Starting phenix.real_space_refine
on Fri Aug 22 20:18:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xd9_38270/08_2025/8xd9_38270_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xd9_38270/08_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_38270/08_2025/8xd9_38270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xd9_38270/08_2025/8xd9_38270.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xd9_38270/08_2025/8xd9_38270_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xd9_38270/08_2025/8xd9_38270_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
          bond proxies already assigned to first conformer: 2594
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.31, per 1000 atoms: 0.30
  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: 0.64
  Conformation dependent library (CDL) restraints added in 746.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.21
  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: 1.18

  Time building geometry restraints manager: 0.88 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  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:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.760
  Find NCS groups from input model:        0.070
  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:6.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.850
-------------------------------------------------------------------------------
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= 0.242
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.009   0.002   ARG A 373 
 TYR   0.009   0.001   TYR C 368 
 PHE   0.017   0.002   PHE C 179 
 TRP   0.014   0.001   TRP A 339 
 HIS   0.003   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 7842)
  covalent geometry    : angle       0.74193 (10770)
  hydrogen bonds       : bond        0.17338 (  465)
  hydrogen bonds       : angle       5.79087 ( 1377)

*********************** 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  : 0.291 
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: 0.5891
  time to fit residues: 92.1418
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  : 0.279 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.082813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.069936 restraints weight = 42760.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 3.93
r_work: 0.2740 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7842  Z= 0.144
  Angle     :  0.673   8.499  10770  Z= 0.329
  Chirality :  0.044   0.151   1281
  Planarity :  0.005   0.040   1305
  Dihedral  :  5.657  42.308   1056
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.27), residues: 990
  helix:  1.01 (0.20), residues: 705
  sheet:  None (None), residues: 0
  loop : -0.02 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG A 373 
 TYR   0.011   0.001   TYR C 368 
 PHE   0.013   0.001   PHE B 300 
 TRP   0.010   0.001   TRP C 339 
 HIS   0.002   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7842)
  covalent geometry    : angle       0.67333 (10770)
  hydrogen bonds       : bond        0.04141 (  465)
  hydrogen bonds       : angle       4.04191 ( 1377)

*********************** 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
  107 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.5303 (tpp-160)
REVERT: A  267 MET cc_start: 0.8680 (tmm) cc_final: 0.8475 (tmm)
REVERT: B  171 ASP cc_start: 0.9061 (t0) cc_final: 0.8768 (t0)
REVERT: B  217 GLN cc_start: 0.8788 (pm20) cc_final: 0.8127 (pm20)
REVERT: B  223 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.5631 (tpp-160)
REVERT: C  217 GLN cc_start: 0.8835 (pm20) cc_final: 0.8515 (pm20)
REVERT: C  223 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.5547 (tpp-160)
  outliers start: 6
  outliers final: 1
  residues processed: 106
  average time/residue: 0.6387
  time to fit residues: 71.0157
Evaluate side-chains
  82 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
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 75 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3080 r_free = 0.3080 target = 0.080120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.067525 restraints weight = 40414.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 3.78
r_work: 0.2693 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7842  Z= 0.184
  Angle     :  0.666   8.058  10770  Z= 0.324
  Chirality :  0.044   0.151   1281
  Planarity :  0.005   0.041   1305
  Dihedral  :  5.490  37.149   1056
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.64 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.27), residues: 990
  helix:  1.37 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.41 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG A 373 
 TYR   0.012   0.001   TYR B 368 
 PHE   0.014   0.001   PHE B 300 
 TRP   0.007   0.001   TRP C 143 
 HIS   0.004   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 7842)
  covalent geometry    : angle       0.66626 (10770)
  hydrogen bonds       : bond        0.03997 (  465)
  hydrogen bonds       : angle       3.83420 ( 1377)

*********************** 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
  97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.5368 (mpt90)
REVERT: A  267 MET cc_start: 0.8729 (tmm) cc_final: 0.8434 (tmm)
REVERT: B  171 ASP cc_start: 0.8909 (t0) cc_final: 0.8548 (t0)
REVERT: B  231 GLN cc_start: 0.8339 (tp40) cc_final: 0.8137 (mm-40)
REVERT: C  152 MET cc_start: 0.9090 (tpp) cc_final: 0.8794 (tpp)
REVERT: C  217 GLN cc_start: 0.8825 (pm20) cc_final: 0.8529 (pm20)
  outliers start: 9
  outliers final: 1
  residues processed: 95
  average time/residue: 0.6802
  time to fit residues: 67.8943
Evaluate side-chains
  79 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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 55 optimal weight:    0.0370
   chunk 72 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0370
   chunk 83 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
B 217 GLN
C 111 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.082950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.071080 restraints weight = 28899.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 3.25
r_work: 0.2772 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    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 = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7842  Z= 0.119
  Angle     :  0.614   8.094  10770  Z= 0.296
  Chirality :  0.041   0.146   1281
  Planarity :  0.005   0.037   1305
  Dihedral  :  4.818  40.154   1048
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.09 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.27), residues: 990
  helix:  1.61 (0.20), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.53 (0.34), residues: 297

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7842)
  covalent geometry    : angle       0.61439 (10770)
  hydrogen bonds       : bond        0.03471 (  465)
  hydrogen bonds       : angle       3.57430 ( 1377)

*********************** 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
  104 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.5334 (mpt90)
REVERT: A  267 MET cc_start: 0.8742 (tmm) cc_final: 0.8501 (tmm)
REVERT: B  171 ASP cc_start: 0.8903 (t0) cc_final: 0.8547 (t0)
REVERT: C  217 GLN cc_start: 0.8825 (pm20) cc_final: 0.8521 (pm20)
  outliers start: 10
  outliers final: 0
  residues processed: 100
  average time/residue: 0.6747
  time to fit residues: 70.8728
Evaluate side-chains
  81 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 19 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 72 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3107 r_free = 0.3107 target = 0.081762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.069265 restraints weight = 42678.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 3.86
r_work: 0.2727 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1922

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= 0.140
  Angle     :  0.625   8.810  10770  Z= 0.299
  Chirality :  0.042   0.149   1281
  Planarity :  0.004   0.032   1305
  Dihedral  :  4.748  41.346   1048
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 15.32 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.27), residues: 990
  helix:  1.64 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.47 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG A  63 
 TYR   0.011   0.001   TYR C 368 
 PHE   0.012   0.001   PHE B 300 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.003   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7842)
  covalent geometry    : angle       0.62497 (10770)
  hydrogen bonds       : bond        0.03483 (  465)
  hydrogen bonds       : angle       3.56460 ( 1377)

*********************** 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
  92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.5319 (mpt90)
REVERT: A  267 MET cc_start: 0.8676 (tmm) cc_final: 0.8338 (tmm)
REVERT: B  171 ASP cc_start: 0.8927 (t0) cc_final: 0.8552 (t0)
REVERT: C  217 GLN cc_start: 0.8836 (pm20) cc_final: 0.8567 (pm20)
  outliers start: 9
  outliers final: 2
  residues processed: 91
  average time/residue: 0.6109
  time to fit residues: 58.4472
Evaluate side-chains
  82 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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 88 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.3110 r_free = 0.3110 target = 0.081935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.069919 restraints weight = 32016.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 3.40
r_work: 0.2752 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.2017

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= 0.133
  Angle     :  0.614   8.498  10770  Z= 0.294
  Chirality :  0.042   0.146   1281
  Planarity :  0.004   0.032   1305
  Dihedral  :  4.704  42.795   1048
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.27), residues: 990
  helix:  1.80 (0.20), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.75 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG A  63 
 TYR   0.010   0.001   TYR C 368 
 PHE   0.012   0.001   PHE A 287 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7842)
  covalent geometry    : angle       0.61359 (10770)
  hydrogen bonds       : bond        0.03395 (  465)
  hydrogen bonds       : angle       3.49958 ( 1377)

*********************** 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
  101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.5162 (mpt90)
REVERT: B  223 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.5381 (tpp-160)
REVERT: C   87 GLN cc_start: 0.9309 (tp40) cc_final: 0.9101 (tp-100)
REVERT: C  217 GLN cc_start: 0.8808 (pm20) cc_final: 0.8560 (pm20)
REVERT: C  223 ARG cc_start: 0.8260 (ttt180) cc_final: 0.5385 (mpt90)
  outliers start: 12
  outliers final: 3
  residues processed: 95
  average time/residue: 0.6786
  time to fit residues: 67.5301
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  : 0.285 
-------------------------------------------------------------------------------
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 A residue  316 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 95 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 43 optimal weight:    0.4980
   chunk 90 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3113 r_free = 0.3113 target = 0.082186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.070034 restraints weight = 33150.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 3.47
r_work: 0.2746 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2045

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= 0.133
  Angle     :  0.623   8.613  10770  Z= 0.297
  Chirality :  0.042   0.146   1281
  Planarity :  0.004   0.030   1305
  Dihedral  :  4.681  44.005   1048
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.27), residues: 990
  helix:  1.86 (0.20), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.81 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG A  63 
 TYR   0.010   0.001   TYR B 368 
 PHE   0.011   0.001   PHE A 287 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7842)
  covalent geometry    : angle       0.62327 (10770)
  hydrogen bonds       : bond        0.03353 (  465)
  hydrogen bonds       : angle       3.48390 ( 1377)

*********************** 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
  97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  223 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.5093 (mpt90)
REVERT: B  112 ASP cc_start: 0.8495 (p0) cc_final: 0.7913 (p0)
REVERT: B  223 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.5358 (tpp-160)
REVERT: C   87 GLN cc_start: 0.9314 (tp40) cc_final: 0.9111 (tp-100)
REVERT: C  217 GLN cc_start: 0.8813 (pm20) cc_final: 0.8576 (pm20)
REVERT: C  223 ARG cc_start: 0.8243 (ttt180) cc_final: 0.5355 (mpt90)
  outliers start: 9
  outliers final: 3
  residues processed: 94
  average time/residue: 0.7112
  time to fit residues: 69.9748
Evaluate side-chains
  86 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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 A residue  316 LEU
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 68 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0970
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5578

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.083237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.070707 restraints weight = 38985.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 3.75
r_work: 0.2751 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    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 = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.2137

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= 0.123
  Angle     :  0.618   9.555  10770  Z= 0.295
  Chirality :  0.041   0.144   1281
  Planarity :  0.004   0.030   1305
  Dihedral  :  4.651  45.202   1048
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 16.91 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.27), residues: 990
  helix:  1.92 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.82 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG A  63 
 TYR   0.011   0.001   TYR A 186 
 PHE   0.011   0.001   PHE A 287 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7842)
  covalent geometry    : angle       0.61806 (10770)
  hydrogen bonds       : bond        0.03262 (  465)
  hydrogen bonds       : angle       3.45107 ( 1377)

*********************** 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
  96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  217 GLN cc_start: 0.8435 (mp10) cc_final: 0.8216 (mp10)
REVERT: A  223 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.5072 (mmp80)
REVERT: A  267 MET cc_start: 0.8696 (tmm) cc_final: 0.8432 (tmm)
REVERT: B  112 ASP cc_start: 0.8475 (p0) cc_final: 0.7910 (p0)
REVERT: C  217 GLN cc_start: 0.8794 (pm20) cc_final: 0.8564 (pm20)
REVERT: C  223 ARG cc_start: 0.8226 (ttt180) cc_final: 0.5383 (mpt90)
  outliers start: 8
  outliers final: 3
  residues processed: 95
  average time/residue: 0.6746
  time to fit residues: 67.3617
Evaluate side-chains
  86 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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 A residue  316 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 16 optimal weight:    0.0980
   chunk 45 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 53 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 217 GLN
C  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.084123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.071530 restraints weight = 40796.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 3.83
r_work: 0.2765 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    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 = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2213

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= 0.120
  Angle     :  0.629  10.960  10770  Z= 0.298
  Chirality :  0.041   0.148   1281
  Planarity :  0.004   0.031   1305
  Dihedral  :  4.620  46.358   1048
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 17.40 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.40 (0.27), residues: 990
  helix:  1.96 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.87 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG A 373 
 TYR   0.010   0.001   TYR A 368 
 PHE   0.011   0.001   PHE A 287 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7842)
  covalent geometry    : angle       0.62905 (10770)
  hydrogen bonds       : bond        0.03163 (  465)
  hydrogen bonds       : angle       3.44997 ( 1377)

*********************** 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  : 0.293 
Fit side-chains
REVERT: A  217 GLN cc_start: 0.8455 (mp10) cc_final: 0.8240 (mp10)
REVERT: A  223 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.5045 (mmp80)
REVERT: A  267 MET cc_start: 0.8695 (tmm) cc_final: 0.8422 (tmm)
REVERT: C  223 ARG cc_start: 0.8201 (ttt180) cc_final: 0.5314 (mpt90)
  outliers start: 6
  outliers final: 3
  residues processed: 90
  average time/residue: 0.7151
  time to fit residues: 67.6055
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  : 0.301 
-------------------------------------------------------------------------------
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 A residue  316 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 15 optimal weight:    0.1980
   chunk 19 optimal weight:    0.7980
   chunk 55 optimal weight:    0.4980
   chunk 42 optimal weight:    0.2980
   chunk 37 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.084553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.071941 restraints weight = 39090.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 3.80
r_work: 0.2775 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2775
-------------------------------------------------------------------------------
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 = 0.48   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 = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2288

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= 0.117
  Angle     :  0.626   9.629  10770  Z= 0.294
  Chirality :  0.041   0.143   1281
  Planarity :  0.004   0.031   1305
  Dihedral  :  4.583  47.220   1048
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 17.77 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.27), residues: 990
  helix:  2.02 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.90 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG A 373 
 TYR   0.009   0.001   TYR B 368 
 PHE   0.011   0.001   PHE A 287 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.002   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7842)
  covalent geometry    : angle       0.62615 (10770)
  hydrogen bonds       : bond        0.03145 (  465)
  hydrogen bonds       : angle       3.40225 ( 1377)

********************** 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: 6
    poor density    : 86
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  217 GLN cc_start: 0.8436 (mp10) cc_final: 0.8219 (mp10)
REVERT: A  223 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.5168 (mmp80)
REVERT: A  267 MET cc_start: 0.8689 (tmm) cc_final: 0.8409 (tmm)
REVERT: B  223 ARG cc_start: 0.8184 (ttt180) cc_final: 0.5120 (tpp-160)
REVERT: C   69 MET cc_start: 0.9163 (mmp) cc_final: 0.8956 (mmt)
REVERT: C  223 ARG cc_start: 0.8174 (ttt180) cc_final: 0.5418 (mpt90)
  outliers start: 6
  outliers final: 4
  residues processed: 89
  average time/residue: 0.7121
  time to fit residues: 66.3239
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  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  112 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 48 optimal weight:    0.0060
   chunk 68 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.084056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.071966 restraints weight = 30683.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.37
r_work: 0.2794 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2794
-------------------------------------------------------------------------------
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: 0.8470
moved from start:          0.2263

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= 0.128
  Angle     :  0.640  11.303  10770  Z= 0.301
  Chirality :  0.041   0.142   1281
  Planarity :  0.004   0.043   1305
  Dihedral  :  4.599  47.299   1048
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 17.65 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.27), residues: 990
  helix:  2.02 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.91 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG B 373 
 TYR   0.010   0.001   TYR A 186 
 PHE   0.012   0.001   PHE A 287 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7842)
  covalent geometry    : angle       0.64045 (10770)
  hydrogen bonds       : bond        0.03185 (  465)
  hydrogen bonds       : angle       3.41049 ( 1377)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2464.44 seconds
wall clock time: 42 minutes 49.96 seconds (2569.96 seconds total)