Starting phenix.real_space_refine
on Tue Jan 14 23:48:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xd9_38270/01_2025/8xd9_38270_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xd9_38270/01_2025/8xd9_38270.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xd9_38270/01_2025/8xd9_38270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xd9_38270/01_2025/8xd9_38270.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xd9_38270/01_2025/8xd9_38270_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xd9_38270/01_2025/8xd9_38270_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
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: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5097      2.51       5
     N    1152      2.21       5
     O    1293      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 7599
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2533
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 331, 2525
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
      Conformer: "B"
        Number of residues, atoms: 331, 2525
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
          bond proxies already assigned to first conformer: 2594
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 5.63, per 1000 atoms: 0.74
  Number of scatterers: 7599
  At special positions: 0
  Unit cell: (90.1, 96.46, 75.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1293      8.00
     N    1152      7.00
     C    5097      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: 1.77
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 0 sheets defined
      77.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 67
      removed outlier: 3.563A  pdb=" N   SER A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLN A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 70
      No H-bonds generated for 'chain 'A' and resid 68 through 70'
    Processing helix  chain 'A' and resid 73 through 88
    Processing helix  chain 'A' and resid 88 through 109
    Processing helix  chain 'A' and resid 113 through 118
    Processing helix  chain 'A' and resid 122 through 135
      removed outlier: 3.776A  pdb=" N   VAL A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LEU A 127 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL A 128 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 145 through 154
      removed outlier: 3.693A  pdb=" N   MET A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 167
      removed outlier: 4.428A  pdb=" N   ILE A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 176 through 191
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 4.013A  pdb=" N   VAL A 216 " --> pdb=" O   TRP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 223
    Processing helix  chain 'A' and resid 223 through 231
    Processing helix  chain 'A' and resid 237 through 252
      removed outlier: 3.667A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 271
      removed outlier: 3.771A  pdb=" N   LEU A 271 " --> pdb=" O   MET A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 281
      removed outlier: 3.589A  pdb=" N   ILE A 280 " --> pdb=" O   PRO A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 298
      removed outlier: 3.533A  pdb=" N   LEU A 291 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLY A 298 " --> pdb=" O   ILE A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 329
      removed outlier: 3.615A  pdb=" N   ALA A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA A 324 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 350
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.806A  pdb=" N   VAL A 366 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 381
    Processing helix  chain 'B' and resid 52 through 67
      removed outlier: 3.562A  pdb=" N   SER B  66 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLN B  67 " --> pdb=" O   ARG B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 70
      No H-bonds generated for 'chain 'B' and resid 68 through 70'
    Processing helix  chain 'B' and resid 73 through 88
    Processing helix  chain 'B' and resid 88 through 109
    Processing helix  chain 'B' and resid 113 through 118
    Processing helix  chain 'B' and resid 122 through 135
      removed outlier: 3.776A  pdb=" N   VAL B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU B 127 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL B 128 " --> pdb=" O   ASN B 124 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 144
      No H-bonds generated for 'chain 'B' and resid 142 through 144'
    Processing helix  chain 'B' and resid 145 through 154
      removed outlier: 3.693A  pdb=" N   MET B 154 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 167
      removed outlier: 4.427A  pdb=" N   ILE B 158 " --> pdb=" O   MET B 154 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ILE B 166 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 176 through 191
    Processing helix  chain 'B' and resid 212 through 216
      removed outlier: 4.013A  pdb=" N   VAL B 216 " --> pdb=" O   TRP B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 223
    Processing helix  chain 'B' and resid 223 through 231
    Processing helix  chain 'B' and resid 237 through 252
      removed outlier: 3.667A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 271
      removed outlier: 3.771A  pdb=" N   LEU B 271 " --> pdb=" O   MET B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 281
      removed outlier: 3.589A  pdb=" N   ILE B 280 " --> pdb=" O   PRO B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.534A  pdb=" N   LEU B 291 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY B 298 " --> pdb=" O   ILE B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 329
      removed outlier: 3.615A  pdb=" N   ALA B 323 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA B 324 " --> pdb=" O   TYR B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 350
    Processing helix  chain 'B' and resid 362 through 366
      removed outlier: 3.806A  pdb=" N   VAL B 366 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 381
    Processing helix  chain 'C' and resid 52 through 67
      removed outlier: 3.562A  pdb=" N   SER C  66 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLN C  67 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 70
      No H-bonds generated for 'chain 'C' and resid 68 through 70'
    Processing helix  chain 'C' and resid 73 through 88
    Processing helix  chain 'C' and resid 88 through 109
    Processing helix  chain 'C' and resid 113 through 118
    Processing helix  chain 'C' and resid 122 through 135
      removed outlier: 3.776A  pdb=" N   VAL C 126 " --> pdb=" O   GLY C 122 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU C 127 " --> pdb=" O   TYR C 123 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL C 128 " --> pdb=" O   ASN C 124 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE C 135 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 144
      No H-bonds generated for 'chain 'C' and resid 142 through 144'
    Processing helix  chain 'C' and resid 145 through 154
      removed outlier: 3.693A  pdb=" N   MET C 154 " --> pdb=" O   ILE C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 167
      removed outlier: 4.427A  pdb=" N   ILE C 158 " --> pdb=" O   MET C 154 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ILE C 166 " --> pdb=" O   ALA C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 170
      No H-bonds generated for 'chain 'C' and resid 168 through 170'
    Processing helix  chain 'C' and resid 176 through 191
    Processing helix  chain 'C' and resid 212 through 216
      removed outlier: 4.013A  pdb=" N   VAL C 216 " --> pdb=" O   TRP C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 223
    Processing helix  chain 'C' and resid 223 through 231
    Processing helix  chain 'C' and resid 237 through 252
      removed outlier: 3.666A  pdb=" N   SER C 251 " --> pdb=" O   ALA C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 271
      removed outlier: 3.771A  pdb=" N   LEU C 271 " --> pdb=" O   MET C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 281
      removed outlier: 3.589A  pdb=" N   ILE C 280 " --> pdb=" O   PRO C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 298
      removed outlier: 3.534A  pdb=" N   LEU C 291 " --> pdb=" O   PHE C 287 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY C 298 " --> pdb=" O   ILE C 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 329
      removed outlier: 3.616A  pdb=" N   ALA C 323 " --> pdb=" O   ALA C 319 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA C 324 " --> pdb=" O   TYR C 320 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 350
    Processing helix  chain 'C' and resid 362 through 366
      removed outlier: 3.806A  pdb=" N   VAL C 366 " --> pdb=" O   LEU C 363 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 368 through 381

    465 hydrogen bonds defined for protein.
    1377 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: 2.01

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1688
        1.33 -     1.45: 1871
        1.45 -     1.57: 4196
        1.57 -     1.70: 0
        1.70 -     1.82: 87
  Bond restraints: 7842
  Sorted by residual:
  bond pdb=" CA  PHE A  57 "
       pdb=" C   PHE A  57 "
    ideal  model  delta    sigma   weight residual
    1.523  1.493  0.030 1.30e-02 5.92e+03 5.40e+00
  bond pdb=" CA  PHE B  57 "
       pdb=" C   PHE B  57 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.030 1.30e-02 5.92e+03 5.16e+00
  bond pdb=" CA  PHE C  57 "
       pdb=" C   PHE C  57 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.30e-02 5.92e+03 4.94e+00
  bond pdb=" CA  GLN B  56 "
       pdb=" C   GLN B  56 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.32e-02 5.74e+03 4.16e+00
  bond pdb=" CA  GLN C  56 "
       pdb=" C   GLN C  56 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.32e-02 5.74e+03 4.15e+00
  ... (remaining 7837 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 10260
        1.50 -     3.00: 386
        3.00 -     4.50: 79
        4.50 -     6.00: 36
        6.00 -     7.50: 9
  Bond angle restraints: 10770
  Sorted by residual:
  angle pdb=" N   ASP C  59 "
        pdb=" CA  ASP C  59 "
        pdb=" C   ASP C  59 "
      ideal   model   delta    sigma   weight residual
     111.28  105.30    5.98 1.09e+00 8.42e-01 3.01e+01
  angle pdb=" N   ASP A  59 "
        pdb=" CA  ASP A  59 "
        pdb=" C   ASP A  59 "
      ideal   model   delta    sigma   weight residual
     111.28  105.30    5.98 1.09e+00 8.42e-01 3.01e+01
  angle pdb=" N   ASP B  59 "
        pdb=" CA  ASP B  59 "
        pdb=" C   ASP B  59 "
      ideal   model   delta    sigma   weight residual
     111.28  105.31    5.97 1.09e+00 8.42e-01 3.00e+01
  angle pdb=" N   PHE C  57 "
        pdb=" CA  PHE C  57 "
        pdb=" C   PHE C  57 "
      ideal   model   delta    sigma   weight residual
     111.28  108.14    3.14 1.09e+00 8.42e-01 8.30e+00
  angle pdb=" N   PHE A  57 "
        pdb=" CA  PHE A  57 "
        pdb=" C   PHE A  57 "
      ideal   model   delta    sigma   weight residual
     111.28  108.16    3.12 1.09e+00 8.42e-01 8.17e+00
  ... (remaining 10765 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.04: 4037
       15.04 -    30.07: 334
       30.07 -    45.11: 72
       45.11 -    60.15: 18
       60.15 -    75.19: 6
  Dihedral angle restraints: 4467
    sinusoidal: 1590
      harmonic: 2877
  Sorted by residual:
  dihedral pdb=" CA  TYR C 368 "
           pdb=" C   TYR C 368 "
           pdb=" N   PRO C 369 "
           pdb=" CA  PRO C 369 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.49  -20.51     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  TYR A 368 "
           pdb=" C   TYR A 368 "
           pdb=" N   PRO A 369 "
           pdb=" CA  PRO A 369 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.51  -20.49     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  TYR B 368 "
           pdb=" C   TYR B 368 "
           pdb=" N   PRO B 369 "
           pdb=" CA  PRO B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.55  -20.45     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 4464 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1098
       0.068 -    0.135: 169
       0.135 -    0.203: 5
       0.203 -    0.271: 6
       0.271 -    0.338: 3
  Chirality restraints: 1281
  Sorted by residual:
  chirality pdb=" CA  PHE B  58 "
            pdb=" N   PHE B  58 "
            pdb=" C   PHE B  58 "
            pdb=" CB  PHE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" CA  PHE C  58 "
            pdb=" N   PHE C  58 "
            pdb=" C   PHE C  58 "
            pdb=" CB  PHE C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  PHE A  58 "
            pdb=" N   PHE A  58 "
            pdb=" C   PHE A  58 "
            pdb=" CB  PHE A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.83e+00
  ... (remaining 1278 not shown)

  Planarity restraints: 1305
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  54 "   -0.011 2.00e-02 2.50e+03   2.11e-02 4.47e+00
        pdb=" C   VAL A  54 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL A  54 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A  55 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  54 "    0.011 2.00e-02 2.50e+03   2.10e-02 4.41e+00
        pdb=" C   VAL B  54 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL B  54 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE B  55 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  84 "    0.010 2.00e-02 2.50e+03   2.10e-02 4.40e+00
        pdb=" C   LEU A  84 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A  84 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A  85 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1302 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 3212
        2.92 -     3.42: 8146
        3.42 -     3.91: 13114
        3.91 -     4.41: 15384
        4.41 -     4.90: 24755
  Nonbonded interactions: 64611
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 237 "
            pdb=" OG1 THR A 240 "
     model   vdw
     2.428 3.040
  nonbonded pdb=" O   ASN B 237 "
            pdb=" OG1 THR B 240 "
     model   vdw
     2.428 3.040
  nonbonded pdb=" O   ASN C 237 "
            pdb=" OG1 THR C 240 "
     model   vdw
     2.428 3.040
  nonbonded pdb=" ND1 HIS C 192 "
            pdb=" O   THR C 199 "
     model   vdw
     2.429 3.120
  nonbonded pdb=" ND1 HIS B 192 "
            pdb=" O   THR B 199 "
     model   vdw
     2.430 3.120
  ... (remaining 64606 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  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:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     22.260
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  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:12.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7842  Z= 0.302
  Angle     :  0.742   7.501  10770  Z= 0.402
  Chirality :  0.051   0.338   1281
  Planarity :  0.005   0.034   1305
  Dihedral  : 12.441  75.187   2625
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  0.74 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 990
  helix:  0.80 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.35 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 339 
 HIS   0.003   0.001   HIS C 258 
 PHE   0.017   0.002   PHE C 179 
 TYR   0.009   0.001   TYR C 368 
 ARG   0.009   0.002   ARG A 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.9371 (tt) cc_final: 0.9093 (tm)
REVERT: A  223 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.5871 (tpp-160)
REVERT: B  217 GLN cc_start: 0.8710 (pm20) cc_final: 0.8012 (pm20)
REVERT: B  223 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.6136 (tpp-160)
REVERT: C   59 ASP cc_start: 0.8131 (t70) cc_final: 0.7919 (t0)
REVERT: C  217 GLN cc_start: 0.8633 (pm20) cc_final: 0.7993 (pm20)
REVERT: C  223 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.5908 (mpt180)
  outliers start: 9
  outliers final: 0
  residues processed: 148
  average time/residue: 1.1842
  time to fit residues: 185.4381
Evaluate side-chains
  94 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain C residue  223 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 41 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0070
   chunk 30 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
A  87 GLN
A 180 ASN
B  87 GLN
B 111 GLN
B 180 ASN
C  72 ASN
C  73 ASN
C  87 GLN
C 111 GLN
C 180 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.083304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.071024 restraints weight = 32763.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 3.45
r_work: 0.2771 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7842  Z= 0.213
  Angle     :  0.668   8.511  10770  Z= 0.326
  Chirality :  0.043   0.149   1281
  Planarity :  0.005   0.040   1305
  Dihedral  :  5.640  42.402   1056
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.05 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.27), residues: 990
  helix:  1.03 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.02 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 339 
 HIS   0.002   0.001   HIS C 258 
 PHE   0.013   0.001   PHE B 300 
 TYR   0.010   0.001   TYR C 368 
 ARG   0.008   0.002   ARG A 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.5297 (tpp-160)
REVERT: A  267 MET cc_start: 0.8654 (tmm) cc_final: 0.8368 (tmm)
REVERT: B  171 ASP cc_start: 0.9044 (t0) cc_final: 0.8746 (t0)
REVERT: B  217 GLN cc_start: 0.8779 (pm20) cc_final: 0.8114 (pm20)
REVERT: B  223 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.5624 (tpp-160)
REVERT: C  152 MET cc_start: 0.8987 (tpp) cc_final: 0.8621 (tpp)
REVERT: C  217 GLN cc_start: 0.8822 (pm20) cc_final: 0.8498 (pm20)
REVERT: C  223 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.5467 (tpp-160)
  outliers start: 6
  outliers final: 1
  residues processed: 105
  average time/residue: 1.5146
  time to fit residues: 166.8452
Evaluate side-chains
  84 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain C residue  223 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   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 = 0.3117 r_free = 0.3117 target = 0.082373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.070931 restraints weight = 22177.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.86
r_work: 0.2788 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7842  Z= 0.223
  Angle     :  0.638   8.156  10770  Z= 0.309
  Chirality :  0.043   0.149   1281
  Planarity :  0.005   0.038   1305
  Dihedral  :  5.399  37.440   1056
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 11.27 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.27), residues: 990
  helix:  1.41 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.37 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.003   0.001   HIS C 258 
 PHE   0.012   0.001   PHE B 300 
 TYR   0.010   0.001   TYR B 368 
 ARG   0.009   0.002   ARG A 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.5364 (mpt90)
REVERT: A  267 MET cc_start: 0.8664 (tmm) cc_final: 0.8445 (tmm)
REVERT: B  171 ASP cc_start: 0.8905 (t0) cc_final: 0.8597 (t0)
REVERT: C  152 MET cc_start: 0.8985 (tpp) cc_final: 0.8685 (tpp)
REVERT: C  217 GLN cc_start: 0.8765 (pm20) cc_final: 0.8491 (pm20)
  outliers start: 8
  outliers final: 1
  residues processed: 99
  average time/residue: 1.4235
  time to fit residues: 148.1385
Evaluate side-chains
  82 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  223 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   chunk 95 optimal weight:    0.9990
   chunk 15 optimal weight:    0.1980
   chunk 49 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 203 GLN
B 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.083569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.071358 restraints weight = 32968.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 3.50
r_work: 0.2773 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7842  Z= 0.182
  Angle     :  0.611   7.971  10770  Z= 0.293
  Chirality :  0.041   0.146   1281
  Planarity :  0.005   0.039   1305
  Dihedral  :  4.747  39.199   1048
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 13.36 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.27), residues: 990
  helix:  1.61 (0.20), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.46 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 258 
 PHE   0.011   0.001   PHE B 300 
 TYR   0.010   0.001   TYR A 123 
 ARG   0.008   0.002   ARG A 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.5263 (mpt90)
REVERT: A  267 MET cc_start: 0.8733 (tmm) cc_final: 0.8381 (tmm)
REVERT: B  171 ASP cc_start: 0.8938 (t0) cc_final: 0.8634 (t0)
REVERT: C  217 GLN cc_start: 0.8806 (pm20) cc_final: 0.8507 (pm20)
  outliers start: 8
  outliers final: 1
  residues processed: 96
  average time/residue: 1.4212
  time to fit residues: 143.5193
Evaluate side-chains
  80 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  223 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 203 GLN
B 217 GLN
B 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.081999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.070098 restraints weight = 29340.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.28
r_work: 0.2761 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2765
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7842  Z= 0.222
  Angle     :  0.623   8.734  10770  Z= 0.299
  Chirality :  0.042   0.150   1281
  Planarity :  0.004   0.030   1305
  Dihedral  :  4.721  40.539   1048
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 14.46 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.27), residues: 990
  helix:  1.69 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.61 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.003   0.001   HIS C 258 
 PHE   0.012   0.001   PHE B 300 
 TYR   0.010   0.001   TYR C 368 
 ARG   0.008   0.002   ARG A  63 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.5272 (mpt90)
REVERT: A  267 MET cc_start: 0.8709 (tmm) cc_final: 0.8366 (tmm)
REVERT: B  171 ASP cc_start: 0.8916 (t0) cc_final: 0.8555 (t0)
REVERT: B  223 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.5341 (tpp-160)
REVERT: C  152 MET cc_start: 0.8916 (tpp) cc_final: 0.8636 (tpp)
REVERT: C  217 GLN cc_start: 0.8837 (pm20) cc_final: 0.8560 (pm20)
  outliers start: 9
  outliers final: 3
  residues processed: 90
  average time/residue: 1.4772
  time to fit residues: 139.5949
Evaluate side-chains
  84 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain B residue  223 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0870
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.083103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.071068 restraints weight = 30972.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 3.37
r_work: 0.2773 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7842  Z= 0.192
  Angle     :  0.609   8.581  10770  Z= 0.291
  Chirality :  0.041   0.145   1281
  Planarity :  0.004   0.033   1305
  Dihedral  :  4.664  42.065   1048
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.44 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.27), residues: 990
  helix:  1.82 (0.20), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.74 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 258 
 PHE   0.011   0.001   PHE B 300 
 TYR   0.010   0.001   TYR C 368 
 ARG   0.007   0.002   ARG A  63 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.5155 (mpt90)
REVERT: A  267 MET cc_start: 0.8752 (tmm) cc_final: 0.8422 (tmm)
REVERT: B  171 ASP cc_start: 0.8866 (t0) cc_final: 0.8498 (t0)
REVERT: B  223 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.5355 (tpp-160)
REVERT: C   87 GLN cc_start: 0.9313 (tp40) cc_final: 0.9108 (tp-100)
REVERT: C  217 GLN cc_start: 0.8783 (pm20) cc_final: 0.8537 (pm20)
  outliers start: 11
  outliers final: 4
  residues processed: 90
  average time/residue: 1.5478
  time to fit residues: 146.4064
Evaluate side-chains
  87 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  223 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0000
   chunk 47 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0370
   chunk 30 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.3462

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.084781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.073434 restraints weight = 22412.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 2.89
r_work: 0.2834 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7842  Z= 0.175
  Angle     :  0.602   8.695  10770  Z= 0.287
  Chirality :  0.040   0.144   1281
  Planarity :  0.004   0.030   1305
  Dihedral  :  4.567  44.201   1048
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 15.93 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.27), residues: 990
  helix:  1.96 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.78 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.002   0.001   HIS B 308 
 PHE   0.011   0.001   PHE C 300 
 TYR   0.010   0.001   TYR A 186 
 ARG   0.007   0.002   ARG A  63 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.5072 (mmp80)
REVERT: A  267 MET cc_start: 0.8790 (tmm) cc_final: 0.8454 (tmm)
REVERT: B  112 ASP cc_start: 0.8429 (p0) cc_final: 0.7904 (p0)
REVERT: B  171 ASP cc_start: 0.8890 (t0) cc_final: 0.8521 (t0)
REVERT: B  217 GLN cc_start: 0.8850 (pm20) cc_final: 0.8265 (pm20)
REVERT: C  217 GLN cc_start: 0.8789 (pm20) cc_final: 0.8542 (pm20)
  outliers start: 8
  outliers final: 3
  residues processed: 103
  average time/residue: 1.5071
  time to fit residues: 163.0368
Evaluate side-chains
  85 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain B residue  223 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0670
   chunk 78 optimal weight:    0.0870
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
C  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.085176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.072990 restraints weight = 32567.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 3.49
r_work: 0.2807 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7842  Z= 0.180
  Angle     :  0.614  10.533  10770  Z= 0.292
  Chirality :  0.041   0.255   1281
  Planarity :  0.004   0.031   1305
  Dihedral  :  4.534  45.295   1048
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 16.79 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.27), residues: 990
  helix:  1.99 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.84 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 308 
 PHE   0.011   0.001   PHE A 287 
 TYR   0.010   0.001   TYR C 368 
 ARG   0.007   0.002   ARG C 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 1.150 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.5199 (mmp80)
REVERT: A  267 MET cc_start: 0.8753 (tmm) cc_final: 0.8390 (tmm)
REVERT: B  112 ASP cc_start: 0.8432 (p0) cc_final: 0.7921 (p0)
REVERT: B  171 ASP cc_start: 0.8883 (t0) cc_final: 0.8514 (t0)
REVERT: B  217 GLN cc_start: 0.8848 (pm20) cc_final: 0.8265 (pm20)
REVERT: C  217 GLN cc_start: 0.8791 (pm20) cc_final: 0.8527 (pm20)
  outliers start: 7
  outliers final: 5
  residues processed: 95
  average time/residue: 1.5627
  time to fit residues: 156.6087
Evaluate side-chains
  92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  229 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0570
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.3150 r_free = 0.3150 target = 0.084321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.072038 restraints weight = 34689.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.59
r_work: 0.2788 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2795
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2795 r_free = 0.2795    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2795 r_free = 0.2795    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2795
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7842  Z= 0.198
  Angle     :  0.628  10.309  10770  Z= 0.298
  Chirality :  0.042   0.222   1281
  Planarity :  0.004   0.037   1305
  Dihedral  :  4.542  45.735   1048
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 17.03 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.27), residues: 990
  helix:  2.00 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.86 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 258 
 PHE   0.011   0.001   PHE A 287 
 TYR   0.010   0.001   TYR C 368 
 ARG   0.008   0.002   ARG B 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.5176 (mmp80)
REVERT: A  267 MET cc_start: 0.8717 (tmm) cc_final: 0.8467 (tmm)
REVERT: B  217 GLN cc_start: 0.8849 (pm20) cc_final: 0.8263 (pm20)
REVERT: C  217 GLN cc_start: 0.8802 (pm20) cc_final: 0.8549 (pm20)
  outliers start: 7
  outliers final: 6
  residues processed: 90
  average time/residue: 1.5100
  time to fit residues: 142.9001
Evaluate side-chains
  91 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  229 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0270
   chunk 82 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0570
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5956

-------------------------------------------------------------------------------
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 = 0.3149 r_free = 0.3149 target = 0.084330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.072725 restraints weight = 24885.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 3.06
r_work: 0.2816 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7842  Z= 0.198
  Angle     :  0.634  10.469  10770  Z= 0.300
  Chirality :  0.042   0.214   1281
  Planarity :  0.004   0.039   1305
  Dihedral  :  4.568  46.796   1048
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.79 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.27), residues: 990
  helix:  2.03 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.86 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 258 
 PHE   0.011   0.001   PHE A 287 
 TYR   0.010   0.001   TYR A 368 
 ARG   0.009   0.003   ARG B 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.5047 (mmp80)
REVERT: A  267 MET cc_start: 0.8711 (tmm) cc_final: 0.8458 (tmm)
REVERT: C  217 GLN cc_start: 0.8793 (pm20) cc_final: 0.8514 (pm20)
  outliers start: 6
  outliers final: 7
  residues processed: 94
  average time/residue: 1.3656
  time to fit residues: 135.3624
Evaluate side-chains
  93 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  229 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0070
   chunk 56 optimal weight:    0.1980
   chunk 34 optimal weight:    0.0670
   chunk 40 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.2336

-------------------------------------------------------------------------------
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 = 0.3170 r_free = 0.3170 target = 0.085533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.073925 restraints weight = 23776.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 3.01
r_work: 0.2835 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7842  Z= 0.176
  Angle     :  0.629  10.437  10770  Z= 0.297
  Chirality :  0.041   0.215   1281
  Planarity :  0.004   0.040   1305
  Dihedral  :  4.566  47.554   1048
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 17.03 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.27), residues: 990
  helix:  2.06 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.87 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.002   0.001   HIS B 308 
 PHE   0.010   0.001   PHE A 287 
 TYR   0.010   0.001   TYR B 368 
 ARG   0.009   0.003   ARG B 373 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5012.48 seconds
wall clock time: 89 minutes 45.67 seconds (5385.67 seconds total)