLIER) cc_final: 0.5054 (mm)
REVERT: B  251 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7262 (pt)
REVERT: B  282 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7383 (mtpm)
REVERT: B  550 MET cc_start: 0.4968 (tpt) cc_final: 0.4477 (tpt)
  outliers start: 37
  outliers final: 9
  residues processed: 156
  average time/residue: 0.4173
  time to fit residues: 69.8656
Evaluate side-chains
  128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 GLN
B 108 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.152562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.117813 restraints weight = 8098.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.17
r_work: 0.3070 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8490  Z= 0.146
  Angle     :  0.650   8.399  11588  Z= 0.318
  Chirality :  0.043   0.188   1422
  Planarity :  0.005   0.045   1352
  Dihedral  : 12.736 131.629   1940
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.12 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.10 (0.26), residues: 1012
  helix:  1.13 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  0.08 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 456 
 TYR   0.014   0.002   TYR B 339 
 PHE   0.021   0.002   PHE B 502 
 TRP   0.015   0.001   TRP A 149 
 HIS   0.003   0.001   HIS B 354 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.15 ( 8488)
  covalent geometry    : angle       0.65042 /  0.32 (11588)
  hydrogen bonds       : bond        0.05271 /  3.77 (  506)
  hydrogen bonds       : angle       5.00948 /  3.59 ( 1452)
  Misc. bond           : bond        0.00020 /  0.01 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A   78 MET cc_start: 0.8756 (tmt) cc_final: 0.8354 (tmt)
REVERT: A  161 MET cc_start: 0.9018 (mtp) cc_final: 0.8587 (mtm)
REVERT: A  172 LEU cc_start: 0.8493 (tp) cc_final: 0.8141 (mt)
REVERT: A  251 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7230 (pt)
REVERT: A  254 MET cc_start: 0.7203 (mtp) cc_final: 0.6997 (mtm)
REVERT: A  550 MET cc_start: 0.4939 (tpt) cc_final: 0.4429 (tpt)
REVERT: B  172 LEU cc_start: 0.8567 (tp) cc_final: 0.8060 (mt)
REVERT: B  251 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7420 (pt)
REVERT: B  282 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7473 (mtpm)
REVERT: B  550 MET cc_start: 0.5034 (tpt) cc_final: 0.4557 (tpt)
  outliers start: 21
  outliers final: 5
  residues processed: 124
  average time/residue: 0.4407
  time to fit residues: 58.5183
Evaluate side-chains
  121 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0170
   chunk 77 optimal weight:    0.0980
   chunk 76 optimal weight:   20.0000
   chunk 43 optimal weight:   10.0000
   overall best weight:    2.0222

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN
B 483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.150853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.113662 restraints weight = 7990.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.26
r_work: 0.3055 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8490  Z= 0.140
  Angle     :  0.627   8.339  11588  Z= 0.304
  Chirality :  0.042   0.141   1422
  Planarity :  0.005   0.050   1352
  Dihedral  : 12.564 134.318   1940
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.71 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.82 (0.26), residues: 1012
  helix:  1.49 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  0.84 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 456 
 TYR   0.009   0.001   TYR B 474 
 PHE   0.016   0.002   PHE A 459 
 TRP   0.014   0.001   TRP A 149 
 HIS   0.002   0.001   HIS B 354 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 8488)
  covalent geometry    : angle       0.62749 /  0.30 (11588)
  hydrogen bonds       : bond        0.05047 /  3.60 (  506)
  hydrogen bonds       : angle       4.85854 /  3.49 ( 1452)
  Misc. bond           : bond        0.00013 /  0.01 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  116 VAL cc_start: 0.8455 (t) cc_final: 0.8208 (t)
REVERT: A  161 MET cc_start: 0.9038 (mtp) cc_final: 0.8616 (mtm)
REVERT: A  172 LEU cc_start: 0.8463 (tp) cc_final: 0.8068 (mt)
REVERT: A  251 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7209 (pt)
REVERT: A  550 MET cc_start: 0.4936 (tpt) cc_final: 0.4454 (tpt)
REVERT: B  116 VAL cc_start: 0.8553 (t) cc_final: 0.8294 (t)
REVERT: B  172 LEU cc_start: 0.8526 (tp) cc_final: 0.8053 (mt)
REVERT: B  251 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7288 (pt)
REVERT: B  282 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7403 (mtpm)
REVERT: B  550 MET cc_start: 0.5029 (tpt) cc_final: 0.4159 (tpt)
  outliers start: 18
  outliers final: 7
  residues processed: 123
  average time/residue: 0.4172
  time to fit residues: 55.1131
Evaluate side-chains
  113 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 87 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.148902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.111692 restraints weight = 7914.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.25
r_work: 0.3067 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8490  Z= 0.170
  Angle     :  0.668   8.081  11588  Z= 0.325
  Chirality :  0.044   0.153   1422
  Planarity :  0.006   0.050   1352
  Dihedral  : 12.780 134.474   1940
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.95 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.89 (0.26), residues: 1012
  helix:  1.49 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop :  1.04 (0.37), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 456 
 TYR   0.012   0.002   TYR A  42 
 PHE   0.019   0.002   PHE A 459 
 TRP   0.015   0.002   TRP A 149 
 HIS   0.003   0.001   HIS B  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.17 ( 8488)
  covalent geometry    : angle       0.66751 /  0.33 (11588)
  hydrogen bonds       : bond        0.05563 /  3.97 (  506)
  hydrogen bonds       : angle       4.96952 /  3.56 ( 1452)
  Misc. bond           : bond        0.00024 /  0.01 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9043 (mtp) cc_final: 0.8616 (mtm)
REVERT: A  172 LEU cc_start: 0.8472 (tp) cc_final: 0.8094 (mt)
REVERT: A  251 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7187 (pt)
REVERT: A  550 MET cc_start: 0.5084 (tpt) cc_final: 0.4353 (tpt)
REVERT: B  172 LEU cc_start: 0.8553 (tp) cc_final: 0.8126 (mt)
REVERT: B  251 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7361 (pt)
REVERT: B  282 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7416 (mtpm)
REVERT: B  550 MET cc_start: 0.5060 (tpt) cc_final: 0.4337 (tpt)
  outliers start: 24
  outliers final: 12
  residues processed: 119
  average time/residue: 0.4063
  time to fit residues: 51.8250
Evaluate side-chains
  118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  344 ARG
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN
B 483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.151255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.114444 restraints weight = 7907.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.25
r_work: 0.3105 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8490  Z= 0.129
  Angle     :  0.615   8.971  11588  Z= 0.294
  Chirality :  0.041   0.135   1422
  Planarity :  0.005   0.048   1352
  Dihedral  : 12.389 135.231   1940
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.31 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.22 (0.27), residues: 1012
  helix:  1.69 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  1.27 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 456 
 TYR   0.009   0.001   TYR A  42 
 PHE   0.015   0.002   PHE A  56 
 TRP   0.014   0.001   TRP A 149 
 HIS   0.002   0.001   HIS A 354 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 8488)
  covalent geometry    : angle       0.61457 /  0.29 (11588)
  hydrogen bonds       : bond        0.04757 /  3.40 (  506)
  hydrogen bonds       : angle       4.78919 /  3.44 ( 1452)
  Misc. bond           : bond        0.00016 /  0.01 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9024 (mtp) cc_final: 0.8605 (mtm)
REVERT: A  167 GLU cc_start: 0.8407 (tt0) cc_final: 0.8175 (tt0)
REVERT: A  172 LEU cc_start: 0.8413 (tp) cc_final: 0.8026 (mt)
REVERT: A  251 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7245 (pt)
REVERT: A  550 MET cc_start: 0.5052 (tpt) cc_final: 0.4258 (tpt)
REVERT: B   78 MET cc_start: 0.8740 (tmt) cc_final: 0.8424 (tmt)
REVERT: B  172 LEU cc_start: 0.8456 (tp) cc_final: 0.8012 (mt)
REVERT: B  251 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7409 (pt)
REVERT: B  282 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7449 (mtpm)
REVERT: B  550 MET cc_start: 0.5026 (tpt) cc_final: 0.4044 (tpt)
  outliers start: 23
  outliers final: 10
  residues processed: 117
  average time/residue: 0.4013
  time to fit residues: 50.3402
Evaluate side-chains
  114 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN
B  76 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.147485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.110342 restraints weight = 7951.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.25
r_work: 0.3010 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8490  Z= 0.222
  Angle     :  0.735   8.192  11588  Z= 0.357
  Chirality :  0.047   0.176   1422
  Planarity :  0.006   0.046   1352
  Dihedral  : 13.075 133.759   1940
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.31 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.72 (0.26), residues: 1012
  helix:  1.33 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  1.02 (0.37), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 456 
 TYR   0.015   0.002   TYR A  42 
 PHE   0.025   0.003   PHE A 200 
 TRP   0.016   0.002   TRP A 149 
 HIS   0.003   0.001   HIS B  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00523 /  0.22 ( 8488)
  covalent geometry    : angle       0.73546 /  0.36 (11588)
  hydrogen bonds       : bond        0.06127 /  4.39 (  506)
  hydrogen bonds       : angle       5.10139 /  3.66 ( 1452)
  Misc. bond           : bond        0.00032 /  0.02 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9065 (mtp) cc_final: 0.8685 (mtm)
REVERT: A  172 LEU cc_start: 0.8555 (tp) cc_final: 0.8119 (mt)
REVERT: A  251 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7156 (pt)
REVERT: A  526 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.6164 (mt0)
REVERT: A  550 MET cc_start: 0.4955 (tpt) cc_final: 0.4071 (tpt)
REVERT: B  172 LEU cc_start: 0.8564 (tp) cc_final: 0.8138 (mt)
REVERT: B  251 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7224 (pt)
REVERT: B  282 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7377 (mtpm)
  outliers start: 19
  outliers final: 11
  residues processed: 117
  average time/residue: 0.4228
  time to fit residues: 53.0924
Evaluate side-chains
  121 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 47 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 52 optimal weight:   10.0000
   overall best weight:    2.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.150822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.116071 restraints weight = 8176.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.19
r_work: 0.3087 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8490  Z= 0.155
  Angle     :  0.645   7.933  11588  Z= 0.313
  Chirality :  0.043   0.149   1422
  Planarity :  0.005   0.044   1352
  Dihedral  : 12.757 133.619   1940
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.79 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.97 (0.27), residues: 1012
  helix:  1.50 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  1.18 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 456 
 TYR   0.012   0.001   TYR A  42 
 PHE   0.017   0.002   PHE A 459 
 TRP   0.016   0.002   TRP A 149 
 HIS   0.002   0.001   HIS A 354 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 8488)
  covalent geometry    : angle       0.64545 /  0.31 (11588)
  hydrogen bonds       : bond        0.05277 /  3.78 (  506)
  hydrogen bonds       : angle       4.94088 /  3.55 ( 1452)
  Misc. bond           : bond        0.00025 /  0.01 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9027 (mtp) cc_final: 0.8600 (mtm)
REVERT: A  172 LEU cc_start: 0.8500 (tp) cc_final: 0.8119 (mt)
REVERT: A  251 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7241 (pt)
REVERT: A  526 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.6133 (mt0)
REVERT: A  550 MET cc_start: 0.4994 (tpt) cc_final: 0.4116 (tpt)
REVERT: B   78 MET cc_start: 0.8796 (tmt) cc_final: 0.8337 (tmt)
REVERT: B  172 LEU cc_start: 0.8509 (tp) cc_final: 0.8114 (mt)
REVERT: B  251 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7364 (pt)
REVERT: B  282 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7498 (mtpm)
  outliers start: 20
  outliers final: 11
  residues processed: 111
  average time/residue: 0.4348
  time to fit residues: 51.6409
Evaluate side-chains
  117 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  313 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 77 optimal weight:    0.4980
   chunk 1 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 13 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   overall best weight:    1.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.151733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.116994 restraints weight = 8139.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.19
r_work: 0.3101 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8490  Z= 0.139
  Angle     :  0.617   7.641  11588  Z= 0.300
  Chirality :  0.042   0.138   1422
  Planarity :  0.005   0.043   1352
  Dihedral  : 12.492 134.390   1940
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.67 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.19 (0.27), residues: 1012
  helix:  1.65 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  1.31 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 456 
 TYR   0.010   0.001   TYR A  42 
 PHE   0.018   0.002   PHE B 420 
 TRP   0.015   0.001   TRP A 149 
 HIS   0.002   0.001   HIS A 354 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 8488)
  covalent geometry    : angle       0.61707 /  0.30 (11588)
  hydrogen bonds       : bond        0.04914 /  3.52 (  506)
  hydrogen bonds       : angle       4.80119 /  3.44 ( 1452)
  Misc. bond           : bond        0.00017 /  0.01 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9020 (mtp) cc_final: 0.8597 (mtm)
REVERT: A  167 GLU cc_start: 0.8409 (tt0) cc_final: 0.8196 (tt0)
REVERT: A  172 LEU cc_start: 0.8466 (tp) cc_final: 0.8079 (mt)
REVERT: A  251 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7182 (pt)
REVERT: A  526 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.6134 (mt0)
REVERT: A  550 MET cc_start: 0.5053 (tpt) cc_final: 0.4160 (tpt)
REVERT: B  172 LEU cc_start: 0.8474 (tp) cc_final: 0.8104 (mt)
REVERT: B  251 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7373 (pt)
REVERT: B  282 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7493 (mtpm)
  outliers start: 20
  outliers final: 13
  residues processed: 115
  average time/residue: 0.4302
  time to fit residues: 52.8174
Evaluate side-chains
  120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 88 optimal weight:    0.7980
   chunk 73 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    2.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
B  50 GLN
B 483 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.150393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.115967 restraints weight = 8130.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.16
r_work: 0.3092 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8490  Z= 0.163
  Angle     :  0.652   7.933  11588  Z= 0.318
  Chirality :  0.044   0.152   1422
  Planarity :  0.005   0.043   1352
  Dihedral  : 12.684 133.828   1940
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.14 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.02 (0.26), residues: 1012
  helix:  1.52 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  1.24 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 456 
 TYR   0.012   0.002   TYR A  42 
 PHE   0.020   0.002   PHE B 420 
 TRP   0.016   0.002   TRP A 149 
 HIS   0.002   0.001   HIS A 354 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 ( 8488)
  covalent geometry    : angle       0.65240 /  0.32 (11588)
  hydrogen bonds       : bond        0.05372 /  3.84 (  506)
  hydrogen bonds       : angle       4.91836 /  3.53 ( 1452)
  Misc. bond           : bond        0.00020 /  0.01 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9029 (mtp) cc_final: 0.8607 (mtm)
REVERT: A  172 LEU cc_start: 0.8469 (tp) cc_final: 0.8100 (mt)
REVERT: A  251 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7230 (pt)
REVERT: A  526 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.6238 (mt0)
REVERT: A  550 MET cc_start: 0.5047 (tpt) cc_final: 0.4143 (tpt)
REVERT: B  172 LEU cc_start: 0.8507 (tp) cc_final: 0.8120 (mt)
REVERT: B  251 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7379 (pt)
REVERT: B  282 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7495 (mtpm)
  outliers start: 17
  outliers final: 13
  residues processed: 106
  average time/residue: 0.4449
  time to fit residues: 50.3976
Evaluate side-chains
  117 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 64 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 74 optimal weight:    0.1980
   chunk 11 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    2.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
B  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.151634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.117011 restraints weight = 8162.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.18
r_work: 0.3097 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8490  Z= 0.143
  Angle     :  0.624   7.754  11588  Z= 0.304
  Chirality :  0.042   0.140   1422
  Planarity :  0.005   0.042   1352
  Dihedral  : 12.544 133.939   1940
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.02 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.14 (0.27), residues: 1012
  helix:  1.61 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  1.29 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 456 
 TYR   0.010   0.001   TYR A  42 
 PHE   0.021   0.002   PHE B 420 
 TRP   0.015   0.001   TRP A 149 
 HIS   0.002   0.001   HIS A 354 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 8488)
  covalent geometry    : angle       0.62420 /  0.30 (11588)
  hydrogen bonds       : bond        0.05015 /  3.59 (  506)
  hydrogen bonds       : angle       4.83619 /  3.47 ( 1452)
  Misc. bond           : bond        0.00018 /  0.01 (    2)

===============================================================================
Job complete
usr+sys time: 2577.88 seconds
wall clock time: 44 minutes 37.91 seconds (2677.91 seconds total)