Starting phenix.real_space_refine
on Thu Mar 13 00:36:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uvc_42615/03_2025/8uvc_42615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uvc_42615/03_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_42615/03_2025/8uvc_42615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uvc_42615/03_2025/8uvc_42615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uvc_42615/03_2025/8uvc_42615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uvc_42615/03_2025/8uvc_42615.cif"
  }
  resolution = 2.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.050
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.98, per 1000 atoms: 0.70
  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: 2.39
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.77
  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: 2.27

  Time building geometry restraints manager: 2.79 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 581 or resid 701 or resid 703 or resid 706 throu \ 
gh 707))
  selection = (chain 'B' and (resid 1 through 581 or resid 701 or resid 703 or resid 706 throu \ 
gh 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:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.790
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:12.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.520
-------------------------------------------------------------------------------
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= 0.330
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (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
 TRP   0.017   0.002   TRP A 418 
 HIS   0.002   0.001   HIS A 109 
 PHE   0.023   0.002   PHE B  72 
 TYR   0.021   0.003   TYR A 301 
 ARG   0.008   0.001   ARG B 228 

*********************** 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  : 0.881 
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: 1.0398
  time to fit residues: 154.5936
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  : 0.985 
-------------------------------------------------------------------------------
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 86 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.9580

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.106867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.075079 restraints weight = 14075.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 2.01
r_work: 0.2769 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2651
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2651 r_free = 0.2651    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2651 r_free = 0.2651    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2651
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8798  Z= 0.223
  Angle     :  0.589   7.655  11964  Z= 0.284
  Chirality :  0.041   0.136   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 11.279  88.364   1852
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  5.47 %
    Favored  : 93.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.27), residues: 1014
  helix:  2.00 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.82 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 418 
 HIS   0.004   0.001   HIS B 109 
 PHE   0.019   0.002   PHE B 363 
 TYR   0.014   0.001   TYR A 226 
 ARG   0.002   0.000   ARG A 227 

*********************** 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: 13
    poor density    : 113
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7314 (tp30)
REVERT: B    1 MET cc_start: 0.5987 (OUTLIER) cc_final: 0.4816 (mmt)
REVERT: B  223 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7285 (tp30)
REVERT: B  330 GLU cc_start: 0.7834 (tp30) cc_final: 0.7316 (tm-30)
REVERT: B  525 VAL cc_start: 0.9140 (m) cc_final: 0.8913 (p)
  outliers start: 13
  outliers final: 5
  residues processed: 117
  average time/residue: 0.9375
  time to fit residues: 119.9781
Evaluate side-chains
  121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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 69 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0570
   chunk 51 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.7902

-------------------------------------------------------------------------------
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 = 0.106965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.073894 restraints weight = 19795.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 2.35
r_work: 0.2740 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2624 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.1428

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= 0.194
  Angle     :  0.532   5.434  11964  Z= 0.262
  Chirality :  0.041   0.156   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.861  89.062   1852
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  6.86 %
    Favored  : 91.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.27), residues: 1014
  helix:  2.14 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop :  1.09 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 418 
 HIS   0.004   0.001   HIS A 109 
 PHE   0.015   0.001   PHE B 363 
 TYR   0.016   0.001   TYR B 226 
 ARG   0.003   0.000   ARG A 227 

*********************** 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
  128 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5485 (OUTLIER) cc_final: 0.3983 (mmt)
REVERT: A  223 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7337 (tp30)
REVERT: A  478 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7837 (t80)
REVERT: B    1 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.4714 (mmt)
REVERT: B  223 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7367 (tp30)
REVERT: B  272 VAL cc_start: 0.9072 (m) cc_final: 0.8802 (p)
REVERT: B  330 GLU cc_start: 0.7881 (tp30) cc_final: 0.7347 (tm-30)
REVERT: B  404 ASP cc_start: 0.7816 (t0) cc_final: 0.7445 (t70)
REVERT: B  525 VAL cc_start: 0.9128 (m) cc_final: 0.8911 (p)
  outliers start: 14
  outliers final: 5
  residues processed: 118
  average time/residue: 0.9325
  time to fit residues: 120.2314
Evaluate side-chains
  122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 30 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0870
   chunk 55 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 63 optimal weight:    0.3980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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
B 552 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.107906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.075294 restraints weight = 19467.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 2.28
r_work: 0.2743 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2627 r_free = 0.2627    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2627 r_free = 0.2627    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8798  Z= 0.158
  Angle     :  0.505   5.350  11964  Z= 0.248
  Chirality :  0.040   0.161   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.805  89.875   1852
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  7.44 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.90 (0.27), residues: 1014
  helix:  2.19 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.17 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 418 
 HIS   0.006   0.001   HIS B 109 
 PHE   0.014   0.001   PHE A 352 
 TYR   0.016   0.001   TYR B 226 
 ARG   0.003   0.000   ARG A 227 

*********************** 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
  133 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.229 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5414 (OUTLIER) cc_final: 0.4051 (mmt)
REVERT: A  223 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7359 (tp30)
REVERT: A  225 GLU cc_start: 0.7984 (tp30) cc_final: 0.7781 (tp30)
REVERT: B    1 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.4716 (mmt)
REVERT: B  223 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7260 (tp30)
REVERT: B  272 VAL cc_start: 0.8956 (m) cc_final: 0.8710 (p)
REVERT: B  330 GLU cc_start: 0.7829 (tp30) cc_final: 0.7306 (tm-30)
REVERT: B  404 ASP cc_start: 0.7767 (t0) cc_final: 0.7470 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 123
  average time/residue: 0.9991
  time to fit residues: 133.9488
Evaluate side-chains
  120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
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    9 LYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  527 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 96 optimal weight:    0.1980
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3376 r_free = 0.3376 target = 0.106654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.074602 restraints weight = 19097.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 2.19
r_work: 0.2726 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2609 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8857
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8798  Z= 0.188
  Angle     :  0.524   5.473  11964  Z= 0.257
  Chirality :  0.041   0.168   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.878  89.768   1852
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  7.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.27), residues: 1014
  helix:  2.19 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.16 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 418 
 HIS   0.007   0.001   HIS B 109 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.017   0.001   TYR B 226 
 ARG   0.002   0.000   ARG A 503 

*********************** 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
  125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.966 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7424 (tp30)
REVERT: A  478 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7912 (t80)
REVERT: B    1 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.4759 (mmt)
REVERT: B  223 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7370 (tp30)
REVERT: B  272 VAL cc_start: 0.9113 (m) cc_final: 0.8875 (p)
REVERT: B  330 GLU cc_start: 0.8019 (tp30) cc_final: 0.7549 (tm-30)
REVERT: B  404 ASP cc_start: 0.7916 (t0) cc_final: 0.7585 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 117
  average time/residue: 1.0924
  time to fit residues: 139.1939
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  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
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   25 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  527 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0970
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.107881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.076418 restraints weight = 14169.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.99
r_work: 0.2842 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2737
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.1692

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= 0.167
  Angle     :  0.512   5.625  11964  Z= 0.251
  Chirality :  0.040   0.176   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.793  88.525   1852
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  8.26 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.95 (0.27), residues: 1014
  helix:  2.24 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.13 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 418 
 HIS   0.007   0.001   HIS B 109 
 PHE   0.014   0.001   PHE A 352 
 TYR   0.018   0.001   TYR B 226 
 ARG   0.002   0.000   ARG B 227 

*********************** 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
  125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.977 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7438 (tp30)
REVERT: A  478 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7968 (t80)
REVERT: B    1 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.4694 (mmt)
REVERT: B  272 VAL cc_start: 0.9131 (m) cc_final: 0.8874 (p)
REVERT: B  330 GLU cc_start: 0.8042 (tp30) cc_final: 0.7479 (mm-30)
REVERT: B  404 ASP cc_start: 0.7959 (t0) cc_final: 0.7611 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 117
  average time/residue: 1.0439
  time to fit residues: 132.4646
Evaluate side-chains
  117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.105343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.073349 restraints weight = 15648.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.05
r_work: 0.2703 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2585 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8798  Z= 0.256
  Angle     :  0.572   7.516  11964  Z= 0.280
  Chirality :  0.043   0.222   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 11.115  89.954   1852
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.27), residues: 1014
  helix:  2.17 (0.19), residues: 774
  sheet:  None (None), residues: 0
  loop :  1.01 (0.43), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 418 
 HIS   0.005   0.001   HIS A 109 
 PHE   0.017   0.002   PHE A 477 
 TYR   0.018   0.001   TYR B 226 
 ARG   0.002   0.000   ARG A 227 

*********************** 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
  123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5462 (OUTLIER) cc_final: 0.3932 (mmm)
REVERT: A  223 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7401 (tp30)
REVERT: A  478 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7993 (t80)
REVERT: B    1 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.4691 (mmt)
REVERT: B  150 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9111 (ttt)
REVERT: B  272 VAL cc_start: 0.9201 (m) cc_final: 0.8906 (p)
REVERT: B  330 GLU cc_start: 0.8097 (tp30) cc_final: 0.7535 (mm-30)
REVERT: B  404 ASP cc_start: 0.7946 (t0) cc_final: 0.7560 (t0)
  outliers start: 15
  outliers final: 6
  residues processed: 112
  average time/residue: 0.8622
  time to fit residues: 105.5878
Evaluate side-chains
  115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
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  478 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  150 MET
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 29 optimal weight:    0.0870
   chunk 94 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0570
   chunk 8 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 98 optimal weight:    0.4980
   chunk 80 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4076

-------------------------------------------------------------------------------
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 = 0.3428 r_free = 0.3428 target = 0.108084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.076412 restraints weight = 16471.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.10
r_work: 0.2838 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8892
moved from start:          0.1817

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= 0.152
  Angle     :  0.517   6.492  11964  Z= 0.252
  Chirality :  0.040   0.172   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.834  87.841   1852
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.53 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.27), residues: 1014
  helix:  2.25 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.14 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 418 
 HIS   0.004   0.001   HIS B 109 
 PHE   0.014   0.001   PHE B 352 
 TYR   0.020   0.001   TYR A 226 
 ARG   0.002   0.000   ARG B 227 

*********************** 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
  117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 1.082 
Fit side-chains
REVERT: B    1 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.4667 (mmt)
REVERT: B  150 MET cc_start: 0.9348 (tmm) cc_final: 0.9131 (ttt)
REVERT: B  272 VAL cc_start: 0.9141 (m) cc_final: 0.8844 (p)
REVERT: B  330 GLU cc_start: 0.8049 (tp30) cc_final: 0.7515 (mm-30)
REVERT: B  404 ASP cc_start: 0.7993 (t0) cc_final: 0.7628 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 114
  average time/residue: 0.8674
  time to fit residues: 109.0154
Evaluate side-chains
  117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.4980
   chunk 56 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 96 optimal weight:    0.1980
   chunk 85 optimal weight:    0.0000
   overall best weight:    0.3984

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.108540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.077123 restraints weight = 15533.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.04
r_work: 0.2852 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8798  Z= 0.151
  Angle     :  0.521   6.964  11964  Z= 0.253
  Chirality :  0.040   0.187   1390
  Planarity :  0.005   0.039   1396
  Dihedral  : 10.700  87.319   1852
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.01 (0.27), residues: 1014
  helix:  2.28 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.15 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 418 
 HIS   0.003   0.001   HIS B 109 
 PHE   0.014   0.001   PHE A 352 
 TYR   0.018   0.001   TYR B 226 
 ARG   0.002   0.000   ARG A  16 

*********************** 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
  120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5653 (OUTLIER) cc_final: 0.3998 (mmm)
REVERT: B    1 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.4582 (mmt)
REVERT: B  150 MET cc_start: 0.9339 (tmm) cc_final: 0.9127 (ttt)
REVERT: B  272 VAL cc_start: 0.9126 (m) cc_final: 0.8852 (p)
REVERT: B  330 GLU cc_start: 0.7975 (tp30) cc_final: 0.7472 (mm-30)
REVERT: B  404 ASP cc_start: 0.7989 (t0) cc_final: 0.7627 (t0)
REVERT: B  522 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8782 (mtm)
  outliers start: 9
  outliers final: 5
  residues processed: 116
  average time/residue: 0.8796
  time to fit residues: 111.8763
Evaluate side-chains
  117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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   25 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  522 MET
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 48 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 80 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 72 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.107579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.076021 restraints weight = 15529.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 2.05
r_work: 0.2753 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.1857

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= 0.179
  Angle     :  0.541   6.885  11964  Z= 0.264
  Chirality :  0.041   0.186   1390
  Planarity :  0.005   0.039   1396
  Dihedral  : 10.734  87.901   1852
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.12 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.92 (0.27), residues: 1014
  helix:  2.22 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.12 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 418 
 HIS   0.003   0.001   HIS A 109 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.019   0.001   TYR B 226 
 ARG   0.001   0.000   ARG A  16 

********************** 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
  119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.3917 (mmm)
REVERT: A  478 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7987 (t80)
REVERT: B    1 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.4548 (mmt)
REVERT: B  150 MET cc_start: 0.9350 (tmm) cc_final: 0.9079 (ttt)
REVERT: B  225 GLU cc_start: 0.8286 (tp30) cc_final: 0.7968 (tp30)
REVERT: B  272 VAL cc_start: 0.9129 (m) cc_final: 0.8836 (p)
REVERT: B  330 GLU cc_start: 0.7996 (tp30) cc_final: 0.7489 (mm-30)
REVERT: B  404 ASP cc_start: 0.7974 (t0) cc_final: 0.7597 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 115
  average time/residue: 0.9888
  time to fit residues: 124.4825
Evaluate side-chains
  119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
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  478 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0970
   chunk 91 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3390 r_free = 0.3390 target = 0.105456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.074267 restraints weight = 13080.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 1.89
r_work: 0.2723 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8798  Z= 0.248
  Angle     :  0.586   9.441  11964  Z= 0.287
  Chirality :  0.043   0.190   1390
  Planarity :  0.005   0.038   1396
  Dihedral  : 11.049  89.421   1852
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.35 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.27), residues: 1014
  helix:  2.14 (0.19), residues: 774
  sheet:  None (None), residues: 0
  loop :  0.96 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 418 
 HIS   0.005   0.001   HIS A 109 
 PHE   0.017   0.001   PHE A 352 
 TYR   0.019   0.002   TYR B 226 
 ARG   0.002   0.000   ARG A 228 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9191.78 seconds
wall clock time: 160 minutes 47.99 seconds (9647.99 seconds total)