Starting phenix.real_space_refine
on Wed Feb 12 23:22:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uvc_42615/02_2025/8uvc_42615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uvc_42615/02_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_42615/02_2025/8uvc_42615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uvc_42615/02_2025/8uvc_42615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uvc_42615/02_2025/8uvc_42615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uvc_42615/02_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-5592/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: 5.83, per 1000 atoms: 0.68
  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: 2.41
  Conformation dependent library (CDL) restraints added in 928.5 milliseconds
  

  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: 0.80
  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: 2.40

  Time building geometry restraints manager: 2.68 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:             3.110
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.330
  Find NCS groups from input model:        0.360
  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:11.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.140
-------------------------------------------------------------------------------
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  : 0.919 
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: 1.1178
  time to fit residues: 165.8353
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  : 0.896 
-------------------------------------------------------------------------------
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 = 0.075078 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: 0.2653 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    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 = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2654
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
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  : 0.942 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7323 (tp30)
REVERT: B    1 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.4824 (mmt)
REVERT: B  223 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7292 (tp30)
REVERT: B  330 GLU cc_start: 0.7839 (tp30) cc_final: 0.7322 (tm-30)
REVERT: B  525 VAL cc_start: 0.9144 (m) cc_final: 0.8917 (p)
  outliers start: 13
  outliers final: 5
  residues processed: 117
  average time/residue: 0.9334
  time to fit residues: 118.8362
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  : 0.900 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 51 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7918

-------------------------------------------------------------------------------
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 = 0.106755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.073809 restraints weight = 20711.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.37
r_work: 0.2739 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.1420

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   5.436  11964  Z= 0.263
  Chirality :  0.041   0.158   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.860  89.019   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 :  1.74 %
    Allowed  :  6.74 %
    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:  2.79 (0.27), residues: 1014
  helix:  2.14 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop :  1.08 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 418 
 HIS   0.003   0.001   HIS A 109 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.015   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
  129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5485 (OUTLIER) cc_final: 0.3956 (mmt)
REVERT: A  223 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7329 (tp30)
REVERT: A  478 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7839 (t80)
REVERT: B    1 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.4698 (mmt)
REVERT: B  223 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7354 (tp30)
REVERT: B  272 VAL cc_start: 0.9074 (m) cc_final: 0.8803 (p)
REVERT: B  330 GLU cc_start: 0.7858 (tp30) cc_final: 0.7321 (tm-30)
REVERT: B  404 ASP cc_start: 0.7775 (t0) cc_final: 0.7412 (t70)
REVERT: B  525 VAL cc_start: 0.9130 (m) cc_final: 0.8909 (p)
  outliers start: 15
  outliers final: 5
  residues processed: 118
  average time/residue: 0.9098
  time to fit residues: 117.0354
Evaluate side-chains
  118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 84 optimal weight:    9.9990
   chunk 30 optimal weight:    0.4980
   chunk 67 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.107059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.074376 restraints weight = 19303.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.27
r_work: 0.2728 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
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 = 0.42   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 = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1538

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= 0.179
  Angle     :  0.515   5.427  11964  Z= 0.254
  Chirality :  0.040   0.159   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.886  89.597   1852
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  :  7.21 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.85 (0.27), residues: 1014
  helix:  2.15 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.18 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   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 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
  135 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7358 (tp30)
REVERT: A  225 GLU cc_start: 0.8001 (tp30) cc_final: 0.7797 (tp30)
REVERT: A  478 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7792 (t80)
REVERT: B    1 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.4715 (mmt)
REVERT: B  223 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7305 (tp30)
REVERT: B  272 VAL cc_start: 0.8981 (m) cc_final: 0.8721 (p)
REVERT: B  330 GLU cc_start: 0.7841 (tp30) cc_final: 0.7321 (tm-30)
REVERT: B  404 ASP cc_start: 0.7784 (t0) cc_final: 0.7487 (t0)
  outliers start: 18
  outliers final: 8
  residues processed: 122
  average time/residue: 0.9569
  time to fit residues: 126.7932
Evaluate side-chains
  121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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    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
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 92 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3384 r_free = 0.3384 target = 0.105004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.072010 restraints weight = 20495.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.31
r_work: 0.2673 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2555 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8798  Z= 0.269
  Angle     :  0.566   6.166  11964  Z= 0.279
  Chirality :  0.043   0.171   1390
  Planarity :  0.005   0.041   1396
  Dihedral  : 11.221  89.277   1852
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  7.56 %
    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:  2.68 (0.27), residues: 1014
  helix:  2.07 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop :  0.99 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 418 
 HIS   0.008   0.002   HIS B 109 
 PHE   0.017   0.002   PHE A 477 
 TYR   0.017   0.001   TYR B 226 
 ARG   0.004   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
  127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7406 (tp30)
REVERT: A  478 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7974 (t80)
REVERT: B    1 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.4787 (mmt)
REVERT: B  223 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7359 (tp30)
REVERT: B  272 VAL cc_start: 0.9190 (m) cc_final: 0.8880 (p)
REVERT: B  330 GLU cc_start: 0.8126 (tp30) cc_final: 0.7682 (tm-30)
REVERT: B  404 ASP cc_start: 0.7902 (t0) cc_final: 0.7579 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 117
  average time/residue: 0.9917
  time to fit residues: 126.2225
Evaluate side-chains
  121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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    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  291 LEU
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 19 optimal weight:    0.0270
   chunk 57 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 63 optimal weight:    0.2980
   chunk 48 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 67 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.4038

-------------------------------------------------------------------------------
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 = 0.3422 r_free = 0.3422 target = 0.107666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.076667 restraints weight = 13929.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 1.94
r_work: 0.2845 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    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 = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1717

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= 0.151
  Angle     :  0.510   5.989  11964  Z= 0.249
  Chirality :  0.040   0.173   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.930  89.057   1852
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  8.49 %
    Favored  : 90.47 %
  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:  2.91 (0.27), residues: 1014
  helix:  2.21 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.13 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 418 
 HIS   0.006   0.001   HIS B 109 
 PHE   0.014   0.001   PHE A 352 
 TYR   0.018   0.001   TYR A 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
  124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.865 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7447 (tp30)
REVERT: A  228 ARG cc_start: 0.8256 (ttm110) cc_final: 0.8029 (mtm-85)
REVERT: B    1 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.4714 (mmt)
REVERT: B  272 VAL cc_start: 0.9130 (m) cc_final: 0.8852 (p)
REVERT: B  330 GLU cc_start: 0.8013 (tp30) cc_final: 0.7461 (mm-30)
REVERT: B  404 ASP cc_start: 0.7948 (t0) cc_final: 0.7591 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 120
  average time/residue: 0.9445
  time to fit residues: 123.4925
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  : 0.950 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.106536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.074838 restraints weight = 15492.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.04
r_work: 0.2730 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2615 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    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 = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.1785

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= 0.193
  Angle     :  0.539   7.224  11964  Z= 0.262
  Chirality :  0.041   0.196   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.973  89.163   1852
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  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 (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:  2.88 (0.27), residues: 1014
  helix:  2.19 (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   0.021   0.002   TRP B 418 
 HIS   0.005   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 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
  119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 1.049 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5494 (OUTLIER) cc_final: 0.3932 (mmm)
REVERT: A  223 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7419 (tp30)
REVERT: A  478 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7950 (t80)
REVERT: B    1 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.4717 (mmt)
REVERT: B  150 MET cc_start: 0.9348 (tmm) cc_final: 0.9066 (ttt)
REVERT: B  272 VAL cc_start: 0.9156 (m) cc_final: 0.8864 (p)
REVERT: B  330 GLU cc_start: 0.8044 (tp30) cc_final: 0.7478 (mm-30)
REVERT: B  404 ASP cc_start: 0.7942 (t0) cc_final: 0.7576 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 115
  average time/residue: 0.9460
  time to fit residues: 118.5923
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  : 0.934 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0770
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.106989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.074839 restraints weight = 16727.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.14
r_work: 0.2730 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2614 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2614
-------------------------------------------------------------------------------
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 = 0.43   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 = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.1816

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= 0.181
  Angle     :  0.530   6.574  11964  Z= 0.258
  Chirality :  0.041   0.180   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.941  88.774   1852
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.19 %
    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 (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:  2.88 (0.27), residues: 1014
  helix:  2.19 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.09 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 418 
 HIS   0.004   0.001   HIS B 109 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.019   0.001   TYR B 226 
 ARG   0.002   0.000   ARG A 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
  125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5492 (OUTLIER) cc_final: 0.3931 (mmm)
REVERT: A  478 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7917 (t80)
REVERT: B    1 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.4651 (mmt)
REVERT: B  150 MET cc_start: 0.9333 (tmm) cc_final: 0.9074 (ttt)
REVERT: B  272 VAL cc_start: 0.9116 (m) cc_final: 0.8812 (p)
REVERT: B  330 GLU cc_start: 0.8001 (tp30) cc_final: 0.7444 (mm-30)
REVERT: B  404 ASP cc_start: 0.7920 (t0) cc_final: 0.7522 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 118
  average time/residue: 0.8949
  time to fit residues: 115.2799
Evaluate side-chains
  118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0470
   chunk 68 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   chunk 96 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0670
   overall best weight:    0.4216

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.108412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.076879 restraints weight = 15698.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.06
r_work: 0.2848 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    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 = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.1824

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= 0.153
  Angle     :  0.520   6.975  11964  Z= 0.252
  Chirality :  0.040   0.184   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.775  87.656   1852
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.88 %
    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 (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:  2.25 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.09 (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   0.019   0.001   TYR B 226 
 ARG   0.001   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
  115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.3958 (mmm)
REVERT: B    1 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.4619 (mmt)
REVERT: B  150 MET cc_start: 0.9343 (tmm) cc_final: 0.9058 (ttt)
REVERT: B  272 VAL cc_start: 0.9132 (m) cc_final: 0.8845 (p)
REVERT: B  330 GLU cc_start: 0.8003 (tp30) cc_final: 0.7475 (mm-30)
REVERT: B  404 ASP cc_start: 0.7976 (t0) cc_final: 0.7596 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 112
  average time/residue: 0.8922
  time to fit residues: 109.3492
Evaluate side-chains
  113 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
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  527 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 48 optimal weight:    0.8980
   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:    0.9990
   chunk 80 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.106922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.075095 restraints weight = 15663.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.06
r_work: 0.2735 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2619 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8938
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8798  Z= 0.195
  Angle     :  0.544   6.863  11964  Z= 0.265
  Chirality :  0.041   0.181   1390
  Planarity :  0.005   0.039   1396
  Dihedral  : 10.866  88.470   1852
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 10.12 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.27), residues: 1014
  helix:  2.19 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.09 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 418 
 HIS   0.004   0.001   HIS B 109 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.019   0.001   TYR B 226 
 ARG   0.001   0.000   ARG A 228 

********************** 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
  113 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.3926 (mmm)
REVERT: B    1 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.4626 (mmt)
REVERT: B  150 MET cc_start: 0.9364 (tmm) cc_final: 0.9116 (ttt)
REVERT: B  225 GLU cc_start: 0.8296 (tp30) cc_final: 0.7985 (tp30)
REVERT: B  272 VAL cc_start: 0.9172 (m) cc_final: 0.8872 (p)
REVERT: B  330 GLU cc_start: 0.8064 (tp30) cc_final: 0.7574 (mm-30)
REVERT: B  404 ASP cc_start: 0.7982 (t0) cc_final: 0.7594 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 110
  average time/residue: 0.9216
  time to fit residues: 110.4613
Evaluate side-chains
  113 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 100 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0970
   chunk 63 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.4916

-------------------------------------------------------------------------------
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 = 0.108090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.077340 restraints weight = 12711.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.87
r_work: 0.2858 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    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 = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2700
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.1870

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= 0.159
  Angle     :  0.525   6.988  11964  Z= 0.255
  Chirality :  0.040   0.181   1390
  Planarity :  0.005   0.040   1396
  Dihedral  : 10.736  87.795   1852
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 10.23 %
    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:  2.23 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.09 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   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   0.001   0.000   ARG B 227 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8465.28 seconds
wall clock time: 149 minutes 36.51 seconds (8976.51 seconds total)