Starting phenix.real_space_refine
on Fri Oct 10 18:34:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uvc_42615/10_2025/8uvc_42615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uvc_42615/10_2025/8uvc_42615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uvc_42615/10_2025/8uvc_42615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uvc_42615/10_2025/8uvc_42615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uvc_42615/10_2025/8uvc_42615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uvc_42615/10_2025/8uvc_42615.cif"
  }
  resolution = 2.09
  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=   0.000 sd=   0.050
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       4      5.49       5
     S      52      5.16       5
     Na      2      4.78       5
     C    5838      2.51       5
     N    1272      2.21       5
     O    1390      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8558
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 4011
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 34, 'TRANS': 478}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 4011
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 34, 'TRANS': 478}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 282
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 12, 272
          Unusual residues: {' NA': 1, '3PE': 2, 'AKG': 1, 'C14': 4, 'CLR': 4}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
      Conformer: "B"
        Number of residues, atoms: 12, 272
          Unusual residues: {' NA': 1, '3PE': 2, 'AKG': 1, 'C14': 4, 'CLR': 4}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
          bond proxies already assigned to first conformer: 267
    Chain: "B"
      Number of atoms: 254
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 10, 244
          Unusual residues: {' NA': 1, '3PE': 2, 'AKG': 1, 'C14': 2, 'CLR': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
      Conformer: "B"
        Number of residues, atoms: 10, 244
          Unusual residues: {' NA': 1, '3PE': 2, 'AKG': 1, 'C14': 2, 'CLR': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
          bond proxies already assigned to first conformer: 241
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" C1 AAKG A 702 " occ=0.50
      ... (18 atoms not shown)
      pdb=" O5 BAKG A 702 " occ=0.50
    residue:
      pdb=" C1 AAKG B 702 " occ=0.50
      ... (18 atoms not shown)
      pdb=" O5 BAKG B 702 " occ=0.50
  Time building chain proxies: 2.17, per 1000 atoms: 0.25
  Number of scatterers: 8558
  At special positions: 0
  Unit cell: (85.8, 106.425, 82.5, 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      52     16.00
     P       4     15.00
     Na      2     11.00
     O    1390      8.00
     N    1272      7.00
     C    5838      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: 0.77
  Conformation dependent library (CDL) restraints added in 300.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1924

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      84.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 14
      removed outlier: 3.831A  pdb=" N   ALA A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 34
      Proline residue:  A  24  - end of helix
      Proline residue:  A  29  - end of helix
      removed outlier: 3.692A  pdb=" N   PHE A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 55
    Processing helix  chain 'A' and resid 58 through 64
    Processing helix  chain 'A' and resid 64 through 73
      removed outlier: 3.805A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 83 through 86
    Processing helix  chain 'A' and resid 87 through 106
      removed outlier: 3.794A  pdb=" N   PHE A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TRP A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 121
      removed outlier: 3.566A  pdb=" N   GLY A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 140
    Processing helix  chain 'A' and resid 143 through 164
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 220 through 247
      removed outlier: 3.782A  pdb=" N   ILE A 238 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
      removed outlier: 3.869A  pdb=" N   THR A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 7.059A  pdb=" N   THR A 251 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 267
      removed outlier: 3.924A  pdb=" N   LEU A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LYS A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER A 265 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 301
      Proline residue:  A 284  - end of helix
    Processing helix  chain 'A' and resid 320 through 334
    Processing helix  chain 'A' and resid 339 through 358
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 377 through 389
      removed outlier: 3.897A  pdb=" N   ILE A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 3.816A  pdb=" N   PHE A 403 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 425
    Processing helix  chain 'A' and resid 426 through 446
    Processing helix  chain 'A' and resid 447 through 456
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 4.257A  pdb=" N   ASN A 461 " --> pdb=" O   PRO A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 479
    Processing helix  chain 'A' and resid 483 through 502
      Proline residue:  A 493  - end of helix
    Processing helix  chain 'A' and resid 505 through 517
      removed outlier: 3.916A  pdb=" N   LEU A 509 " --> pdb=" O   HIS A 505 " (cutoff:3.500A)
      Proline residue:  A 512  - end of helix
    Processing helix  chain 'A' and resid 527 through 535
    Processing helix  chain 'A' and resid 540 through 566
      removed outlier: 4.149A  pdb=" N   LEU A 550 " --> pdb=" O   ARG A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 572
    Processing helix  chain 'B' and resid 2 through 14
    Processing helix  chain 'B' and resid 14 through 34
      Proline residue:  B  24  - end of helix
      Proline residue:  B  29  - end of helix
      removed outlier: 3.693A  pdb=" N   PHE B  32 " --> pdb=" O   LEU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 55
    Processing helix  chain 'B' and resid 58 through 64
    Processing helix  chain 'B' and resid 64 through 73
      removed outlier: 3.805A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      Proline residue:  B  71  - end of helix
    Processing helix  chain 'B' and resid 77 through 82
    Processing helix  chain 'B' and resid 83 through 86
    Processing helix  chain 'B' and resid 87 through 106
      removed outlier: 3.794A  pdb=" N   PHE B  91 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TRP B 106 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 121
      removed outlier: 3.567A  pdb=" N   GLY B 121 " --> pdb=" O   LEU B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 140
    Processing helix  chain 'B' and resid 143 through 164
      Proline residue:  B 153  - end of helix
    Processing helix  chain 'B' and resid 220 through 247
      removed outlier: 3.782A  pdb=" N   ILE B 238 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      Proline residue:  B 239  - end of helix
      removed outlier: 3.869A  pdb=" N   THR B 247 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 252
      removed outlier: 7.059A  pdb=" N   THR B 251 " --> pdb=" O   ALA B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 267
      removed outlier: 3.924A  pdb=" N   LEU B 257 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER B 265 " --> pdb=" O   GLY B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 301
      Proline residue:  B 284  - end of helix
    Processing helix  chain 'B' and resid 320 through 334
    Processing helix  chain 'B' and resid 339 through 358
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 377 through 389
      removed outlier: 3.897A  pdb=" N   ILE B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
      removed outlier: 3.815A  pdb=" N   PHE B 403 " --> pdb=" O   LEU B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 425
    Processing helix  chain 'B' and resid 426 through 446
    Processing helix  chain 'B' and resid 447 through 456
    Processing helix  chain 'B' and resid 457 through 462
      removed outlier: 4.257A  pdb=" N   ASN B 461 " --> pdb=" O   PRO B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 479
    Processing helix  chain 'B' and resid 483 through 502
      Proline residue:  B 493  - end of helix
    Processing helix  chain 'B' and resid 505 through 517
      removed outlier: 3.916A  pdb=" N   LEU B 509 " --> pdb=" O   HIS B 505 " (cutoff:3.500A)
      Proline residue:  B 512  - end of helix
    Processing helix  chain 'B' and resid 527 through 535
    Processing helix  chain 'B' and resid 540 through 566
      removed outlier: 4.149A  pdb=" N   LEU B 550 " --> pdb=" O   ARG B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 572

    550 hydrogen bonds defined for protein.
    1608 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: 1.26

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1228
        1.30 -     1.43: 2188
        1.43 -     1.55: 5266
        1.55 -     1.68: 26
        1.68 -     1.81: 90
  Bond restraints: 8798
  Sorted by residual:
  bond pdb=" C   ARG B 126 "
       pdb=" O   ARG B 126 "
    ideal  model  delta    sigma   weight residual
    1.236  1.173  0.064 1.25e-02 6.40e+03 2.60e+01
  bond pdb=" C   ARG A 126 "
       pdb=" O   ARG A 126 "
    ideal  model  delta    sigma   weight residual
    1.236  1.173  0.064 1.25e-02 6.40e+03 2.59e+01
  bond pdb=" C   LEU B 129 "
       pdb=" O   LEU B 129 "
    ideal  model  delta    sigma   weight residual
    1.236  1.194  0.043 1.15e-02 7.56e+03 1.39e+01
  bond pdb=" C   LEU A 129 "
       pdb=" O   LEU A 129 "
    ideal  model  delta    sigma   weight residual
    1.236  1.194  0.043 1.15e-02 7.56e+03 1.39e+01
  bond pdb=" C   GLN A  84 "
       pdb=" O   GLN A  84 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.043 1.28e-02 6.10e+03 1.11e+01
  ... (remaining 8793 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 11503
        1.71 -     3.43: 370
        3.43 -     5.14: 65
        5.14 -     6.85: 18
        6.85 -     8.57: 8
  Bond angle restraints: 11964
  Sorted by residual:
  angle pdb=" C   LEU B  87 "
        pdb=" N   ASP B  88 "
        pdb=" CA  ASP B  88 "
      ideal   model   delta    sigma   weight residual
     120.60  129.17   -8.57 1.60e+00 3.91e-01 2.87e+01
  angle pdb=" C   LEU A  87 "
        pdb=" N   ASP A  88 "
        pdb=" CA  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     120.60  129.16   -8.56 1.60e+00 3.91e-01 2.86e+01
  angle pdb=" CA  LEU B  87 "
        pdb=" C   LEU B  87 "
        pdb=" O   LEU B  87 "
      ideal   model   delta    sigma   weight residual
     121.87  116.15    5.72 1.10e+00 8.26e-01 2.70e+01
  angle pdb=" CA  LEU A  87 "
        pdb=" C   LEU A  87 "
        pdb=" O   LEU A  87 "
      ideal   model   delta    sigma   weight residual
     121.87  116.17    5.70 1.10e+00 8.26e-01 2.69e+01
  angle pdb=" CA  LEU B  87 "
        pdb=" C   LEU B  87 "
        pdb=" N   ASP B  88 "
      ideal   model   delta    sigma   weight residual
     115.30  121.61   -6.31 1.33e+00 5.65e-01 2.25e+01
  ... (remaining 11959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.25: 5330
       24.25 -    48.50: 202
       48.50 -    72.75: 48
       72.75 -    96.99: 6
       96.99 -   121.24: 12
  Dihedral angle restraints: 5598
    sinusoidal: 2640
      harmonic: 2958
  Sorted by residual:
  dihedral pdb=" C   PHE B  86 "
           pdb=" N   PHE B  86 "
           pdb=" CA  PHE B  86 "
           pdb=" CB  PHE B  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.30   12.70     0      2.50e+00 1.60e-01 2.58e+01
  dihedral pdb=" C   PHE A  86 "
           pdb=" N   PHE A  86 "
           pdb=" CA  PHE A  86 "
           pdb=" CB  PHE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.28   12.68     0      2.50e+00 1.60e-01 2.57e+01
  dihedral pdb=" N   PHE B  86 "
           pdb=" C   PHE B  86 "
           pdb=" CA  PHE B  86 "
           pdb=" CB  PHE B  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.02  -11.22     0      2.50e+00 1.60e-01 2.01e+01
  ... (remaining 5595 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1321
       0.093 -    0.187: 64
       0.187 -    0.280: 3
       0.280 -    0.374: 0
       0.374 -    0.467: 2
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CA  PHE B  86 "
            pdb=" N   PHE B  86 "
            pdb=" C   PHE B  86 "
            pdb=" CB  PHE B  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" CA  PHE A  86 "
            pdb=" N   PHE A  86 "
            pdb=" C   PHE A  86 "
            pdb=" CB  PHE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.45e+00
  chirality pdb=" CA  LEU B  87 "
            pdb=" N   LEU B  87 "
            pdb=" C   LEU B  87 "
            pdb=" CB  LEU B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1387 not shown)

  Planarity restraints: 1396
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 133 "    0.014 2.00e-02 2.50e+03   2.95e-02 8.72e+00
        pdb=" C   VAL B 133 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL B 133 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR B 134 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 133 "   -0.014 2.00e-02 2.50e+03   2.95e-02 8.71e+00
        pdb=" C   VAL A 133 "    0.051 2.00e-02 2.50e+03
        pdb=" O   VAL A 133 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR A 134 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 132 "    0.014 2.00e-02 2.50e+03   2.91e-02 8.47e+00
        pdb=" C   MET B 132 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   MET B 132 "    0.019 2.00e-02 2.50e+03
        pdb=" N   VAL B 133 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1393 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1943
        2.79 -     3.32: 8603
        3.32 -     3.84: 14966
        3.84 -     4.37: 17900
        4.37 -     4.90: 30108
  Nonbonded interactions: 73520
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 139 "
            pdb=" OD1 ASN B 144 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG  SER A 139 "
            pdb=" OD1 ASN A 144 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   LEU A 561 "
            pdb=" OG1 THR A 565 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   LEU B 561 "
            pdb=" OG1 THR B 565 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OH  TYR B 240 "
            pdb=" O   PHE B 521 "
     model   vdw
     2.339 3.040
  ... (remaining 73515 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' and (resid 1 through 701 or resid 703 or resid 706 through 707))
  selection = (chain 'B' and (resid 1 through 701 or resid 703 or resid 706 through 707))
}

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=0.50 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:             2.270
  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:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.850
  Find NCS groups from input model:        0.130
  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:6.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
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      :  0.005   0.064   8798  Z= 0.298
  Angle     :  0.732   8.567  11964  Z= 0.414
  Chirality :  0.047   0.467   1390
  Planarity :  0.005   0.037   1396
  Dihedral  : 14.953 121.241   3674
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  1.40 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.21 %
  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 aren not related in a simple way.
  whole:  2.48 (0.27), residues: 1014
  helix:  1.95 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop :  0.79 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 228 
 TYR   0.021   0.003   TYR A 301 
 PHE   0.023   0.002   PHE B  72 
 TRP   0.017   0.002   TRP A 418 
 HIS   0.002   0.001   HIS A 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 8798)
  covalent geometry    : angle       0.73168 (11964)
  hydrogen bonds       : bond        0.11590 (  550)
  hydrogen bonds       : angle       4.47670 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  123 GLN cc_start: 0.6894 (mp10) cc_final: 0.6486 (mp10)
REVERT: A  223 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7265 (tp30)
REVERT: B  223 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7303 (tp30)
  outliers start: 4
  outliers final: 2
  residues processed: 138
  average time/residue: 0.5185
  time to fit residues: 76.8621
Evaluate side-chains
  113 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain B residue   86 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
B 333 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.108600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.076883 restraints weight = 14787.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 2.07
r_work: 0.2800 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2683 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8798  Z= 0.126
  Angle     :  0.562   7.100  11964  Z= 0.271
  Chirality :  0.040   0.137   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 11.100  88.886   1852
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  5.47 %
    Favored  : 93.14 %
  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 aren not related in a simple way.
  whole:  2.64 (0.27), residues: 1014
  helix:  2.07 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.81 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 227 
 TYR   0.015   0.001   TYR A 226 
 PHE   0.019   0.001   PHE B 363 
 TRP   0.017   0.002   TRP B 418 
 HIS   0.003   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8798)
  covalent geometry    : angle       0.56175 (11964)
  hydrogen bonds       : bond        0.03873 (  550)
  hydrogen bonds       : angle       3.85462 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7307 (tp30)
REVERT: A  554 MET cc_start: 0.9204 (mtm) cc_final: 0.8989 (mtm)
REVERT: B    1 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.4796 (mmt)
REVERT: B  223 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7309 (tp30)
REVERT: B  272 VAL cc_start: 0.9022 (m) cc_final: 0.8780 (p)
REVERT: B  404 ASP cc_start: 0.7766 (t0) cc_final: 0.7561 (t0)
REVERT: B  525 VAL cc_start: 0.9139 (m) cc_final: 0.8910 (p)
  outliers start: 12
  outliers final: 5
  residues processed: 118
  average time/residue: 0.4300
  time to fit residues: 55.2568
Evaluate side-chains
  116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0570
   chunk 36 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0970
   chunk 84 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.109289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.077090 restraints weight = 18092.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.25
r_work: 0.2800 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2686 r_free = 0.2686    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2686 r_free = 0.2686    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8798  Z= 0.108
  Angle     :  0.503   5.347  11964  Z= 0.247
  Chirality :  0.039   0.154   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.622  89.840   1852
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  7.79 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.27), residues: 1014
  helix:  2.20 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.27 (0.45), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 227 
 TYR   0.015   0.001   TYR B 226 
 PHE   0.015   0.001   PHE B 363 
 TRP   0.018   0.001   TRP B 418 
 HIS   0.003   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8798)
  covalent geometry    : angle       0.50277 (11964)
  hydrogen bonds       : bond        0.03477 (  550)
  hydrogen bonds       : angle       3.77411 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.3940 (mmt)
REVERT: A   86 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.7742 (t80)
REVERT: A  223 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7358 (tp30)
REVERT: B    1 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.4836 (mmt)
REVERT: B  223 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7305 (tp30)
REVERT: B  272 VAL cc_start: 0.8966 (m) cc_final: 0.8751 (p)
REVERT: B  330 GLU cc_start: 0.7892 (tp30) cc_final: 0.7328 (tm-30)
REVERT: B  404 ASP cc_start: 0.7691 (t0) cc_final: 0.7394 (t0)
REVERT: B  525 VAL cc_start: 0.9152 (m) cc_final: 0.8946 (p)
  outliers start: 11
  outliers final: 3
  residues processed: 117
  average time/residue: 0.4001
  time to fit residues: 50.9767
Evaluate side-chains
  115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0060
   chunk 34 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 72 optimal weight:    0.4980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.108400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.075727 restraints weight = 20697.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.38
r_work: 0.2771 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8798  Z= 0.113
  Angle     :  0.508   5.391  11964  Z= 0.249
  Chirality :  0.040   0.160   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.701  89.607   1852
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  7.21 %
    Favored  : 91.05 %
  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 aren not related in a simple way.
  whole:  2.98 (0.27), residues: 1014
  helix:  2.24 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.23 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.015   0.001   TYR B 226 
 PHE   0.014   0.001   PHE A 352 
 TRP   0.019   0.001   TRP B 418 
 HIS   0.003   0.001   HIS A 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8798)
  covalent geometry    : angle       0.50795 (11964)
  hydrogen bonds       : bond        0.03488 (  550)
  hydrogen bonds       : angle       3.77496 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.4057 (mmt)
REVERT: A   86 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.7498 (t80)
REVERT: A  223 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7321 (tp30)
REVERT: A  225 GLU cc_start: 0.8030 (tp30) cc_final: 0.7823 (tp30)
REVERT: A  544 MET cc_start: 0.8708 (ttm) cc_final: 0.8448 (ttp)
REVERT: B    1 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.4696 (mmt)
REVERT: B  223 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7327 (tp30)
REVERT: B  272 VAL cc_start: 0.9010 (m) cc_final: 0.8786 (p)
REVERT: B  330 GLU cc_start: 0.7924 (tp30) cc_final: 0.7420 (tm-30)
REVERT: B  404 ASP cc_start: 0.7692 (t0) cc_final: 0.7368 (t0)
REVERT: B  525 VAL cc_start: 0.9115 (m) cc_final: 0.8913 (p)
  outliers start: 15
  outliers final: 7
  residues processed: 118
  average time/residue: 0.4281
  time to fit residues: 54.7706
Evaluate side-chains
  120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  549 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.0980
   chunk 84 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    0.2980
   chunk 58 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.108613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.077430 restraints weight = 15093.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.00
r_work: 0.2780 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8826
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8798  Z= 0.111
  Angle     :  0.505   5.485  11964  Z= 0.246
  Chirality :  0.040   0.166   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.674  88.672   1852
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  :  7.67 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.99 (0.27), residues: 1014
  helix:  2.27 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.16 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 227 
 TYR   0.016   0.001   TYR B 226 
 PHE   0.014   0.001   PHE A 352 
 TRP   0.019   0.001   TRP B 418 
 HIS   0.007   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8798)
  covalent geometry    : angle       0.50546 (11964)
  hydrogen bonds       : bond        0.03386 (  550)
  hydrogen bonds       : angle       3.73946 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   86 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7354 (t80)
REVERT: A  223 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7398 (tp30)
REVERT: A  478 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7875 (t80)
REVERT: B    1 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.4691 (mmt)
REVERT: B  223 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7377 (tp30)
REVERT: B  272 VAL cc_start: 0.9050 (m) cc_final: 0.8849 (p)
REVERT: B  330 GLU cc_start: 0.7965 (tp30) cc_final: 0.7512 (tm-30)
REVERT: B  404 ASP cc_start: 0.7777 (t0) cc_final: 0.7428 (t0)
  outliers start: 18
  outliers final: 7
  residues processed: 119
  average time/residue: 0.4652
  time to fit residues: 59.9124
Evaluate side-chains
  116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  478 PHE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  549 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0170
   chunk 63 optimal weight:    0.2980
   chunk 41 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
A 552 ASN
B 333 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.077061 restraints weight = 17928.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.15
r_work: 0.2771 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2654
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8798  Z= 0.108
  Angle     :  0.506   7.316  11964  Z= 0.246
  Chirality :  0.040   0.188   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.620  87.774   1852
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.37 %
    Favored  : 89.88 %
  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 aren not related in a simple way.
  whole:  3.02 (0.27), residues: 1014
  helix:  2.29 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.15 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 503 
 TYR   0.018   0.001   TYR A 226 
 PHE   0.014   0.001   PHE A 352 
 TRP   0.018   0.001   TRP B 418 
 HIS   0.003   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8798)
  covalent geometry    : angle       0.50569 (11964)
  hydrogen bonds       : bond        0.03327 (  550)
  hydrogen bonds       : angle       3.74008 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7355 (tp30)
REVERT: A  478 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7897 (t80)
REVERT: A  544 MET cc_start: 0.8770 (ttm) cc_final: 0.8522 (ttp)
REVERT: B    1 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.4684 (mmt)
REVERT: B  223 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7369 (tp30)
REVERT: B  272 VAL cc_start: 0.9041 (m) cc_final: 0.8832 (p)
REVERT: B  330 GLU cc_start: 0.7985 (tp30) cc_final: 0.7388 (mm-30)
REVERT: B  404 ASP cc_start: 0.7800 (t0) cc_final: 0.7459 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 118
  average time/residue: 0.4165
  time to fit residues: 53.3283
Evaluate side-chains
  116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  478 PHE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  549 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0770
   chunk 17 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.107621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.076539 restraints weight = 14855.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 1.96
r_work: 0.2765 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2649 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2651
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2651 r_free = 0.2651    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2651 r_free = 0.2651    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2651
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8798  Z= 0.118
  Angle     :  0.517   5.731  11964  Z= 0.253
  Chirality :  0.040   0.180   1390
  Planarity :  0.005   0.039   1396
  Dihedral  : 10.668  87.709   1852
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  8.84 %
    Favored  : 89.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.02 (0.27), residues: 1014
  helix:  2.29 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.17 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 503 
 TYR   0.018   0.001   TYR B 226 
 PHE   0.014   0.001   PHE A 352 
 TRP   0.020   0.001   TRP B 418 
 HIS   0.007   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8798)
  covalent geometry    : angle       0.51728 (11964)
  hydrogen bonds       : bond        0.03485 (  550)
  hydrogen bonds       : angle       3.77794 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7429 (tp30)
REVERT: A  478 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7920 (t80)
REVERT: A  544 MET cc_start: 0.8767 (ttm) cc_final: 0.8561 (ttp)
REVERT: B    1 MET cc_start: 0.6183 (OUTLIER) cc_final: 0.4629 (mmt)
REVERT: B  223 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7367 (tp30)
REVERT: B  272 VAL cc_start: 0.9054 (m) cc_final: 0.8833 (p)
REVERT: B  330 GLU cc_start: 0.7997 (tp30) cc_final: 0.7377 (mm-30)
REVERT: B  404 ASP cc_start: 0.7837 (t0) cc_final: 0.7492 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 117
  average time/residue: 0.4859
  time to fit residues: 61.3907
Evaluate side-chains
  122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  478 PHE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  549 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0070
   overall best weight:    0.9400

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.106459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.074570 restraints weight = 15503.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 2.06
r_work: 0.2808 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8916
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8798  Z= 0.140
  Angle     :  0.544   6.148  11964  Z= 0.265
  Chirality :  0.041   0.185   1390
  Planarity :  0.005   0.039   1396
  Dihedral  : 10.839  88.314   1852
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  8.84 %
    Favored  : 89.53 %
  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 aren not related in a simple way.
  whole:  2.95 (0.27), residues: 1014
  helix:  2.24 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.16 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.018   0.001   TYR B 226 
 PHE   0.018   0.001   PHE A 477 
 TRP   0.022   0.002   TRP B 418 
 HIS   0.006   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8798)
  covalent geometry    : angle       0.54387 (11964)
  hydrogen bonds       : bond        0.03730 (  550)
  hydrogen bonds       : angle       3.84017 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5541 (OUTLIER) cc_final: 0.3945 (mmm)
REVERT: A  478 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7970 (t80)
REVERT: B    1 MET cc_start: 0.6228 (OUTLIER) cc_final: 0.4615 (mmt)
REVERT: B  272 VAL cc_start: 0.9178 (m) cc_final: 0.8909 (p)
REVERT: B  330 GLU cc_start: 0.8051 (tp30) cc_final: 0.7435 (mm-30)
REVERT: B  404 ASP cc_start: 0.7926 (t0) cc_final: 0.7599 (t0)
  outliers start: 14
  outliers final: 6
  residues processed: 112
  average time/residue: 0.4434
  time to fit residues: 54.0157
Evaluate side-chains
  119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  478 PHE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  549 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0980
   chunk 80 optimal weight:    0.0980
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.108847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.077552 restraints weight = 14284.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.99
r_work: 0.2862 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8798  Z= 0.106
  Angle     :  0.513   6.535  11964  Z= 0.250
  Chirality :  0.040   0.188   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.631  86.777   1852
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.53 %
    Favored  : 89.53 %
  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 aren not related in a simple way.
  whole:  3.07 (0.27), residues: 1014
  helix:  2.32 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.20 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 227 
 TYR   0.019   0.001   TYR A 226 
 PHE   0.018   0.001   PHE A 477 
 TRP   0.017   0.001   TRP B 418 
 HIS   0.006   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8798)
  covalent geometry    : angle       0.51253 (11964)
  hydrogen bonds       : bond        0.03264 (  550)
  hydrogen bonds       : angle       3.72495 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.3986 (mmm)
REVERT: A  478 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.7974 (t80)
REVERT: B    1 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.4549 (mmt)
REVERT: B  225 GLU cc_start: 0.8280 (tp30) cc_final: 0.7992 (tp30)
REVERT: B  272 VAL cc_start: 0.9115 (m) cc_final: 0.8863 (p)
REVERT: B  330 GLU cc_start: 0.8027 (tp30) cc_final: 0.7409 (mm-30)
REVERT: B  404 ASP cc_start: 0.7934 (t0) cc_final: 0.7619 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 112
  average time/residue: 0.4414
  time to fit residues: 53.9300
Evaluate side-chains
  114 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  478 PHE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.106954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.074749 restraints weight = 17189.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.16
r_work: 0.2808 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8911
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8798  Z= 0.131
  Angle     :  0.543   6.641  11964  Z= 0.265
  Chirality :  0.041   0.179   1390
  Planarity :  0.005   0.039   1396
  Dihedral  : 10.762  87.681   1852
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.42 %
    Favored  : 89.42 %
  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 aren not related in a simple way.
  whole:  2.97 (0.27), residues: 1014
  helix:  2.24 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.19 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  16 
 TYR   0.019   0.001   TYR B 226 
 PHE   0.018   0.001   PHE A 477 
 TRP   0.021   0.001   TRP B 418 
 HIS   0.007   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8798)
  covalent geometry    : angle       0.54271 (11964)
  hydrogen bonds       : bond        0.03615 (  550)
  hydrogen bonds       : angle       3.79981 ( 1608)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.3915 (mmm)
REVERT: A  478 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8600 (m-80)
REVERT: B    1 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.4545 (mmt)
REVERT: B  225 GLU cc_start: 0.8273 (tp30) cc_final: 0.7994 (tp30)
REVERT: B  272 VAL cc_start: 0.9154 (m) cc_final: 0.8880 (p)
REVERT: B  330 GLU cc_start: 0.8077 (tp30) cc_final: 0.7481 (mm-30)
REVERT: B  404 ASP cc_start: 0.7925 (t0) cc_final: 0.7587 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 112
  average time/residue: 0.4282
  time to fit residues: 52.2735
Evaluate side-chains
  114 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  478 PHE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  527 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.2980
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    0.2980
   chunk 76 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.106752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.074961 restraints weight = 15295.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.04
r_work: 0.2737 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8798  Z= 0.132
  Angle     :  0.546   6.862  11964  Z= 0.267
  Chirality :  0.041   0.185   1390
  Planarity :  0.005   0.039   1396
  Dihedral  : 10.822  88.271   1852
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.77 %
    Favored  : 89.30 %
  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 aren not related in a simple way.
  whole:  2.94 (0.27), residues: 1014
  helix:  2.22 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.18 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 503 
 TYR   0.020   0.001   TYR A 226 
 PHE   0.017   0.001   PHE A 477 
 TRP   0.021   0.002   TRP B 418 
 HIS   0.010   0.002   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8798)
  covalent geometry    : angle       0.54635 (11964)
  hydrogen bonds       : bond        0.03648 (  550)
  hydrogen bonds       : angle       3.80650 ( 1608)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4454.52 seconds
wall clock time: 76 minutes 16.89 seconds (4576.89 seconds total)