Starting phenix.real_space_refine
on Wed Mar 12 08:59:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xd9_38270/03_2025/8xd9_38270_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xd9_38270/03_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_38270/03_2025/8xd9_38270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xd9_38270/03_2025/8xd9_38270.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xd9_38270/03_2025/8xd9_38270_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xd9_38270/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.95, per 1000 atoms: 0.78
  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: 1.81
  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: 0.73
  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: 2.26

  Time building geometry restraints manager: 2.19 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:             1.070
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.580
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:14.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.330
-------------------------------------------------------------------------------
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  : 0.765 
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: 1.1328
  time to fit residues: 177.7338
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  : 0.905 
-------------------------------------------------------------------------------
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 = 0.083303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.071035 restraints weight = 32779.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 3.46
r_work: 0.2770 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
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: 0.8491
moved from start:          0.1353

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     :  0.667   8.498  10770  Z= 0.326
  Chirality :  0.043   0.149   1281
  Planarity :  0.005   0.040   1305
  Dihedral  :  5.640  42.414   1056
  Min Nonbonded Distance : 2.329

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:  1.00 (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  : 0.858 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.5295 (tpp-160)
REVERT: A  267 MET cc_start: 0.8651 (tmm) cc_final: 0.8366 (tmm)
REVERT: B  171 ASP cc_start: 0.9045 (t0) cc_final: 0.8780 (t0)
REVERT: B  217 GLN cc_start: 0.8777 (pm20) cc_final: 0.8112 (pm20)
REVERT: B  223 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.5623 (tpp-160)
REVERT: C  152 MET cc_start: 0.8986 (tpp) cc_final: 0.8620 (tpp)
REVERT: C  217 GLN cc_start: 0.8820 (pm20) cc_final: 0.8497 (pm20)
REVERT: C  223 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.5467 (tpp-160)
  outliers start: 6
  outliers final: 1
  residues processed: 105
  average time/residue: 1.4310
  time to fit residues: 157.9173
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  : 0.893 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3119 r_free = 0.3119 target = 0.082500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.071118 restraints weight = 22194.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.84
r_work: 0.2791 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    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 = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1557

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= 0.221
  Angle     :  0.639   8.223  10770  Z= 0.309
  Chirality :  0.043   0.148   1281
  Planarity :  0.005   0.037   1305
  Dihedral  :  5.416  37.949   1056
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.15 %
    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:  1.55 (0.27), residues: 990
  helix:  1.39 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.35 (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 A 258 
 PHE   0.012   0.001   PHE B 300 
 TYR   0.010   0.001   TYR B 368 
 ARG   0.008   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
  101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.5323 (mpt90)
REVERT: A  267 MET cc_start: 0.8656 (tmm) cc_final: 0.8353 (tmm)
REVERT: B  171 ASP cc_start: 0.8905 (t0) cc_final: 0.8595 (t0)
REVERT: C  152 MET cc_start: 0.8989 (tpp) cc_final: 0.8593 (tpp)
REVERT: C  217 GLN cc_start: 0.8759 (pm20) cc_final: 0.8461 (pm20)
  outliers start: 9
  outliers final: 1
  residues processed: 100
  average time/residue: 1.4185
  time to fit residues: 149.0771
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  : 0.917 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0980
   chunk 49 optimal weight:    0.0570
   chunk 66 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.5702

-------------------------------------------------------------------------------
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 = 0.3134 r_free = 0.3134 target = 0.083370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.071186 restraints weight = 33054.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 3.51
r_work: 0.2771 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    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 = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
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   0.036   7842  Z= 0.191
  Angle     :  0.614   7.983  10770  Z= 0.296
  Chirality :  0.042   0.147   1281
  Planarity :  0.005   0.040   1305
  Dihedral  :  4.758  39.116   1048
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 13.48 %
    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:  1.79 (0.27), residues: 990
  helix:  1.58 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.42 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   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 B 368 
 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
  98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.5263 (mpt90)
REVERT: A  267 MET cc_start: 0.8738 (tmm) cc_final: 0.8384 (tmm)
REVERT: B  171 ASP cc_start: 0.8923 (t0) cc_final: 0.8603 (t0)
REVERT: C  217 GLN cc_start: 0.8811 (pm20) cc_final: 0.8516 (pm20)
  outliers start: 7
  outliers final: 1
  residues processed: 95
  average time/residue: 1.4617
  time to fit residues: 146.2369
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  : 0.878 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 57 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.083129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.071258 restraints weight = 29213.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 3.26
r_work: 0.2779 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    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 = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7842  Z= 0.194
  Angle     :  0.610   8.974  10770  Z= 0.292
  Chirality :  0.041   0.146   1281
  Planarity :  0.004   0.038   1305
  Dihedral  :  4.677  40.776   1048
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 14.58 %
    Favored  : 84.31 %
  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:  2.03 (0.27), residues: 990
  helix:  1.73 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.60 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   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 186 
 ARG   0.009   0.002   ARG C 373 

*********************** 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
  95 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.5211 (mpt90)
REVERT: A  267 MET cc_start: 0.8722 (tmm) cc_final: 0.8468 (tmm)
REVERT: B  171 ASP cc_start: 0.8898 (t0) cc_final: 0.8558 (t0)
REVERT: C  217 GLN cc_start: 0.8794 (pm20) cc_final: 0.8529 (pm20)
REVERT: C  223 ARG cc_start: 0.8226 (ttt180) cc_final: 0.5399 (tpp-160)
  outliers start: 9
  outliers final: 2
  residues processed: 92
  average time/residue: 1.4278
  time to fit residues: 138.1578
Evaluate side-chains
  85 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0270
   chunk 71 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0470
   chunk 33 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.4736

-------------------------------------------------------------------------------
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 = 0.3144 r_free = 0.3144 target = 0.083944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.071929 restraints weight = 30962.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 3.38
r_work: 0.2792 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2799
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2799 r_free = 0.2799    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 = 0.2799 r_free = 0.2799    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2799
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7842  Z= 0.182
  Angle     :  0.611   8.723  10770  Z= 0.291
  Chirality :  0.041   0.144   1281
  Planarity :  0.004   0.030   1305
  Dihedral  :  4.612  42.084   1048
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.18 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.27), residues: 990
  helix:  1.85 (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   0.008   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 258 
 PHE   0.011   0.001   PHE B 300 
 TYR   0.009   0.001   TYR A 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
  98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.5175 (mpt90)
REVERT: A  267 MET cc_start: 0.8780 (tmm) cc_final: 0.8505 (tmm)
REVERT: B  171 ASP cc_start: 0.8906 (t0) cc_final: 0.8542 (t0)
REVERT: B  223 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.5288 (tpp-160)
REVERT: C   87 GLN cc_start: 0.9315 (tp40) cc_final: 0.9113 (tp-100)
REVERT: C  217 GLN cc_start: 0.8827 (pm20) cc_final: 0.8603 (pm20)
REVERT: C  223 ARG cc_start: 0.8207 (ttt180) cc_final: 0.5364 (mpt90)
  outliers start: 9
  outliers final: 2
  residues processed: 94
  average time/residue: 1.4915
  time to fit residues: 147.0724
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  : 0.849 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0470
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0170
   chunk 30 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.4716

-------------------------------------------------------------------------------
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 = 0.084331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.073023 restraints weight = 22523.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 2.89
r_work: 0.2822 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    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 = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7842  Z= 0.188
  Angle     :  0.611   9.065  10770  Z= 0.292
  Chirality :  0.041   0.238   1281
  Planarity :  0.004   0.032   1305
  Dihedral  :  4.567  43.632   1048
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.30 %
    Favored  : 82.97 %
  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:  2.33 (0.27), residues: 990
  helix:  1.94 (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   0.007   0.001   TRP B 339 
 HIS   0.002   0.001   HIS B 258 
 PHE   0.010   0.001   PHE A 287 
 TYR   0.010   0.001   TYR B 368 
 ARG   0.007   0.002   ARG C 373 

*********************** 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
  98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.5095 (mmp80)
REVERT: A  267 MET cc_start: 0.8762 (tmm) cc_final: 0.8387 (tmm)
REVERT: B  112 ASP cc_start: 0.8433 (p0) cc_final: 0.7909 (p0)
REVERT: B  171 ASP cc_start: 0.8894 (t0) cc_final: 0.8523 (t0)
REVERT: B  217 GLN cc_start: 0.8863 (pm20) cc_final: 0.8297 (pm20)
REVERT: B  373 ARG cc_start: 0.9104 (mmm-85) cc_final: 0.8782 (mmm-85)
REVERT: C   87 GLN cc_start: 0.9313 (tp40) cc_final: 0.9112 (tp-100)
REVERT: C  217 GLN cc_start: 0.8857 (pm20) cc_final: 0.8606 (pm20)
REVERT: C  223 ARG cc_start: 0.8177 (ttt180) cc_final: 0.5311 (mpt90)
  outliers start: 6
  outliers final: 3
  residues processed: 96
  average time/residue: 1.4113
  time to fit residues: 142.3985
Evaluate side-chains
  88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 24 optimal weight:    0.0020
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.4788

-------------------------------------------------------------------------------
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 = 0.3154 r_free = 0.3154 target = 0.084509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.072425 restraints weight = 32685.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 3.46
r_work: 0.2798 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2801
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    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 = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2801
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2181

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= 0.186
  Angle     :  0.615  10.512  10770  Z= 0.292
  Chirality :  0.041   0.202   1281
  Planarity :  0.004   0.031   1305
  Dihedral  :  4.542  44.810   1048
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.91 %
    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:  2.40 (0.27), residues: 990
  helix:  1.98 (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 B 258 
 PHE   0.011   0.001   PHE A 287 
 TYR   0.009   0.001   TYR A 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
  98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.5199 (mmp80)
REVERT: A  267 MET cc_start: 0.8766 (tmm) cc_final: 0.8394 (tmm)
REVERT: B  112 ASP cc_start: 0.8437 (p0) cc_final: 0.7930 (p0)
REVERT: B  171 ASP cc_start: 0.8909 (t0) cc_final: 0.8545 (t0)
REVERT: B  217 GLN cc_start: 0.8855 (pm20) cc_final: 0.8280 (pm20)
REVERT: C  217 GLN cc_start: 0.8866 (pm20) cc_final: 0.8619 (pm20)
REVERT: C  223 ARG cc_start: 0.8153 (ttt180) cc_final: 0.5366 (mpt90)
  outliers start: 6
  outliers final: 4
  residues processed: 96
  average time/residue: 1.9691
  time to fit residues: 198.0664
Evaluate side-chains
  87 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3151 r_free = 0.3151 target = 0.083872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.071671 restraints weight = 34536.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 3.47
r_work: 0.2781 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    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 = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2162

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= 0.212
  Angle     :  0.628   9.218  10770  Z= 0.299
  Chirality :  0.042   0.191   1281
  Planarity :  0.004   0.034   1305
  Dihedral  :  4.584  45.300   1048
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.30 %
    Favored  : 82.97 %
  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:  1.98 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.85 (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   0.012   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
  92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 1.115 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.5006 (mmp80)
REVERT: B  112 ASP cc_start: 0.8428 (p0) cc_final: 0.7927 (p0)
REVERT: B  217 GLN cc_start: 0.8854 (pm20) cc_final: 0.8333 (pm20)
REVERT: C   69 MET cc_start: 0.9142 (mmp) cc_final: 0.8916 (mmt)
REVERT: C  217 GLN cc_start: 0.8834 (pm20) cc_final: 0.8597 (pm20)
REVERT: C  223 ARG cc_start: 0.8142 (ttt180) cc_final: 0.5335 (mpt90)
  outliers start: 6
  outliers final: 5
  residues processed: 89
  average time/residue: 1.5551
  time to fit residues: 145.2764
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  : 1.343 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   chunk 82 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3142 r_free = 0.3142 target = 0.083597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.071944 restraints weight = 24947.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 3.05
r_work: 0.2802 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    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 = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7842  Z= 0.205
  Angle     :  0.633  11.072  10770  Z= 0.300
  Chirality :  0.042   0.191   1281
  Planarity :  0.004   0.039   1305
  Dihedral  :  4.587  45.910   1048
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 16.54 %
    Favored  : 82.60 %
  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:  2.43 (0.27), residues: 990
  helix:  2.00 (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   0.007   0.001   TRP B 339 
 HIS   0.002   0.001   HIS B 258 
 PHE   0.011   0.001   PHE B 287 
 TYR   0.011   0.001   TYR A 186 
 ARG   0.009   0.002   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
  92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A  217 GLN cc_start: 0.8448 (mp10) cc_final: 0.8219 (mp10)
REVERT: A  223 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.5024 (mmp80)
REVERT: A  267 MET cc_start: 0.8696 (tmm) cc_final: 0.8480 (tmm)
REVERT: C  217 GLN cc_start: 0.8833 (pm20) cc_final: 0.8594 (pm20)
REVERT: C  223 ARG cc_start: 0.8163 (ttt180) cc_final: 0.5356 (mpt90)
  outliers start: 7
  outliers final: 5
  residues processed: 88
  average time/residue: 1.7788
  time to fit residues: 163.8318
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  : 1.105 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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 = 0.3124 r_free = 0.3124 target = 0.082026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.070727 restraints weight = 23981.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.90
r_work: 0.2781 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    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 = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7842  Z= 0.242
  Angle     :  0.652  10.576  10770  Z= 0.309
  Chirality :  0.043   0.180   1281
  Planarity :  0.004   0.040   1305
  Dihedral  :  4.696  45.872   1048
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 17.03 %
    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:  2.35 (0.27), residues: 990
  helix:  1.92 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.86 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 144 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.012   0.001   PHE C 287 
 TYR   0.012   0.001   TYR C 368 
 ARG   0.009   0.002   ARG B 373 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5637.55 seconds
wall clock time: 100 minutes 8.25 seconds (6008.25 seconds total)