Starting phenix.real_space_refine
on Tue Feb  3 16:04:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ynf_39423/02_2026/8ynf_39423.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ynf_39423/02_2026/8ynf_39423.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ynf_39423/02_2026/8ynf_39423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ynf_39423/02_2026/8ynf_39423.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ynf_39423/02_2026/8ynf_39423.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ynf_39423/02_2026/8ynf_39423.cif"
  }
  resolution = 3.65
  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=  -0.002 sd=   0.052
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      30      5.16       5
     C    2962      2.51       5
     N     808      2.21       5
     O     836      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4636
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1606
          Classifications: {'peptide': 249}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 13, 'TRANS': 235}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 264
          Unresolved non-hydrogen angles: 345
          Unresolved non-hydrogen dihedrals: 225
          Unresolved non-hydrogen chiralities: 35
          Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1, 'TRP:plan': 3}
          Unresolved non-hydrogen planarities: 127
    Chain: "D"
      Number of atoms: 327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 327
          Classifications: {'peptide': 48}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 2, 'TRANS': 45}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "E"
      Number of atoms: 382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 382
          Classifications: {'peptide': 59}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 3, 'TRANS': 55}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 56
    Chain: "A"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1612
          Classifications: {'peptide': 249}
          Incomplete info: {'truncation_to_alanine': 68}
          Link IDs: {'PTRANS': 13, 'TRANS': 235}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 257
          Unresolved non-hydrogen angles: 336
          Unresolved non-hydrogen dihedrals: 218
          Unresolved non-hydrogen chiralities: 35
          Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1, 'TRP:plan': 3}
          Unresolved non-hydrogen planarities: 121
    Chain: "G"
      Number of atoms: 382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 382
          Classifications: {'peptide': 59}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 3, 'TRANS': 55}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 56
    Chain: "H"
      Number of atoms: 327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 327
          Classifications: {'peptide': 48}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 2, 'TRANS': 45}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 39
  Time building chain proxies: 1.20, per 1000 atoms: 0.26
  Number of scatterers: 4636
  At special positions: 0
  Unit cell: (138.017, 78.8668, 58.2112, 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      30     16.00
     O     836      8.00
     N     808      7.00
     C    2962      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  51 " - pdb=" SG  CYS B 276 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS B 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   7 " - pdb=" SG  CYS E  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS A 276 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 129 " - pdb=" SG  CYS A 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G   7 " - pdb=" SG  CYS G  34 " distance=2.03

  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: 0.67
  Conformation dependent library (CDL) restraints added in 489.0 milliseconds
  

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1328

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 5 sheets defined
      56.3% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 65 through 82
    Processing helix  chain 'B' and resid 95 through 117
      removed outlier: 3.574A  pdb=" N   LEU B  99 " --> pdb=" O   GLY B  95 " (cutoff:3.500A)
      Proline residue:  B 114  - end of helix
    Processing helix  chain 'B' and resid 125 through 153
    Processing helix  chain 'B' and resid 163 through 181
      removed outlier: 4.622A  pdb=" N   LEU B 167 " --> pdb=" O   PRO B 163 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 187
    Processing helix  chain 'B' and resid 200 through 202
      No H-bonds generated for 'chain 'B' and resid 200 through 202'
    Processing helix  chain 'B' and resid 203 through 219
    Processing helix  chain 'B' and resid 219 through 227
    Processing helix  chain 'B' and resid 246 through 268
      removed outlier: 4.393A  pdb=" N   PHE B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      Proline residue:  B 255  - end of helix
    Processing helix  chain 'B' and resid 275 through 295
      removed outlier: 3.693A  pdb=" N   GLN B 279 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 311
      Proline residue:  B 301  - end of helix
      removed outlier: 3.848A  pdb=" N   ALA B 311 " --> pdb=" O   PHE B 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 68
    Processing helix  chain 'E' and resid 63 through 68
    Processing helix  chain 'A' and resid 65 through 81
    Processing helix  chain 'A' and resid 95 through 117
      removed outlier: 3.592A  pdb=" N   LEU A  99 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      Proline residue:  A 114  - end of helix
    Processing helix  chain 'A' and resid 125 through 153
    Processing helix  chain 'A' and resid 163 through 181
      removed outlier: 4.566A  pdb=" N   LEU A 167 " --> pdb=" O   PRO A 163 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU A 169 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
    Processing helix  chain 'A' and resid 200 through 202
      No H-bonds generated for 'chain 'A' and resid 200 through 202'
    Processing helix  chain 'A' and resid 203 through 227
      removed outlier: 4.608A  pdb=" N   LEU A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      Proline residue:  A 222  - end of helix
    Processing helix  chain 'A' and resid 246 through 268
      removed outlier: 4.391A  pdb=" N   PHE A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      Proline residue:  A 255  - end of helix
    Processing helix  chain 'A' and resid 275 through 295
    Processing helix  chain 'A' and resid 295 through 311
      Proline residue:  A 301  - end of helix
      removed outlier: 3.838A  pdb=" N   ALA A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 63 through 68
    Processing helix  chain 'H' and resid 58 through 68
      removed outlier: 4.636A  pdb=" N   VAL H  62 " --> pdb=" O   VAL H  58 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   GLU H  63 " --> pdb=" O   GLN H  59 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   LYS H  64 " --> pdb=" O   ARG H  60 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 188 through 191
      removed outlier: 3.651A  pdb=" N   SER B 191 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU B 194 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 49 through 51
      removed outlier: 4.043A  pdb=" N   LEU D  49 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL D  41 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   VAL D  27 " --> pdb=" O   LEU E  25 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU E  25 " --> pdb=" O   VAL D  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 191
      removed outlier: 3.634A  pdb=" N   SER A 191 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LEU A 194 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 38 through 38
      removed outlier: 3.739A  pdb=" N   GLU G  38 " --> pdb=" O   ILE G  28 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ILE G  28 " --> pdb=" O   GLU G  38 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU G  24 " --> pdb=" O   LYS G  42 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 38 through 38
      removed outlier: 3.739A  pdb=" N   GLU G  38 " --> pdb=" O   ILE G  28 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ILE G  28 " --> pdb=" O   GLU G  38 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU G  25 " --> pdb=" O   VAL H  27 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL H  27 " --> pdb=" O   LEU G  25 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   VAL H  41 " --> pdb=" O   LEU H  49 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LEU H  49 " --> pdb=" O   VAL H  41 " (cutoff:3.500A)

    288 hydrogen bonds defined for protein.
    852 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: 0.75

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 812
        1.32 -     1.45: 1156
        1.45 -     1.57: 2723
        1.57 -     1.70: 0
        1.70 -     1.83: 32
  Bond restraints: 4723
  Sorted by residual:
  bond pdb=" N   LEU B 146 "
       pdb=" CA  LEU B 146 "
    ideal  model  delta    sigma   weight residual
    1.458  1.512 -0.055 1.28e-02 6.10e+03 1.83e+01
  bond pdb=" C   ILE B 173 "
       pdb=" N   TRP B 174 "
    ideal  model  delta    sigma   weight residual
    1.334  1.283  0.052 1.27e-02 6.20e+03 1.66e+01
  bond pdb=" C   ILE A 173 "
       pdb=" N   TRP A 174 "
    ideal  model  delta    sigma   weight residual
    1.334  1.283  0.051 1.27e-02 6.20e+03 1.61e+01
  bond pdb=" C   TRP A 174 "
       pdb=" O   TRP A 174 "
    ideal  model  delta    sigma   weight residual
    1.236  1.197  0.039 1.15e-02 7.56e+03 1.17e+01
  bond pdb=" C   TRP B 174 "
       pdb=" O   TRP B 174 "
    ideal  model  delta    sigma   weight residual
    1.236  1.197  0.039 1.15e-02 7.56e+03 1.16e+01
  ... (remaining 4718 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 6218
        1.79 -     3.59: 198
        3.59 -     5.38: 53
        5.38 -     7.18: 15
        7.18 -     8.97: 3
  Bond angle restraints: 6487
  Sorted by residual:
  angle pdb=" C   ALA A  61 "
        pdb=" CA  ALA A  61 "
        pdb=" CB  ALA A  61 "
      ideal   model   delta    sigma   weight residual
     117.23  109.33    7.90 1.36e+00 5.41e-01 3.37e+01
  angle pdb=" C   ALA B  61 "
        pdb=" CA  ALA B  61 "
        pdb=" CB  ALA B  61 "
      ideal   model   delta    sigma   weight residual
     117.23  109.35    7.88 1.36e+00 5.41e-01 3.36e+01
  angle pdb=" C   PHE A  81 "
        pdb=" CA  PHE A  81 "
        pdb=" CB  PHE A  81 "
      ideal   model   delta    sigma   weight residual
     110.37  119.34   -8.97 1.78e+00 3.16e-01 2.54e+01
  angle pdb=" C   ILE A 173 "
        pdb=" N   TRP A 174 "
        pdb=" CA  TRP A 174 "
      ideal   model   delta    sigma   weight residual
     120.44  113.92    6.52 1.30e+00 5.92e-01 2.51e+01
  angle pdb=" C   ILE B 173 "
        pdb=" N   TRP B 174 "
        pdb=" CA  TRP B 174 "
      ideal   model   delta    sigma   weight residual
     120.44  114.02    6.42 1.30e+00 5.92e-01 2.44e+01
  ... (remaining 6482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 2457
       17.28 -    34.56: 222
       34.56 -    51.84: 48
       51.84 -    69.11: 10
       69.11 -    86.39: 5
  Dihedral angle restraints: 2742
    sinusoidal: 722
      harmonic: 2020
  Sorted by residual:
  dihedral pdb=" CB  CYS B  51 "
           pdb=" SG  CYS B  51 "
           pdb=" SG  CYS B 276 "
           pdb=" CB  CYS B 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.09  -52.09     1      1.00e+01 1.00e-02 3.70e+01
  dihedral pdb=" CA  CYS A  54 "
           pdb=" C   CYS A  54 "
           pdb=" N   ASN A  55 "
           pdb=" CA  ASN A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.74  -22.26     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" SG  CYS A 129 "
           pdb=" CB  CYS A 195 "
           pdb=" SG  CYS A 195 "
           pdb=" CA  CYS A 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    3.84   75.16     1      2.00e+01 2.50e-03 1.79e+01
  ... (remaining 2739 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 599
       0.045 -    0.089: 152
       0.089 -    0.134: 50
       0.134 -    0.179: 7
       0.179 -    0.223: 4
  Chirality restraints: 812
  Sorted by residual:
  chirality pdb=" CA  LEU B 145 "
            pdb=" N   LEU B 145 "
            pdb=" C   LEU B 145 "
            pdb=" CB  LEU B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  LEU B 146 "
            pdb=" N   LEU B 146 "
            pdb=" C   LEU B 146 "
            pdb=" CB  LEU B 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.02e-01
  chirality pdb=" CA  THR A 300 "
            pdb=" N   THR A 300 "
            pdb=" C   THR A 300 "
            pdb=" CB  THR A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.26e-01
  ... (remaining 809 not shown)

  Planarity restraints: 829
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  62 "   -0.060 5.00e-02 4.00e+02   8.96e-02 1.29e+01
        pdb=" N   PRO A  63 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A  63 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A  63 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  62 "   -0.059 5.00e-02 4.00e+02   8.92e-02 1.27e+01
        pdb=" N   PRO B  63 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO B  63 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B  63 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 146 "   -0.017 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   LEU B 146 "    0.061 2.00e-02 2.50e+03
        pdb=" O   LEU B 146 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B 147 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 826 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1030
        2.78 -     3.31: 4545
        3.31 -     3.84: 7560
        3.84 -     4.37: 7506
        4.37 -     4.90: 12886
  Nonbonded interactions: 33527
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS G  42 "
            pdb=" O   LEU G  43 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" NZ  LYS E  42 "
            pdb=" O   LEU E  43 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   PHE A 264 "
            pdb=" OG  SER A 268 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ASN A  55 "
            pdb=" ND2 ASN A 287 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" O   ASN B  55 "
            pdb=" ND2 ASN B 287 "
     model   vdw
     2.309 3.120
  ... (remaining 33522 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 46 through 80 or (resid 81 through 82 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 83 through 311))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             2.140
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.300
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6288
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   4729  Z= 0.241
  Angle     :  0.826   8.974   6499  Z= 0.504
  Chirality :  0.046   0.223    812
  Planarity :  0.008   0.090    829
  Dihedral  : 14.761  86.393   1396
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 25.76 %
    Favored  : 73.13 %
  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 are not related in a simple way.
  whole: -1.16 (0.32), residues: 664
  helix:  0.41 (0.27), residues: 362
  sheet: -0.32 (0.80), residues: 34
  loop : -2.56 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  89 
 TYR   0.001   0.000   TYR B 137 
 PHE   0.024   0.001   PHE A 264 
 TRP   0.010   0.002   TRP B 136 
 HIS   0.005   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 4723)
  covalent geometry    : angle       0.82238 ( 6487)
  SS BOND              : bond        0.00122 (    6)
  SS BOND              : angle       2.03449 (   12)
  hydrogen bonds       : bond        0.14851 (  288)
  hydrogen bonds       : angle       6.60351 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.247 
Fit side-chains
REVERT: B  207 GLN cc_start: 0.6423 (tp40) cc_final: 0.5619 (pt0)
REVERT: A  207 GLN cc_start: 0.6441 (tp40) cc_final: 0.5754 (pt0)
  outliers start: 4
  outliers final: 1
  residues processed: 60
  average time/residue: 0.0445
  time to fit residues: 3.9688
Evaluate side-chains
  54 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E   8 GLN
A 207 GLN
G   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.242540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.208234 restraints weight = 7603.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.210695 restraints weight = 5791.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.211949 restraints weight = 4850.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.213125 restraints weight = 4363.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.214098 restraints weight = 4001.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.4393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6316
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4729  Z= 0.151
  Angle     :  0.645   6.245   6499  Z= 0.333
  Chirality :  0.044   0.166    812
  Planarity :  0.006   0.067    829
  Dihedral  :  5.027  22.239    701
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 26.04 %
    Favored  : 70.91 %
  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 are not related in a simple way.
  whole: -0.91 (0.32), residues: 664
  helix:  0.62 (0.27), residues: 370
  sheet: -0.74 (0.86), residues: 34
  loop : -2.45 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  89 
 TYR   0.003   0.001   TYR A 137 
 PHE   0.007   0.001   PHE A 141 
 TRP   0.015   0.001   TRP B 174 
 HIS   0.003   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4723)
  covalent geometry    : angle       0.64164 ( 6487)
  SS BOND              : bond        0.00258 (    6)
  SS BOND              : angle       1.65655 (   12)
  hydrogen bonds       : bond        0.04279 (  288)
  hydrogen bonds       : angle       5.16784 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B   56 LEU cc_start: 0.8198 (mt) cc_final: 0.7939 (mt)
  outliers start: 11
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0241
  time to fit residues: 2.6301
Evaluate side-chains
  60 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  251 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0870
   chunk 48 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
B  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.242653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.208942 restraints weight = 7532.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.211396 restraints weight = 5772.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.213021 restraints weight = 4835.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.213342 restraints weight = 4301.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.213342 restraints weight = 4122.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6313
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4729  Z= 0.134
  Angle     :  0.614   7.062   6499  Z= 0.315
  Chirality :  0.043   0.169    812
  Planarity :  0.005   0.058    829
  Dihedral  :  4.800  22.081    700
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 26.87 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.33), residues: 664
  helix:  0.93 (0.27), residues: 368
  sheet: -0.41 (0.93), residues: 34
  loop : -2.40 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  89 
 TYR   0.003   0.001   TYR B 137 
 PHE   0.013   0.001   PHE H  17 
 TRP   0.007   0.001   TRP A  96 
 HIS   0.003   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4723)
  covalent geometry    : angle       0.61249 ( 6487)
  SS BOND              : bond        0.00194 (    6)
  SS BOND              : angle       1.28605 (   12)
  hydrogen bonds       : bond        0.03795 (  288)
  hydrogen bonds       : angle       4.78318 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   66 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6403 (mm)
REVERT: H   29 GLU cc_start: 0.6516 (tm-30) cc_final: 0.5981 (tm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 56
  average time/residue: 0.0359
  time to fit residues: 3.0861
Evaluate side-chains
  53 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  217 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0370
   chunk 59 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0980
   chunk 47 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 39 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   overall best weight:    0.3858

-------------------------------------------------------------------------------
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 = 0.4700 r_free = 0.4700 target = 0.244298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.210714 restraints weight = 7624.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.213340 restraints weight = 5798.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.214607 restraints weight = 4854.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.214923 restraints weight = 4353.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.214923 restraints weight = 4182.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.4394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6281
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4729  Z= 0.120
  Angle     :  0.579   5.385   6499  Z= 0.297
  Chirality :  0.042   0.166    812
  Planarity :  0.005   0.056    829
  Dihedral  :  4.579  21.827    700
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 25.76 %
    Favored  : 69.25 %
  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 are not related in a simple way.
  whole: -0.31 (0.33), residues: 664
  helix:  1.21 (0.27), residues: 368
  sheet: -0.56 (0.90), residues: 34
  loop : -2.32 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  89 
 TYR   0.004   0.001   TYR B 137 
 PHE   0.008   0.001   PHE A 264 
 TRP   0.007   0.001   TRP A  96 
 HIS   0.002   0.000   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4723)
  covalent geometry    : angle       0.57757 ( 6487)
  SS BOND              : bond        0.00344 (    6)
  SS BOND              : angle       1.13144 (   12)
  hydrogen bonds       : bond        0.03362 (  288)
  hydrogen bonds       : angle       4.40185 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   66 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6334 (mm)
REVERT: A  133 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6243 (t80)
REVERT: H   29 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6088 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 59
  average time/residue: 0.0375
  time to fit residues: 3.4436
Evaluate side-chains
  54 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   96 TRP
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  251 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0070
   chunk 25 optimal weight:   10.0000
   chunk 2 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.9000

-------------------------------------------------------------------------------
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 = 0.4665 r_free = 0.4665 target = 0.240410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.206221 restraints weight = 7559.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.208600 restraints weight = 5775.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.210336 restraints weight = 4866.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.211460 restraints weight = 4314.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.211891 restraints weight = 3971.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4729  Z= 0.149
  Angle     :  0.612   5.398   6499  Z= 0.315
  Chirality :  0.043   0.165    812
  Planarity :  0.005   0.056    829
  Dihedral  :  4.783  22.705    700
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 27.98 %
    Favored  : 67.59 %
  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 are not related in a simple way.
  whole: -0.48 (0.33), residues: 664
  helix:  1.03 (0.27), residues: 368
  sheet: -0.57 (0.95), residues: 34
  loop : -2.34 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D  60 
 TYR   0.002   0.001   TYR A 133 
 PHE   0.011   0.002   PHE H  17 
 TRP   0.008   0.001   TRP B  90 
 HIS   0.002   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4723)
  covalent geometry    : angle       0.61067 ( 6487)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       1.15137 (   12)
  hydrogen bonds       : bond        0.03808 (  288)
  hydrogen bonds       : angle       4.64000 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.193 
Fit side-chains
REVERT: B  282 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7826 (tp)
REVERT: A   46 GLU cc_start: 0.5523 (pm20) cc_final: 0.5240 (pt0)
REVERT: A   66 ILE cc_start: 0.6803 (mp) cc_final: 0.6444 (mm)
REVERT: H   29 GLU cc_start: 0.6555 (tm-30) cc_final: 0.6110 (tm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 64
  average time/residue: 0.0345
  time to fit residues: 3.4767
Evaluate side-chains
  56 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   96 TRP
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain H residue   52 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 63 optimal weight:    0.0570
   chunk 8 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.9100

-------------------------------------------------------------------------------
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 = 0.4660 r_free = 0.4660 target = 0.240014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.205883 restraints weight = 7800.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.208493 restraints weight = 5953.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.210223 restraints weight = 4956.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.211018 restraints weight = 4373.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.211167 restraints weight = 4070.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.4350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4729  Z= 0.150
  Angle     :  0.606   5.393   6499  Z= 0.312
  Chirality :  0.043   0.162    812
  Planarity :  0.005   0.055    829
  Dihedral  :  4.790  22.034    700
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 29.64 %
    Favored  : 66.76 %
  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 are not related in a simple way.
  whole: -0.48 (0.33), residues: 664
  helix:  1.07 (0.27), residues: 366
  sheet: -0.55 (0.96), residues: 34
  loop : -2.38 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 TYR   0.003   0.001   TYR A 133 
 PHE   0.013   0.001   PHE A 264 
 TRP   0.009   0.001   TRP A  96 
 HIS   0.002   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4723)
  covalent geometry    : angle       0.60430 ( 6487)
  SS BOND              : bond        0.00314 (    6)
  SS BOND              : angle       1.19711 (   12)
  hydrogen bonds       : bond        0.03735 (  288)
  hydrogen bonds       : angle       4.63237 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A   66 ILE cc_start: 0.6853 (mp) cc_final: 0.6507 (mm)
REVERT: H   29 GLU cc_start: 0.6343 (tm-30) cc_final: 0.5928 (tm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 57
  average time/residue: 0.0361
  time to fit residues: 3.2574
Evaluate side-chains
  53 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   96 TRP
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain H residue   52 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.4631 r_free = 0.4631 target = 0.236965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.204311 restraints weight = 7647.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.206472 restraints weight = 5684.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.208492 restraints weight = 4757.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.209484 restraints weight = 4147.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.209781 restraints weight = 3813.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6404
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4729  Z= 0.165
  Angle     :  0.633   6.309   6499  Z= 0.325
  Chirality :  0.044   0.165    812
  Planarity :  0.005   0.053    829
  Dihedral  :  4.945  22.594    700
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 29.09 %
    Favored  : 67.04 %
  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 are not related in a simple way.
  whole: -0.70 (0.33), residues: 664
  helix:  0.87 (0.27), residues: 366
  sheet: -0.63 (0.97), residues: 34
  loop : -2.45 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 TYR   0.003   0.001   TYR A 133 
 PHE   0.014   0.001   PHE A 264 
 TRP   0.011   0.002   TRP B  96 
 HIS   0.002   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 4723)
  covalent geometry    : angle       0.63135 ( 6487)
  SS BOND              : bond        0.00313 (    6)
  SS BOND              : angle       1.31634 (   12)
  hydrogen bonds       : bond        0.03967 (  288)
  hydrogen bonds       : angle       4.81292 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A   66 ILE cc_start: 0.6881 (mp) cc_final: 0.6522 (mm)
REVERT: A  262 LEU cc_start: 0.7983 (mm) cc_final: 0.7577 (tp)
REVERT: H   29 GLU cc_start: 0.6351 (tm-30) cc_final: 0.5662 (tm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 59
  average time/residue: 0.0370
  time to fit residues: 3.4473
Evaluate side-chains
  56 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   96 TRP
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain H residue   52 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0970
   chunk 54 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:   10.0000
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.4662 r_free = 0.4662 target = 0.240388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.206638 restraints weight = 7734.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.209167 restraints weight = 5831.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.210432 restraints weight = 4862.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.210755 restraints weight = 4363.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.211954 restraints weight = 4185.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6369
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4729  Z= 0.135
  Angle     :  0.592   5.414   6499  Z= 0.305
  Chirality :  0.042   0.159    812
  Planarity :  0.005   0.053    829
  Dihedral  :  4.711  21.779    700
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 28.81 %
    Favored  : 67.04 %
  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 are not related in a simple way.
  whole: -0.47 (0.33), residues: 664
  helix:  1.10 (0.27), residues: 366
  sheet: -0.49 (1.00), residues: 34
  loop : -2.43 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 TYR   0.002   0.001   TYR A 137 
 PHE   0.015   0.001   PHE A 264 
 TRP   0.010   0.001   TRP B  96 
 HIS   0.002   0.001   HIS D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4723)
  covalent geometry    : angle       0.59050 ( 6487)
  SS BOND              : bond        0.00222 (    6)
  SS BOND              : angle       1.12297 (   12)
  hydrogen bonds       : bond        0.03600 (  288)
  hydrogen bonds       : angle       4.55887 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.171 
Fit side-chains
REVERT: B  262 LEU cc_start: 0.7971 (mm) cc_final: 0.7594 (tp)
REVERT: A   66 ILE cc_start: 0.6869 (mp) cc_final: 0.6522 (mm)
REVERT: A  262 LEU cc_start: 0.7887 (mm) cc_final: 0.7525 (tp)
REVERT: H   29 GLU cc_start: 0.6310 (tm-30) cc_final: 0.5599 (tm-30)
  outliers start: 15
  outliers final: 13
  residues processed: 55
  average time/residue: 0.0372
  time to fit residues: 3.2423
Evaluate side-chains
  54 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   96 TRP
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  294 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 61 optimal weight:    0.0060
   chunk 32 optimal weight:    0.0980
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0980
   overall best weight:    0.5398

-------------------------------------------------------------------------------
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 = 0.4660 r_free = 0.4660 target = 0.240730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.207132 restraints weight = 7701.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.209709 restraints weight = 5789.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.211052 restraints weight = 4832.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.212595 restraints weight = 4329.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.212962 restraints weight = 3934.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4729  Z= 0.128
  Angle     :  0.588   5.397   6499  Z= 0.304
  Chirality :  0.042   0.161    812
  Planarity :  0.005   0.052    829
  Dihedral  :  4.607  22.394    700
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 28.25 %
    Favored  : 67.87 %
  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 are not related in a simple way.
  whole: -0.29 (0.33), residues: 664
  helix:  1.26 (0.27), residues: 366
  sheet: -0.45 (1.01), residues: 34
  loop : -2.38 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 TYR   0.002   0.000   TYR B 137 
 PHE   0.016   0.001   PHE A 264 
 TRP   0.008   0.001   TRP B  96 
 HIS   0.001   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4723)
  covalent geometry    : angle       0.58666 ( 6487)
  SS BOND              : bond        0.00202 (    6)
  SS BOND              : angle       0.97631 (   12)
  hydrogen bonds       : bond        0.03421 (  288)
  hydrogen bonds       : angle       4.38482 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.175 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.5773 (mp0) cc_final: 0.5489 (mp0)
REVERT: A   66 ILE cc_start: 0.6847 (mp) cc_final: 0.6512 (mm)
REVERT: A  262 LEU cc_start: 0.7893 (mm) cc_final: 0.7533 (tp)
REVERT: H   29 GLU cc_start: 0.6328 (tm-30) cc_final: 0.5657 (tm-30)
  outliers start: 14
  outliers final: 14
  residues processed: 55
  average time/residue: 0.0351
  time to fit residues: 3.0968
Evaluate side-chains
  54 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   96 TRP
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  294 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4651 r_free = 0.4651 target = 0.239891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.205971 restraints weight = 7696.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.208204 restraints weight = 5851.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.210153 restraints weight = 4944.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.211016 restraints weight = 4377.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.211211 restraints weight = 4057.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4729  Z= 0.137
  Angle     :  0.595   5.390   6499  Z= 0.308
  Chirality :  0.042   0.161    812
  Planarity :  0.005   0.053    829
  Dihedral  :  4.587  22.091    700
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 28.53 %
    Favored  : 67.59 %
  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 are not related in a simple way.
  whole: -0.26 (0.34), residues: 664
  helix:  1.27 (0.27), residues: 366
  sheet: -0.31 (1.03), residues: 34
  loop : -2.34 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 TYR   0.002   0.001   TYR B 137 
 PHE   0.015   0.001   PHE A 264 
 TRP   0.008   0.001   TRP B  96 
 HIS   0.002   0.001   HIS G  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 4723)
  covalent geometry    : angle       0.59367 ( 6487)
  SS BOND              : bond        0.00203 (    6)
  SS BOND              : angle       0.97315 (   12)
  hydrogen bonds       : bond        0.03547 (  288)
  hydrogen bonds       : angle       4.41559 (  852)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.098 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.5825 (mp0) cc_final: 0.5552 (mp0)
REVERT: A   66 ILE cc_start: 0.6849 (mp) cc_final: 0.6511 (mm)
REVERT: A  262 LEU cc_start: 0.7915 (mm) cc_final: 0.7521 (tp)
REVERT: H   29 GLU cc_start: 0.6334 (tm-30) cc_final: 0.5702 (tm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 55
  average time/residue: 0.0295
  time to fit residues: 2.5468
Evaluate side-chains
  53 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   96 TRP
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   96 TRP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  251 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0010
   chunk 44 optimal weight:    0.8980
   chunk 51 optimal weight:    0.3980
   chunk 32 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0970
   chunk 43 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.2984

-------------------------------------------------------------------------------
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 = 0.4674 r_free = 0.4674 target = 0.242597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.209195 restraints weight = 7782.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.212004 restraints weight = 5859.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.213794 restraints weight = 4831.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.214444 restraints weight = 4240.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.215261 restraints weight = 3963.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6272
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4729  Z= 0.115
  Angle     :  0.569   5.306   6499  Z= 0.293
  Chirality :  0.041   0.159    812
  Planarity :  0.005   0.052    829
  Dihedral  :  4.371  21.410    700
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 29.09 %
    Favored  : 67.87 %
  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 are not related in a simple way.
  whole:  0.04 (0.34), residues: 664
  helix:  1.53 (0.27), residues: 370
  sheet: -0.17 (1.03), residues: 34
  loop : -2.30 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  89 
 TYR   0.004   0.001   TYR B 137 
 PHE   0.016   0.001   PHE A 264 
 TRP   0.006   0.001   TRP A  96 
 HIS   0.002   0.000   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4723)
  covalent geometry    : angle       0.56897 ( 6487)
  SS BOND              : bond        0.00179 (    6)
  SS BOND              : angle       0.72748 (   12)
  hydrogen bonds       : bond        0.03156 (  288)
  hydrogen bonds       : angle       4.10369 (  852)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 797.89 seconds
wall clock time: 14 minutes 28.67 seconds (868.67 seconds total)