Starting phenix.real_space_refine
on Mon May 12 02:50:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b4i_15849/05_2025/8b4i_15849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b4i_15849/05_2025/8b4i_15849.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b4i_15849/05_2025/8b4i_15849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b4i_15849/05_2025/8b4i_15849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b4i_15849/05_2025/8b4i_15849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b4i_15849/05_2025/8b4i_15849.cif"
  }
  resolution = 3.32
  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=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      24      5.16       5
     C    5322      2.51       5
     N    1347      2.21       5
     O    1548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8242
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 2515
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 325, 2507
          Classifications: {'peptide': 325}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315}
      Conformer: "B"
        Number of residues, atoms: 325, 2507
          Classifications: {'peptide': 325}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315}
          bond proxies already assigned to first conformer: 2547
    Chain: "B"
      Number of atoms: 2515
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 325, 2507
          Classifications: {'peptide': 325}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315}
      Conformer: "B"
        Number of residues, atoms: 325, 2507
          Classifications: {'peptide': 325}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315}
          bond proxies already assigned to first conformer: 2547
    Chain: "C"
      Number of atoms: 450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 450
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 58}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "D"
      Number of atoms: 450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 450
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 58}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "E"
      Number of atoms: 290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 290
          Classifications: {'peptide': 38}
          Link IDs: {'PTRANS': 1, 'TRANS': 36}
    Chain: "F"
      Number of atoms: 290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 290
          Classifications: {'peptide': 38}
          Link IDs: {'PTRANS': 1, 'TRANS': 36}
    Chain: "G"
      Number of atoms: 289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 289
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
    Chain: "H"
      Number of atoms: 289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 289
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
    Chain: "I"
      Number of atoms: 408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 408
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
    Chain: "J"
      Number of atoms: 408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 408
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'DU0': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 79
          Unusual residues: {'DU0': 1, 'PLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 111
          Unusual residues: {'DU0': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 111
          Unusual residues: {'DU0': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 8.81, per 1000 atoms: 1.07
  Number of scatterers: 8242
  At special positions: 0
  Unit cell: (123.876, 106.299, 99.603, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P       1     15.00
     O    1548      8.00
     N    1347      7.00
     C    5322      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: 2.53
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1900

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      38.9% alpha, 35.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 34
      removed outlier: 3.832A  pdb=" N   PHE A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 47
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 334 through 343
      removed outlier: 4.345A  pdb=" N   GLU A 340 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   GLY A 341 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 34
    Processing helix  chain 'B' and resid 43 through 47
    Processing helix  chain 'B' and resid 48 through 53
    Processing helix  chain 'B' and resid 334 through 343
      removed outlier: 4.344A  pdb=" N   GLU B 340 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   GLY B 341 " --> pdb=" O   GLU B 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 122
      Proline residue:  C  99  - end of helix
    Processing helix  chain 'D' and resid 64 through 122
      Proline residue:  D  99  - end of helix
    Processing helix  chain 'E' and resid 11 through 46
      Proline residue:  E  40  - end of helix
    Processing helix  chain 'F' and resid 11 through 46
      Proline residue:  F  40  - end of helix
    Processing helix  chain 'G' and resid 23 through 28
      removed outlier: 3.978A  pdb=" N   THR G  28 " --> pdb=" O   TYR G  24 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 51
    Processing helix  chain 'G' and resid 52 through 58
    Processing helix  chain 'H' and resid 23 through 28
      removed outlier: 4.072A  pdb=" N   THR H  28 " --> pdb=" O   TYR H  24 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 31 through 50
      removed outlier: 4.727A  pdb=" N   VAL H  35 " --> pdb=" O   GLU H  31 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 51 through 58
    Processing helix  chain 'I' and resid 5 through 39
      removed outlier: 3.655A  pdb=" N   ARG I  11 " --> pdb=" O   GLU I   7 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   LEU I  28 " --> pdb=" O   HIS I  24 " (cutoff:3.500A)
      Proline residue:  I  29  - end of helix
    Processing helix  chain 'I' and resid 44 through 49
      removed outlier: 3.775A  pdb=" N   LEU I  48 " --> pdb=" O   SER I  44 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   LEU I  49 " --> pdb=" O   ILE I  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 44 through 49'
    Processing helix  chain 'J' and resid 5 through 39
      removed outlier: 3.552A  pdb=" N   ARG J  11 " --> pdb=" O   GLU J   7 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LEU J  28 " --> pdb=" O   HIS J  24 " (cutoff:3.500A)
      Proline residue:  J  29  - end of helix
    Processing helix  chain 'J' and resid 46 through 50
      removed outlier: 3.922A  pdb=" N   LEU J  49 " --> pdb=" O   ILE J  46 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 74
      removed outlier: 6.345A  pdb=" N   PHE A  79 " --> pdb=" O   PHE A  73 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE A 135 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A 147 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ALA A 144 " --> pdb=" O   ASN A 163 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 159 " --> pdb=" O   HIS A 148 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   THR A 172 " --> pdb=" O   PRO A 164 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   LEU A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA A 207 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   VAL A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   SER A 280 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLN A 319 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   GLY A  64 " --> pdb=" O   MET A 324 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   VAL A 326 " --> pdb=" O   GLY A  64 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ARG A  66 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   ILE A 328 " --> pdb=" O   ARG A  66 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASP A  68 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   ALA A 330 " --> pdb=" O   ASP A  68 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   THR A  70 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 74
      removed outlier: 6.295A  pdb=" N   PHE B  79 " --> pdb=" O   PHE B  73 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   PHE B 135 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ALA B 144 " --> pdb=" O   ASN B 163 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   THR B 172 " --> pdb=" O   PRO B 164 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   LEU B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA B 207 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN B 319 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   GLY B  64 " --> pdb=" O   MET B 324 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   VAL B 326 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ARG B  66 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 8.192A  pdb=" N   ILE B 328 " --> pdb=" O   ARG B  66 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   ASP B  68 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   ALA B 330 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   THR B  70 " --> pdb=" O   ALA B 330 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1600 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: 2.45

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1384
        1.32 -     1.44: 2230
        1.44 -     1.56: 4773
        1.56 -     1.68: 2
        1.68 -     1.80: 46
  Bond restraints: 8435
  Sorted by residual:
  bond pdb=" C22 DU0 B 402 "
       pdb=" O23 DU0 B 402 "
    ideal  model  delta    sigma   weight residual
    1.412  1.439 -0.027 2.00e-02 2.50e+03 1.77e+00
  bond pdb=" C22 DU0 A 401 "
       pdb=" O23 DU0 A 401 "
    ideal  model  delta    sigma   weight residual
    1.412  1.437 -0.025 2.00e-02 2.50e+03 1.56e+00
  bond pdb=" C09 DU0 C 201 "
       pdb=" O16 DU0 C 201 "
    ideal  model  delta    sigma   weight residual
    1.404  1.429 -0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C09 DU0 B 402 "
       pdb=" O16 DU0 B 402 "
    ideal  model  delta    sigma   weight residual
    1.404  1.428 -0.024 2.00e-02 2.50e+03 1.48e+00
  bond pdb=" C24 DU0 C 201 "
       pdb=" O23 DU0 C 201 "
    ideal  model  delta    sigma   weight residual
    1.409  1.433 -0.024 2.00e-02 2.50e+03 1.48e+00
  ... (remaining 8430 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 11083
        1.40 -     2.80: 318
        2.80 -     4.21: 58
        4.21 -     5.61: 24
        5.61 -     7.01: 4
  Bond angle restraints: 11487
  Sorted by residual:
  angle pdb=" N   SER A 288 "
        pdb=" CA  SER A 288 "
        pdb=" C   SER A 288 "
      ideal   model   delta    sigma   weight residual
     113.28  110.33    2.95 1.22e+00 6.72e-01 5.84e+00
  angle pdb=" N   SER B 288 "
        pdb=" CA  SER B 288 "
        pdb=" C   SER B 288 "
      ideal   model   delta    sigma   weight residual
     113.28  110.35    2.93 1.22e+00 6.72e-01 5.76e+00
  angle pdb=" O10 DU0 C 201 "
        pdb=" C09 DU0 C 201 "
        pdb=" O16 DU0 C 201 "
      ideal   model   delta    sigma   weight residual
     110.24  103.23    7.01 3.00e+00 1.11e-01 5.46e+00
  angle pdb=" O10 DU0 D 201 "
        pdb=" C09 DU0 D 201 "
        pdb=" O16 DU0 D 201 "
      ideal   model   delta    sigma   weight residual
     110.24  103.50    6.74 3.00e+00 1.11e-01 5.05e+00
  angle pdb=" O10 DU0 C 202 "
        pdb=" C09 DU0 C 202 "
        pdb=" O16 DU0 C 202 "
      ideal   model   delta    sigma   weight residual
     110.24  103.85    6.39 3.00e+00 1.11e-01 4.53e+00
  ... (remaining 11482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.75: 5349
       25.75 -    51.50: 108
       51.50 -    77.25: 43
       77.25 -   103.00: 36
      103.00 -   128.74: 13
  Dihedral angle restraints: 5549
    sinusoidal: 2597
      harmonic: 2952
  Sorted by residual:
  dihedral pdb=" C76 DU0 D 201 "
           pdb=" C22 DU0 D 201 "
           pdb=" C75 DU0 D 201 "
           pdb=" O23 DU0 D 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -179.09  -50.35 -128.74     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" C76 DU0 C 201 "
           pdb=" C22 DU0 C 201 "
           pdb=" C75 DU0 C 201 "
           pdb=" O23 DU0 C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -179.09  -50.59 -128.50     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" C21 DU0 D 201 "
           pdb=" C22 DU0 D 201 "
           pdb=" C75 DU0 D 201 "
           pdb=" C76 DU0 D 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      56.15  -68.09  124.24     1      3.00e+01 1.11e-03 1.67e+01
  ... (remaining 5546 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 983
       0.039 -    0.077: 256
       0.077 -    0.116: 55
       0.116 -    0.154: 15
       0.154 -    0.193: 12
  Chirality restraints: 1321
  Sorted by residual:
  chirality pdb=" C07 DU0 C 203 "
            pdb=" C06 DU0 C 203 "
            pdb=" C08 DU0 C 203 "
            pdb=" C09 DU0 C 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.76   -0.19 2.00e-01 2.50e+01 9.27e-01
  chirality pdb=" C07 DU0 D 203 "
            pdb=" C06 DU0 D 203 "
            pdb=" C08 DU0 D 203 "
            pdb=" C09 DU0 D 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.75   -0.19 2.00e-01 2.50e+01 8.78e-01
  chirality pdb=" C07 DU0 A 401 "
            pdb=" C06 DU0 A 401 "
            pdb=" C08 DU0 A 401 "
            pdb=" C09 DU0 A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.75   -0.19 2.00e-01 2.50e+01 8.66e-01
  ... (remaining 1318 not shown)

  Planarity restraints: 1412
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU I  28 "    0.019 5.00e-02 4.00e+02   2.93e-02 1.37e+00
        pdb=" N   PRO I  29 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO I  29 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO I  29 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL J  40 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO J  41 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO J  41 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO J  41 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  40 "    0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO B  41 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B  41 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  41 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1409 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1013
        2.74 -     3.28: 8101
        3.28 -     3.82: 12385
        3.82 -     4.36: 14931
        4.36 -     4.90: 27112
  Nonbonded interactions: 63542
  Sorted by model distance:
  nonbonded pdb=" O   GLY I  35 "
            pdb=" OG  SER I  39 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O23 DU0 D 202 "
            pdb=" O52 DU0 D 202 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NZ  LYS A 132 "
            pdb=" OE1 GLU A 149 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" N   GLN A 228 "
            pdb=" OE1 GLN A 228 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   GLY J  35 "
            pdb=" OG  SER J  39 "
     model   vdw
     2.271 3.040
  ... (remaining 63537 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 25 through 308 or resid 310 through 349))
  selection = (chain 'B' and (resid 25 through 308 or resid 310 through 349))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}

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=0.00 max=1.00 mean=0.99
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:             4.530
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.410
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8435  Z= 0.210
  Angle     :  0.618   7.008  11487  Z= 0.310
  Chirality :  0.041   0.193   1321
  Planarity :  0.003   0.029   1412
  Dihedral  : 16.412 128.745   3649
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.68 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.59 (0.28), residues: 1008
  helix:  2.10 (0.27), residues: 352
  sheet: -0.41 (0.26), residues: 398
  loop : -0.48 (0.46), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.001   HIS I  24 
 PHE   0.008   0.001   PHE A 271 
 TYR   0.007   0.001   TYR H  24 
 ARG   0.002   0.000   ARG H  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18956 (  560)
  hydrogen bonds       : angle       7.82458 ( 1600)
  covalent geometry    : bond        0.00440 ( 8435)
  covalent geometry    : angle       0.61829 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 225
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8119 (tm-30)
REVERT: A   49 ARG cc_start: 0.8428 (ptt90) cc_final: 0.8227 (ptt-90)
REVERT: A  143 MET cc_start: 0.8488 (ttp) cc_final: 0.7991 (tmm)
REVERT: A  215 LYS cc_start: 0.8861 (tttt) cc_final: 0.8638 (tttm)
REVERT: A  321 LYS cc_start: 0.8521 (mttt) cc_final: 0.8212 (mtmt)
REVERT: A  329 GLU cc_start: 0.8222 (tt0) cc_final: 0.7891 (mt-10)
REVERT: B  215 LYS cc_start: 0.8960 (tttt) cc_final: 0.8702 (tttp)
REVERT: B  291 LYS cc_start: 0.8877 (tttt) cc_final: 0.8501 (tttp)
REVERT: B  312 ASP cc_start: 0.7717 (t0) cc_final: 0.7177 (t0)
REVERT: B  321 LYS cc_start: 0.8675 (mttt) cc_final: 0.8365 (mtpp)
REVERT: B  324 MET cc_start: 0.8374 (mmm) cc_final: 0.8079 (tpp)
REVERT: B  329 GLU cc_start: 0.8341 (tt0) cc_final: 0.7194 (tm-30)
REVERT: D  115 GLN cc_start: 0.8667 (tp40) cc_final: 0.8434 (tp40)
REVERT: E   13 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8392 (pm20)
REVERT: E   27 GLN cc_start: 0.8613 (mt0) cc_final: 0.8277 (mt0)
REVERT: F   13 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8269 (pm20)
REVERT: H   56 MET cc_start: 0.8913 (ttp) cc_final: 0.8663 (ttt)
REVERT: J   36 TYR cc_start: 0.8481 (t80) cc_final: 0.8259 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 226
  average time/residue: 0.2319
  time to fit residues: 68.2479
Evaluate side-chains
  185 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    0.1980
   chunk 57 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
A 150 HIS
A 163 ASN
B  84 GLN
B 145 GLN
B 150 HIS
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  24 HIS
J  24 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.122915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.081505 restraints weight = 40713.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 5.39
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       94 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       94 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8435  Z= 0.179
  Angle     :  0.706   7.592  11487  Z= 0.345
  Chirality :  0.043   0.188   1321
  Planarity :  0.004   0.038   1412
  Dihedral  : 12.362 102.084   1887
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.07 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.00 (0.28), residues: 1008
  helix:  2.56 (0.26), residues: 358
  sheet: -0.23 (0.26), residues: 402
  loop : -0.45 (0.45), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 236 
 HIS   0.002   0.001   HIS B 150 
 PHE   0.015   0.001   PHE A 135 
 TYR   0.019   0.002   TYR I  33 
 ARG   0.009   0.001   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (  560)
  hydrogen bonds       : angle       5.09780 ( 1600)
  covalent geometry    : bond        0.00400 ( 8435)
  covalent geometry    : angle       0.70607 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 173
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8080 (tm-30)
REVERT: A   49 ARG cc_start: 0.8335 (ptt90) cc_final: 0.7970 (ptt-90)
REVERT: A  215 LYS cc_start: 0.8834 (tttt) cc_final: 0.8440 (tttp)
REVERT: A  321 LYS cc_start: 0.8458 (mttt) cc_final: 0.8136 (mtmm)
REVERT: A  329 GLU cc_start: 0.8103 (tt0) cc_final: 0.7777 (mt-10)
REVERT: B   71 LYS cc_start: 0.8316 (tttp) cc_final: 0.7861 (ttmm)
REVERT: B  143 MET cc_start: 0.8266 (ttt) cc_final: 0.7827 (tmm)
REVERT: B  215 LYS cc_start: 0.8928 (tttt) cc_final: 0.8691 (tttm)
REVERT: B  321 LYS cc_start: 0.8576 (mttt) cc_final: 0.8234 (mtpp)
REVERT: B  329 GLU cc_start: 0.8082 (tt0) cc_final: 0.7244 (tm-30)
REVERT: E   27 GLN cc_start: 0.8317 (mt0) cc_final: 0.7689 (mp10)
REVERT: F   23 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8136 (t)
REVERT: F   27 GLN cc_start: 0.8283 (mt0) cc_final: 0.7726 (mp10)
REVERT: H   56 MET cc_start: 0.8877 (ttp) cc_final: 0.8639 (ttt)
REVERT: I    6 GLU cc_start: 0.8503 (pm20) cc_final: 0.7494 (pm20)
REVERT: I    7 GLU cc_start: 0.8832 (tt0) cc_final: 0.8617 (pm20)
REVERT: J    6 GLU cc_start: 0.8161 (pm20) cc_final: 0.7071 (pm20)
REVERT: J    7 GLU cc_start: 0.8928 (tt0) cc_final: 0.8723 (pm20)
  outliers start: 12
  outliers final: 5
  residues processed: 180
  average time/residue: 0.2352
  time to fit residues: 56.1781
Evaluate side-chains
  164 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 158
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain F residue   23 THR
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain H residue   26 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0870
   chunk 46 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0270
   chunk 31 optimal weight:    8.9990
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.5216

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.126321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.082965 restraints weight = 37208.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 5.52
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       94 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.3089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8435  Z= 0.133
  Angle     :  0.658   8.382  11487  Z= 0.318
  Chirality :  0.041   0.175   1321
  Planarity :  0.004   0.042   1412
  Dihedral  : 11.043  92.133   1887
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.02 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.22 (0.28), residues: 1008
  helix:  2.82 (0.26), residues: 350
  sheet: -0.10 (0.26), residues: 402
  loop : -0.40 (0.44), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 195 
 HIS   0.001   0.000   HIS A 315 
 PHE   0.012   0.001   PHE A 135 
 TYR   0.019   0.001   TYR C  68 
 ARG   0.006   0.001   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  560)
  hydrogen bonds       : angle       4.63688 ( 1600)
  covalent geometry    : bond        0.00292 ( 8435)
  covalent geometry    : angle       0.65849 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 168
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: A   49 ARG cc_start: 0.8272 (ptt90) cc_final: 0.7893 (ptt-90)
REVERT: A  215 LYS cc_start: 0.8849 (tttt) cc_final: 0.8561 (tttm)
REVERT: A  321 LYS cc_start: 0.8450 (mttt) cc_final: 0.8096 (mtpp)
REVERT: A  329 GLU cc_start: 0.7996 (tt0) cc_final: 0.6987 (tm-30)
REVERT: B  143 MET cc_start: 0.8360 (ttt) cc_final: 0.7921 (tmm)
REVERT: B  215 LYS cc_start: 0.8932 (tttt) cc_final: 0.8676 (tttp)
REVERT: B  321 LYS cc_start: 0.8543 (mttt) cc_final: 0.8178 (mtpp)
REVERT: B  329 GLU cc_start: 0.8037 (tt0) cc_final: 0.7217 (tm-30)
REVERT: E   13 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8259 (pm20)
REVERT: E   23 THR cc_start: 0.8655 (t) cc_final: 0.8104 (t)
REVERT: E   27 GLN cc_start: 0.8280 (mt0) cc_final: 0.7723 (mp10)
REVERT: F   23 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8164 (t)
REVERT: F   27 GLN cc_start: 0.8248 (mt0) cc_final: 0.7729 (mp10)
REVERT: H   56 MET cc_start: 0.8913 (ttp) cc_final: 0.8683 (ttt)
REVERT: I    6 GLU cc_start: 0.8510 (pm20) cc_final: 0.7807 (pm20)
REVERT: I    7 GLU cc_start: 0.8813 (tt0) cc_final: 0.8609 (pm20)
REVERT: I   42 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8300 (mmm-85)
REVERT: J    6 GLU cc_start: 0.8116 (pm20) cc_final: 0.7504 (pm20)
REVERT: J    7 GLU cc_start: 0.8905 (tt0) cc_final: 0.8704 (pm20)
REVERT: J   36 TYR cc_start: 0.7899 (t80) cc_final: 0.7634 (t80)
REVERT: J   42 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8001 (mmm-85)
  outliers start: 13
  outliers final: 4
  residues processed: 172
  average time/residue: 0.2058
  time to fit residues: 48.7690
Evaluate side-chains
  161 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 156
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain F residue   23 THR
Chi-restraints excluded: chain F residue   43 ILE
Chi-restraints excluded: chain H residue   51 SER
Chi-restraints excluded: chain I residue   18 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0370
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.1260

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.124703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.083158 restraints weight = 38455.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 5.33
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8435  Z= 0.182
  Angle     :  0.653   7.041  11487  Z= 0.319
  Chirality :  0.041   0.141   1321
  Planarity :  0.004   0.043   1412
  Dihedral  : 10.291  92.200   1887
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.14 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.20 (0.28), residues: 1008
  helix:  2.82 (0.26), residues: 350
  sheet: -0.15 (0.26), residues: 412
  loop : -0.35 (0.44), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 236 
 HIS   0.002   0.000   HIS J  24 
 PHE   0.012   0.001   PHE A 135 
 TYR   0.019   0.002   TYR D  68 
 ARG   0.010   0.001   ARG C 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03081 (  560)
  hydrogen bonds       : angle       4.50141 ( 1600)
  covalent geometry    : bond        0.00419 ( 8435)
  covalent geometry    : angle       0.65344 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8075 (tm-30)
REVERT: A  215 LYS cc_start: 0.8874 (tttt) cc_final: 0.8539 (tttm)
REVERT: A  321 LYS cc_start: 0.8474 (mttt) cc_final: 0.8133 (mtpp)
REVERT: A  329 GLU cc_start: 0.8104 (tt0) cc_final: 0.7056 (tm-30)
REVERT: B  215 LYS cc_start: 0.8934 (tttt) cc_final: 0.8662 (tttm)
REVERT: B  321 LYS cc_start: 0.8497 (mttt) cc_final: 0.8145 (mtpp)
REVERT: B  329 GLU cc_start: 0.8072 (tt0) cc_final: 0.7219 (tm-30)
REVERT: C  115 GLN cc_start: 0.8842 (tp40) cc_final: 0.8587 (tp40)
REVERT: E   23 THR cc_start: 0.8707 (t) cc_final: 0.8156 (t)
REVERT: E   27 GLN cc_start: 0.8346 (mt0) cc_final: 0.7778 (mp10)
REVERT: F   23 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8178 (t)
REVERT: F   27 GLN cc_start: 0.8311 (mt0) cc_final: 0.7768 (mp10)
REVERT: H   56 MET cc_start: 0.8901 (ttp) cc_final: 0.8659 (ttt)
REVERT: I    6 GLU cc_start: 0.8396 (pm20) cc_final: 0.7805 (pm20)
REVERT: I   42 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8097 (mmm-85)
REVERT: J    6 GLU cc_start: 0.8145 (pm20) cc_final: 0.7554 (pm20)
REVERT: J   33 TYR cc_start: 0.8386 (t80) cc_final: 0.8183 (t80)
REVERT: J   36 TYR cc_start: 0.7938 (t80) cc_final: 0.7706 (t80)
REVERT: J   42 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.8088 (mmm-85)
  outliers start: 16
  outliers final: 10
  residues processed: 167
  average time/residue: 0.2156
  time to fit residues: 49.4886
Evaluate side-chains
  169 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 158
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain E residue   43 ILE
Chi-restraints excluded: chain F residue   23 THR
Chi-restraints excluded: chain F residue   43 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain H residue   51 SER
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain J residue   18 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0970
   chunk 65 optimal weight:    0.6980
   chunk 82 optimal weight:    9.9990
   chunk 68 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.125527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.082087 restraints weight = 35171.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 5.44
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8435  Z= 0.139
  Angle     :  0.633   7.408  11487  Z= 0.310
  Chirality :  0.040   0.185   1321
  Planarity :  0.004   0.040   1412
  Dihedral  : 10.117 102.105   1887
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 13.14 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.22 (0.28), residues: 1008
  helix:  2.77 (0.26), residues: 350
  sheet: -0.13 (0.25), residues: 416
  loop : -0.23 (0.45), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 236 
 HIS   0.002   0.000   HIS A  83 
 PHE   0.011   0.001   PHE A 135 
 TYR   0.019   0.001   TYR D  68 
 ARG   0.012   0.001   ARG D 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02897 (  560)
  hydrogen bonds       : angle       4.40247 ( 1600)
  covalent geometry    : bond        0.00316 ( 8435)
  covalent geometry    : angle       0.63322 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8051 (tm-30)
REVERT: A   84 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7678 (tt0)
REVERT: A  215 LYS cc_start: 0.8861 (tttt) cc_final: 0.8566 (tttm)
REVERT: A  321 LYS cc_start: 0.8462 (mttt) cc_final: 0.8118 (mtpp)
REVERT: A  329 GLU cc_start: 0.8089 (tt0) cc_final: 0.7750 (mt-10)
REVERT: B   45 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: B  215 LYS cc_start: 0.8934 (tttt) cc_final: 0.8659 (tttm)
REVERT: B  321 LYS cc_start: 0.8509 (mttt) cc_final: 0.8163 (mtpp)
REVERT: B  329 GLU cc_start: 0.8051 (tt0) cc_final: 0.7205 (tm-30)
REVERT: C  115 GLN cc_start: 0.8843 (tp40) cc_final: 0.8640 (tp40)
REVERT: E   23 THR cc_start: 0.8686 (t) cc_final: 0.8158 (t)
REVERT: E   27 GLN cc_start: 0.8317 (mt0) cc_final: 0.7771 (mp10)
REVERT: F   23 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8172 (t)
REVERT: F   27 GLN cc_start: 0.8295 (mt0) cc_final: 0.7765 (mp10)
REVERT: H   56 MET cc_start: 0.8909 (ttp) cc_final: 0.8669 (ttt)
REVERT: I   42 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8137 (mmm-85)
REVERT: J   36 TYR cc_start: 0.7737 (t80) cc_final: 0.7478 (t80)
REVERT: J   42 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8115 (mmm-85)
  outliers start: 11
  outliers final: 8
  residues processed: 164
  average time/residue: 0.2202
  time to fit residues: 49.5280
Evaluate side-chains
  169 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  265 LYS
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain E residue   43 ILE
Chi-restraints excluded: chain F residue   23 THR
Chi-restraints excluded: chain F residue   43 ILE
Chi-restraints excluded: chain G residue   56 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.079987 restraints weight = 44651.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 5.81
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3057
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.3057
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8435  Z= 0.175
  Angle     :  0.633   7.271  11487  Z= 0.313
  Chirality :  0.040   0.143   1321
  Planarity :  0.004   0.035   1412
  Dihedral  : 10.040 106.397   1887
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.50 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.21 (0.28), residues: 1008
  helix:  2.75 (0.26), residues: 350
  sheet: -0.13 (0.25), residues: 416
  loop : -0.26 (0.45), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 236 
 HIS   0.001   0.001   HIS A  83 
 PHE   0.012   0.001   PHE A 135 
 TYR   0.018   0.001   TYR D  68 
 ARG   0.005   0.000   ARG J  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02880 (  560)
  hydrogen bonds       : angle       4.37301 ( 1600)
  covalent geometry    : bond        0.00404 ( 8435)
  covalent geometry    : angle       0.63307 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 157
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: A   84 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7810 (tt0)
REVERT: A  215 LYS cc_start: 0.8871 (tttt) cc_final: 0.8573 (tttm)
REVERT: A  321 LYS cc_start: 0.8462 (mttt) cc_final: 0.8117 (mtpp)
REVERT: A  329 GLU cc_start: 0.8131 (tt0) cc_final: 0.7068 (tm-30)
REVERT: B   45 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8134 (tm-30)
REVERT: B  215 LYS cc_start: 0.8925 (tttt) cc_final: 0.8658 (tttm)
REVERT: B  321 LYS cc_start: 0.8504 (mttt) cc_final: 0.8145 (mtpp)
REVERT: B  329 GLU cc_start: 0.8069 (tt0) cc_final: 0.7217 (tm-30)
REVERT: C  115 GLN cc_start: 0.8862 (tp40) cc_final: 0.8284 (tp40)
REVERT: C  119 MET cc_start: 0.8518 (mmp) cc_final: 0.8070 (mmp)
REVERT: E   23 THR cc_start: 0.8701 (t) cc_final: 0.8177 (t)
REVERT: E   27 GLN cc_start: 0.8342 (mt0) cc_final: 0.7797 (mp10)
REVERT: F   27 GLN cc_start: 0.8327 (mt0) cc_final: 0.7791 (mp10)
REVERT: H   56 MET cc_start: 0.8907 (ttp) cc_final: 0.8682 (ttt)
REVERT: I   42 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8216 (mmm-85)
REVERT: J   42 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8085 (mmm-85)
  outliers start: 12
  outliers final: 8
  residues processed: 163
  average time/residue: 0.1984
  time to fit residues: 44.5155
Evaluate side-chains
  163 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  265 LYS
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain E residue   43 ILE
Chi-restraints excluded: chain F residue   43 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain I residue   19 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 70 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.125155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.081278 restraints weight = 43633.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 5.81
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8435  Z= 0.150
  Angle     :  0.627   7.408  11487  Z= 0.309
  Chirality :  0.040   0.140   1321
  Planarity :  0.004   0.034   1412
  Dihedral  :  9.855 108.344   1887
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.99 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.25 (0.28), residues: 1008
  helix:  2.78 (0.26), residues: 350
  sheet: -0.11 (0.25), residues: 416
  loop : -0.20 (0.45), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 236 
 HIS   0.001   0.000   HIS J  24 
 PHE   0.011   0.001   PHE A 135 
 TYR   0.021   0.001   TYR D  68 
 ARG   0.004   0.000   ARG I  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02750 (  560)
  hydrogen bonds       : angle       4.30444 ( 1600)
  covalent geometry    : bond        0.00347 ( 8435)
  covalent geometry    : angle       0.62693 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: A  215 LYS cc_start: 0.8868 (tttt) cc_final: 0.8574 (tttm)
REVERT: A  321 LYS cc_start: 0.8460 (mttt) cc_final: 0.8117 (mtpp)
REVERT: A  329 GLU cc_start: 0.8124 (tt0) cc_final: 0.7097 (tm-30)
REVERT: B   45 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8138 (tm-30)
REVERT: B  215 LYS cc_start: 0.8924 (tttt) cc_final: 0.8667 (tttm)
REVERT: B  321 LYS cc_start: 0.8487 (mttt) cc_final: 0.8127 (mtpp)
REVERT: B  329 GLU cc_start: 0.8053 (tt0) cc_final: 0.7212 (tm-30)
REVERT: C  115 GLN cc_start: 0.8861 (tp40) cc_final: 0.8251 (tp40)
REVERT: C  119 MET cc_start: 0.8539 (mmp) cc_final: 0.8111 (mmp)
REVERT: E   23 THR cc_start: 0.8699 (t) cc_final: 0.8178 (t)
REVERT: E   27 GLN cc_start: 0.8339 (mt0) cc_final: 0.7793 (mp10)
REVERT: F   27 GLN cc_start: 0.8317 (mt0) cc_final: 0.7777 (mp10)
REVERT: H   56 MET cc_start: 0.8906 (ttp) cc_final: 0.8683 (ttt)
REVERT: I   42 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8276 (mmm-85)
REVERT: J   42 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8098 (mmm-85)
  outliers start: 10
  outliers final: 10
  residues processed: 161
  average time/residue: 0.1898
  time to fit residues: 42.2197
Evaluate side-chains
  163 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  265 LYS
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain E residue   43 ILE
Chi-restraints excluded: chain F residue   43 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain H residue   51 SER
Chi-restraints excluded: chain I residue   19 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 55 optimal weight:    0.3980
   chunk 81 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0970
   chunk 31 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.086012 restraints weight = 36083.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 5.15
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8435  Z= 0.133
  Angle     :  0.615   7.789  11487  Z= 0.304
  Chirality :  0.039   0.140   1321
  Planarity :  0.004   0.034   1412
  Dihedral  :  9.553 107.690   1887
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.75 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.39 (0.28), residues: 1008
  helix:  2.86 (0.26), residues: 350
  sheet:  0.03 (0.25), residues: 412
  loop : -0.22 (0.45), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 195 
 HIS   0.001   0.000   HIS J  24 
 PHE   0.010   0.001   PHE A 135 
 TYR   0.021   0.001   TYR D  68 
 ARG   0.003   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02584 (  560)
  hydrogen bonds       : angle       4.20974 ( 1600)
  covalent geometry    : bond        0.00308 ( 8435)
  covalent geometry    : angle       0.61548 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8018 (tm-30)
REVERT: A   84 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7689 (tt0)
REVERT: A  215 LYS cc_start: 0.8862 (tttt) cc_final: 0.8581 (tttm)
REVERT: A  321 LYS cc_start: 0.8400 (mttt) cc_final: 0.8065 (mtpp)
REVERT: A  329 GLU cc_start: 0.8079 (tt0) cc_final: 0.7021 (tm-30)
REVERT: B   45 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: B  215 LYS cc_start: 0.8933 (tttt) cc_final: 0.8688 (tttm)
REVERT: B  321 LYS cc_start: 0.8474 (mttt) cc_final: 0.8127 (mtpp)
REVERT: B  329 GLU cc_start: 0.8090 (tt0) cc_final: 0.7252 (tm-30)
REVERT: C  115 GLN cc_start: 0.8901 (tp40) cc_final: 0.8333 (tp40)
REVERT: C  119 MET cc_start: 0.8508 (mmp) cc_final: 0.8086 (mmp)
REVERT: E   23 THR cc_start: 0.8692 (t) cc_final: 0.8146 (t)
REVERT: E   27 GLN cc_start: 0.8375 (mt0) cc_final: 0.7820 (mp10)
REVERT: F   27 GLN cc_start: 0.8360 (mt0) cc_final: 0.7868 (mp10)
REVERT: H   55 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8338 (mm-30)
REVERT: H   56 MET cc_start: 0.8858 (ttp) cc_final: 0.8649 (ttt)
REVERT: I   42 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8292 (mmm-85)
REVERT: J   42 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8213 (mmm-85)
  outliers start: 13
  outliers final: 11
  residues processed: 169
  average time/residue: 0.2052
  time to fit residues: 47.4613
Evaluate side-chains
  162 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  265 LYS
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain J residue   16 ILE
Chi-restraints excluded: chain J residue   18 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 55 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 45 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.127300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.087480 restraints weight = 41507.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 5.29
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8435  Z= 0.158
  Angle     :  0.630   7.627  11487  Z= 0.314
  Chirality :  0.040   0.143   1321
  Planarity :  0.004   0.035   1412
  Dihedral  :  9.448 104.200   1887
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.60 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.46 (0.28), residues: 1008
  helix:  2.90 (0.26), residues: 350
  sheet:  0.03 (0.26), residues: 410
  loop : -0.05 (0.44), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 236 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.027   0.001   PHE A  85 
 TYR   0.020   0.002   TYR D  68 
 ARG   0.009   0.000   ARG D 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02664 (  560)
  hydrogen bonds       : angle       4.20171 ( 1600)
  covalent geometry    : bond        0.00371 ( 8435)
  covalent geometry    : angle       0.62986 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8004 (tm-30)
REVERT: A  215 LYS cc_start: 0.8848 (tttt) cc_final: 0.8575 (tttm)
REVERT: A  321 LYS cc_start: 0.8408 (mttt) cc_final: 0.8063 (mtpp)
REVERT: A  329 GLU cc_start: 0.8098 (tt0) cc_final: 0.7072 (tm-30)
REVERT: B   45 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: B  215 LYS cc_start: 0.8923 (tttt) cc_final: 0.8682 (tttm)
REVERT: B  321 LYS cc_start: 0.8460 (mttt) cc_final: 0.8073 (mtpp)
REVERT: B  329 GLU cc_start: 0.8114 (tt0) cc_final: 0.7266 (tm-30)
REVERT: C  115 GLN cc_start: 0.8920 (tp40) cc_final: 0.8379 (tp40)
REVERT: C  119 MET cc_start: 0.8529 (mmp) cc_final: 0.8109 (mmp)
REVERT: E   23 THR cc_start: 0.8714 (t) cc_final: 0.8166 (t)
REVERT: E   27 GLN cc_start: 0.8394 (mt0) cc_final: 0.7837 (mp10)
REVERT: F   27 GLN cc_start: 0.8378 (mt0) cc_final: 0.7829 (mp10)
REVERT: H   55 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8336 (mm-30)
REVERT: H   56 MET cc_start: 0.8869 (ttp) cc_final: 0.8657 (ttt)
REVERT: I   42 ARG cc_start: 0.8671 (mmm-85) cc_final: 0.8292 (mmm-85)
REVERT: J   42 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8245 (mmm-85)
  outliers start: 12
  outliers final: 11
  residues processed: 159
  average time/residue: 0.2041
  time to fit residues: 44.5937
Evaluate side-chains
  161 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  265 LYS
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain F residue   23 THR
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain J residue   18 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0000
   chunk 23 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
C 115 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.126044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.082380 restraints weight = 42839.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 5.71
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8435  Z= 0.156
  Angle     :  0.636   7.651  11487  Z= 0.318
  Chirality :  0.040   0.179   1321
  Planarity :  0.004   0.037   1412
  Dihedral  :  9.289 100.118   1887
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.96 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.45 (0.28), residues: 1008
  helix:  2.88 (0.26), residues: 350
  sheet:  0.03 (0.26), residues: 410
  loop : -0.06 (0.44), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 236 
 HIS   0.001   0.000   HIS J  24 
 PHE   0.011   0.001   PHE A 135 
 TYR   0.019   0.002   TYR D  68 
 ARG   0.015   0.000   ARG D 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02659 (  560)
  hydrogen bonds       : angle       4.21631 ( 1600)
  covalent geometry    : bond        0.00365 ( 8435)
  covalent geometry    : angle       0.63632 (11487)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8015 (tm-30)
REVERT: A  215 LYS cc_start: 0.8851 (tttt) cc_final: 0.8547 (tttm)
REVERT: A  321 LYS cc_start: 0.8374 (mttt) cc_final: 0.8025 (mtpp)
REVERT: A  329 GLU cc_start: 0.8114 (tt0) cc_final: 0.7080 (tm-30)
REVERT: B   45 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: B  215 LYS cc_start: 0.8935 (tttt) cc_final: 0.8672 (tttm)
REVERT: B  321 LYS cc_start: 0.8433 (mttt) cc_final: 0.8041 (mtpp)
REVERT: B  329 GLU cc_start: 0.8135 (tt0) cc_final: 0.7275 (tm-30)
REVERT: C  115 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8425 (tp40)
REVERT: C  119 MET cc_start: 0.8573 (mmp) cc_final: 0.8140 (mmp)
REVERT: E   23 THR cc_start: 0.8692 (t) cc_final: 0.8179 (t)
REVERT: E   27 GLN cc_start: 0.8362 (mt0) cc_final: 0.7815 (mp10)
REVERT: F   27 GLN cc_start: 0.8343 (mt0) cc_final: 0.7803 (mp10)
REVERT: H   55 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8339 (mm-30)
REVERT: H   56 MET cc_start: 0.8907 (ttp) cc_final: 0.8692 (ttt)
REVERT: I   42 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8285 (mmm-85)
REVERT: J   42 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8267 (mmm-85)
REVERT: J   47 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6847 (mtm-85)
  outliers start: 13
  outliers final: 12
  residues processed: 158
  average time/residue: 0.1987
  time to fit residues: 43.0707
Evaluate side-chains
  161 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  265 LYS
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain F residue   23 THR
Chi-restraints excluded: chain H residue   51 SER
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain J residue   18 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 69 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.126407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.082567 restraints weight = 40433.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 5.71
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|
r_final: 0.3076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8435  Z= 0.149
  Angle     :  0.628   7.684  11487  Z= 0.315
  Chirality :  0.040   0.187   1321
  Planarity :  0.004   0.037   1412
  Dihedral  :  9.064  94.448   1887
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.09 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.45 (0.28), residues: 1008
  helix:  2.86 (0.27), residues: 350
  sheet:  0.04 (0.25), residues: 410
  loop : -0.04 (0.44), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 195 
 HIS   0.001   0.000   HIS J  24 
 PHE   0.011   0.001   PHE A 135 
 TYR   0.019   0.001   TYR D  68 
 ARG   0.007   0.000   ARG D 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02747 (  560)
  hydrogen bonds       : angle       4.22204 ( 1600)
  covalent geometry    : bond        0.00347 ( 8435)
  covalent geometry    : angle       0.62757 (11487)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4083.11 seconds
wall clock time: 71 minutes 35.64 seconds (4295.64 seconds total)