Starting phenix.real_space_refine
on Tue Mar  3 14:34:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dl6_27497/03_2026/8dl6_27497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dl6_27497/03_2026/8dl6_27497.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dl6_27497/03_2026/8dl6_27497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dl6_27497/03_2026/8dl6_27497.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dl6_27497/03_2026/8dl6_27497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dl6_27497/03_2026/8dl6_27497.cif"
  }
  resolution = 3.0
  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=   0.014 sd=   0.076
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      34      5.16       5
     C    3944      2.51       5
     N    1045      2.21       5
     O    1147      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6171
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3384
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 442, 3377
          Classifications: {'peptide': 442}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 431}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 442, 3377
          Classifications: {'peptide': 442}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 431}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 3439
    Chain: "C"
      Number of atoms: 1348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1348
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 319
          Unresolved non-hydrogen angles: 411
          Unresolved non-hydrogen dihedrals: 270
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 8, 'TYR:plan': 4, 'ASP:plan': 6, 'TRP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 177
    Chain: "D"
      Number of atoms: 1437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1437
          Classifications: {'peptide': 219}
          Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 81}
          Link IDs: {'PTRANS': 14, 'TRANS': 204}
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 252
          Unresolved non-hydrogen angles: 336
          Unresolved non-hydrogen dihedrals: 208
          Unresolved non-hydrogen chiralities: 40
          Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 91
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATHR A 334 " occ=0.71
      ... (12 atoms not shown)
      pdb=" CG2BTHR A 334 " occ=0.29
  Time building chain proxies: 2.02, per 1000 atoms: 0.33
  Number of scatterers: 6171
  At special positions: 0
  Unit cell: (75.9, 72.6, 141.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      34     16.00
     O    1147      8.00
     N    1045      7.00
     C    3944      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 367 " - pdb=" SG  CYS A 553 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 108 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  41 " - pdb=" SG  CYS D 115 " 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: 0.52
  Conformation dependent library (CDL) restraints added in 300.8 milliseconds
  

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 9 sheets defined
      49.9% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 23
    Processing helix  chain 'A' and resid 24 through 55
      removed outlier: 4.066A  pdb=" N   LEU A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 85
      removed outlier: 3.882A  pdb=" N   VAL A  74 " --> pdb=" O   GLY A  70 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ASP A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
    Processing helix  chain 'A' and resid 116 through 124
      removed outlier: 4.664A  pdb=" N   TYR A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 163
      removed outlier: 4.387A  pdb=" N   THR A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 197
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 200 through 228
      removed outlier: 3.911A  pdb=" N   GLY A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 6.527A  pdb=" N   ALA A 232 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 305
    Processing helix  chain 'A' and resid 307 through 317
      removed outlier: 3.523A  pdb=" N   ALA A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 317 " --> pdb=" O   GLY A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 335
    Processing helix  chain 'A' and resid 340 through 368
      removed outlier: 3.628A  pdb=" N   ILE A 344 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 393
      removed outlier: 3.583A  pdb=" N   THR A 372 " --> pdb=" O   GLY A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 484
      removed outlier: 3.550A  pdb=" N   VAL A 484 " --> pdb=" O   LEU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 489
    Processing helix  chain 'A' and resid 490 through 514
      removed outlier: 3.919A  pdb=" N   ALA A 514 " --> pdb=" O   MET A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 544
    Processing helix  chain 'C' and resid 141 through 147
    Processing helix  chain 'C' and resid 202 through 208
    Processing helix  chain 'D' and resid 47 through 51
    Processing helix  chain 'D' and resid 81 through 85
      removed outlier: 3.570A  pdb=" N   GLN D  84 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   GLY D  85 " --> pdb=" O   LYS D  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 81 through 85'
    Processing helix  chain 'D' and resid 106 through 110
      removed outlier: 3.876A  pdb=" N   THR D 110 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 183
      removed outlier: 3.653A  pdb=" N   GLY D 182 " --> pdb=" O   TRP D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 213
    Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25
      removed outlier: 3.683A  pdb=" N   ASP C  90 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33
      removed outlier: 6.697A  pdb=" N   MET C  31 " --> pdb=" O   GLU C 125 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ILE C  68 " --> pdb=" O   TRP C  55 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   GLN C  57 " --> pdb=" O   LEU C  66 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   LEU C  66 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 137 through 138
      removed outlier: 3.567A  pdb=" N   VAL C 153 " --> pdb=" O   PHE C 138 " (cutoff:3.500A)
      removed outlier: 5.048A  pdb=" N   SER C 151 " --> pdb=" O   LEU C 201 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   LEU C 201 " --> pdb=" O   SER C 151 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   VAL C 153 " --> pdb=" O   LEU C 199 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   LEU C 199 " --> pdb=" O   VAL C 153 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   PHE C 155 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   SER C 197 " --> pdb=" O   PHE C 155 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ASN C 157 " --> pdb=" O   MET C 195 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   MET C 195 " --> pdb=" O   ASN C 157 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170
      removed outlier: 3.512A  pdb=" N   CYS C 214 " --> pdb=" O   LYS C 227 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE C 225 " --> pdb=" O   ALA C 216 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25
      removed outlier: 3.812A  pdb=" N   VAL D  37 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU D 102 " --> pdb=" O   VAL D  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 31
      removed outlier: 6.636A  pdb=" N   MET D  53 " --> pdb=" O   TRP D  69 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP D  69 " --> pdb=" O   MET D  53 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   TRP D  55 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 146
      removed outlier: 4.951A  pdb=" N   GLY D 164 " --> pdb=" O   VAL D 206 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL D 206 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   LEU D 166 " --> pdb=" O   SER D 204 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   SER D 204 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   LYS D 168 " --> pdb=" O   LEU D 202 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU D 202 " --> pdb=" O   LYS D 168 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 146
      removed outlier: 4.951A  pdb=" N   GLY D 164 " --> pdb=" O   VAL D 206 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL D 206 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   LEU D 166 " --> pdb=" O   SER D 204 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   SER D 204 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   LYS D 168 " --> pdb=" O   LEU D 202 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU D 202 " --> pdb=" O   LYS D 168 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 219 through 222

    414 hydrogen bonds defined for protein.
    1165 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: 0.87

  Time building geometry restraints manager: 0.65 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: 1254
        1.33 -     1.45: 1461
        1.45 -     1.57: 3512
        1.57 -     1.69: 0
        1.69 -     1.82: 55
  Bond restraints: 6282
  Sorted by residual:
  bond pdb=" C   LEU A 213 "
       pdb=" O   LEU A 213 "
    ideal  model  delta    sigma   weight residual
    1.236  1.303 -0.066 1.15e-02 7.56e+03 3.34e+01
  bond pdb=" C   ALA A 379 "
       pdb=" O   ALA A 379 "
    ideal  model  delta    sigma   weight residual
    1.236  1.298 -0.061 1.15e-02 7.56e+03 2.85e+01
  bond pdb=" C   SER A 382 "
       pdb=" O   SER A 382 "
    ideal  model  delta    sigma   weight residual
    1.236  1.297 -0.061 1.15e-02 7.56e+03 2.78e+01
  bond pdb=" C   ASP A 166 "
       pdb=" O   ASP A 166 "
    ideal  model  delta    sigma   weight residual
    1.235  1.294 -0.058 1.22e-02 6.72e+03 2.28e+01
  bond pdb=" C   CYS A 217 "
       pdb=" O   CYS A 217 "
    ideal  model  delta    sigma   weight residual
    1.236  1.289 -0.053 1.15e-02 7.56e+03 2.14e+01
  ... (remaining 6277 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 8185
        2.46 -     4.91: 346
        4.91 -     7.37: 29
        7.37 -     9.82: 6
        9.82 -    12.28: 3
  Bond angle restraints: 8569
  Sorted by residual:
  angle pdb=" N   PRO A 397 "
        pdb=" CA  PRO A 397 "
        pdb=" C   PRO A 397 "
      ideal   model   delta    sigma   weight residual
     113.47  101.19   12.28 1.43e+00 4.89e-01 7.37e+01
  angle pdb=" N   PRO D 192 "
        pdb=" CA  PRO D 192 "
        pdb=" CB  PRO D 192 "
      ideal   model   delta    sigma   weight residual
     103.31  110.26   -6.95 8.90e-01 1.26e+00 6.11e+01
  angle pdb=" N   PRO D 148 "
        pdb=" CA  PRO D 148 "
        pdb=" CB  PRO D 148 "
      ideal   model   delta    sigma   weight residual
     103.25  111.41   -8.16 1.05e+00 9.07e-01 6.04e+01
  angle pdb=" N   PRO D 174 "
        pdb=" CA  PRO D 174 "
        pdb=" CB  PRO D 174 "
      ideal   model   delta    sigma   weight residual
     103.25  111.13   -7.88 1.05e+00 9.07e-01 5.64e+01
  angle pdb=" N   PRO D 151 "
        pdb=" CA  PRO D 151 "
        pdb=" CB  PRO D 151 "
      ideal   model   delta    sigma   weight residual
     103.25  110.81   -7.56 1.05e+00 9.07e-01 5.19e+01
  ... (remaining 8564 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 3291
       17.11 -    34.22: 269
       34.22 -    51.33: 73
       51.33 -    68.44: 19
       68.44 -    85.55: 5
  Dihedral angle restraints: 3657
    sinusoidal: 1157
      harmonic: 2500
  Sorted by residual:
  dihedral pdb=" CB  CYS A 367 "
           pdb=" SG  CYS A 367 "
           pdb=" SG  CYS A 553 "
           pdb=" CB  CYS A 553 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.53  -55.53     1      1.00e+01 1.00e-02 4.17e+01
  dihedral pdb=" CA  ASP C 102 "
           pdb=" CB  ASP C 102 "
           pdb=" CG  ASP C 102 "
           pdb=" OD1 ASP C 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.93   59.93     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" CA  GLU D 108 "
           pdb=" C   GLU D 108 "
           pdb=" N   ASP D 109 "
           pdb=" CA  ASP D 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.09  -15.91     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 3654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 652
       0.047 -    0.093: 209
       0.093 -    0.139: 123
       0.139 -    0.185: 27
       0.185 -    0.232: 14
  Chirality restraints: 1025
  Sorted by residual:
  chirality pdb=" CA  PRO D 225 "
            pdb=" N   PRO D 225 "
            pdb=" C   PRO D 225 "
            pdb=" CB  PRO D 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  VAL A 192 "
            pdb=" N   VAL A 192 "
            pdb=" C   VAL A 192 "
            pdb=" CB  VAL A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  ILE A 385 "
            pdb=" CA  ILE A 385 "
            pdb=" CG1 ILE A 385 "
            pdb=" CG2 ILE A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1022 not shown)

  Planarity restraints: 1088
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  86 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.19e+00
        pdb=" C   ASN A  86 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ASN A  86 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA A  87 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 165 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.23e+00
        pdb=" C   GLU A 165 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLU A 165 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASP A 166 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 515 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.05e+00
        pdb=" C   PRO A 515 "    0.039 2.00e-02 2.50e+03
        pdb=" O   PRO A 515 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASN A 516 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1085 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 232
        2.71 -     3.26: 6318
        3.26 -     3.81: 9660
        3.81 -     4.35: 10689
        4.35 -     4.90: 19124
  Nonbonded interactions: 46023
  Sorted by model distance:
  nonbonded pdb=" N   GLU C 101 "
            pdb=" OE1 GLU C 101 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" N   ALA C 131 "
            pdb=" CB  TYR C 160 "
     model   vdw
     2.175 3.520
  nonbonded pdb=" OD1 ASN A 100 "
            pdb="CA    CA A 601 "
     model   vdw
     2.220 2.510
  nonbonded pdb=" O   SER D  26 "
            pdb=" OG1 THR D 133 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OE1 GLU A 165 "
            pdb=" OH  TYR D  51 "
     model   vdw
     2.311 3.040
  ... (remaining 46018 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.29 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.830
  Find NCS groups from input model:        0.020
  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:8.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
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      :  0.008   0.066   6285  Z= 0.608
  Angle     :  1.089  12.276   8575  Z= 0.787
  Chirality :  0.063   0.232   1025
  Planarity :  0.004   0.042   1088
  Dihedral  : 14.534  85.547   2050
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  :  6.94 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 20.93 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.55 (0.28), residues: 867
  helix:  0.61 (0.25), residues: 393
  sheet: -0.13 (0.39), residues: 185
  loop : -1.81 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  59 
 TYR   0.012   0.001   TYR D  51 
 PHE   0.014   0.002   PHE C  91 
 TRP   0.015   0.002   TRP A 127 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00808 ( 6282)
  covalent geometry    : angle       1.08887 ( 8569)
  SS BOND              : bond        0.00295 (    3)
  SS BOND              : angle       1.28008 (    6)
  hydrogen bonds       : bond        0.14583 (  410)
  hydrogen bonds       : angle       6.59621 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9258 (mm)
REVERT: A  112 MET cc_start: 0.8870 (ttt) cc_final: 0.8645 (tmm)
  outliers start: 18
  outliers final: 5
  residues processed: 54
  average time/residue: 0.5485
  time to fit residues: 31.1243
Evaluate side-chains
  40 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  553 CYS
Chi-restraints excluded: chain D residue  106 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:   40.0000
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.068327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.049660 restraints weight = 74213.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 5.99
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6285  Z= 0.180
  Angle     :  0.647   8.307   8575  Z= 0.341
  Chirality :  0.044   0.145   1025
  Planarity :  0.005   0.055   1088
  Dihedral  :  5.453  59.127    934
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  5.32 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.36 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.83 (0.29), residues: 867
  helix:  2.21 (0.25), residues: 390
  sheet:  0.49 (0.40), residues: 179
  loop : -1.75 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  40 
 TYR   0.011   0.001   TYR A 538 
 PHE   0.011   0.001   PHE C  91 
 TRP   0.027   0.002   TRP A 127 
 HIS   0.004   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6282)
  covalent geometry    : angle       0.64645 ( 8569)
  SS BOND              : bond        0.00292 (    3)
  SS BOND              : angle       1.44235 (    6)
  hydrogen bonds       : bond        0.06644 (  410)
  hydrogen bonds       : angle       4.81929 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 6
  residues processed: 47
  average time/residue: 0.5250
  time to fit residues: 26.1331
Evaluate side-chains
  38 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain C residue   57 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 13 optimal weight:    0.1980
   chunk 33 optimal weight:    5.9990
   chunk 55 optimal weight:   50.0000
   chunk 82 optimal weight:   40.0000
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.069378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.050753 restraints weight = 87683.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 6.43
r_work: 0.2722 rms_B_bonded: 6.42 restraints_weight: 2.0000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6285  Z= 0.134
  Angle     :  0.576   8.811   8575  Z= 0.300
  Chirality :  0.041   0.151   1025
  Planarity :  0.004   0.047   1088
  Dihedral  :  5.098  59.457    932
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.79 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.00 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.52 (0.30), residues: 867
  helix:  2.94 (0.25), residues: 386
  sheet:  0.63 (0.40), residues: 183
  loop : -1.48 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  40 
 TYR   0.008   0.001   TYR A 538 
 PHE   0.010   0.001   PHE C  91 
 TRP   0.017   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6282)
  covalent geometry    : angle       0.57510 ( 8569)
  SS BOND              : bond        0.00335 (    3)
  SS BOND              : angle       1.30245 (    6)
  hydrogen bonds       : bond        0.05357 (  410)
  hydrogen bonds       : angle       4.42499 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 42
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 4
  residues processed: 58
  average time/residue: 0.5770
  time to fit residues: 35.1520
Evaluate side-chains
  38 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  498 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 = 0.3413 r_free = 0.3413 target = 0.065533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.047460 restraints weight = 43003.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 4.66
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6285  Z= 0.215
  Angle     :  0.650   8.989   8575  Z= 0.339
  Chirality :  0.043   0.169   1025
  Planarity :  0.004   0.045   1088
  Dihedral  :  4.793  58.884    930
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.25 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.69 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.50 (0.30), residues: 867
  helix:  2.81 (0.25), residues: 388
  sheet:  0.69 (0.40), residues: 185
  loop : -1.39 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  59 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.016   0.001   TRP A 127 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 6282)
  covalent geometry    : angle       0.64895 ( 8569)
  SS BOND              : bond        0.00382 (    3)
  SS BOND              : angle       1.37160 (    6)
  hydrogen bonds       : bond        0.07055 (  410)
  hydrogen bonds       : angle       4.63558 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9141 (m) cc_final: 0.8895 (m)
  outliers start: 15
  outliers final: 8
  residues processed: 48
  average time/residue: 0.5501
  time to fit residues: 27.7742
Evaluate side-chains
  43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 79 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 60 optimal weight:   40.0000
   chunk 82 optimal weight:   40.0000
   chunk 41 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.068154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.050008 restraints weight = 81157.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 6.14
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
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   0.034   6285  Z= 0.149
  Angle     :  0.603   8.325   8575  Z= 0.310
  Chirality :  0.042   0.157   1025
  Planarity :  0.004   0.050   1088
  Dihedral  :  4.657  59.706    930
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.21 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 24.51 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.76 (0.30), residues: 867
  helix:  3.06 (0.25), residues: 386
  sheet:  0.79 (0.40), residues: 185
  loop : -1.29 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  59 
 TYR   0.009   0.001   TYR A 538 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.011   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6282)
  covalent geometry    : angle       0.60224 ( 8569)
  SS BOND              : bond        0.00377 (    3)
  SS BOND              : angle       1.16551 (    6)
  hydrogen bonds       : bond        0.05739 (  410)
  hydrogen bonds       : angle       4.34949 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9160 (m) cc_final: 0.8836 (m)
REVERT: A  165 GLU cc_start: 0.8990 (mp0) cc_final: 0.8750 (mt-10)
REVERT: C   51 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9309 (m)
REVERT: D   29 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7629 (mm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 54
  average time/residue: 0.5706
  time to fit residues: 32.3907
Evaluate side-chains
  49 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  553 CYS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 54 optimal weight:    0.4980
   chunk 44 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:   30.0000
   overall best weight:    2.2988

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.067434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.049244 restraints weight = 68860.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 5.71
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6285  Z= 0.164
  Angle     :  0.618   9.284   8575  Z= 0.317
  Chirality :  0.042   0.155   1025
  Planarity :  0.004   0.052   1088
  Dihedral  :  4.630  58.876    930
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.90 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.61 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.80 (0.30), residues: 867
  helix:  3.05 (0.25), residues: 385
  sheet:  0.84 (0.40), residues: 185
  loop : -1.20 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  59 
 TYR   0.010   0.001   TYR A 501 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.010   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6282)
  covalent geometry    : angle       0.61754 ( 8569)
  SS BOND              : bond        0.00377 (    3)
  SS BOND              : angle       1.19566 (    6)
  hydrogen bonds       : bond        0.05984 (  410)
  hydrogen bonds       : angle       4.37562 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9134 (m) cc_final: 0.8886 (m)
REVERT: C   51 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9257 (m)
REVERT: D   29 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7737 (mm-30)
REVERT: D   59 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8659 (tpp80)
  outliers start: 17
  outliers final: 12
  residues processed: 54
  average time/residue: 0.5862
  time to fit residues: 33.2388
Evaluate side-chains
  50 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 36
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  553 CYS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain D residue   59 ARG
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  106 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 85 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.066050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.048236 restraints weight = 51565.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 4.97
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2819
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2819 r_free = 0.2819    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2819 r_free = 0.2819    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2819
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6285  Z= 0.216
  Angle     :  0.670   9.914   8575  Z= 0.345
  Chirality :  0.043   0.164   1025
  Planarity :  0.004   0.054   1088
  Dihedral  :  4.691  57.805    930
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.25 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.79 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.71 (0.30), residues: 867
  helix:  2.85 (0.25), residues: 388
  sheet:  0.82 (0.40), residues: 181
  loop : -1.08 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  59 
 TYR   0.013   0.001   TYR A 501 
 PHE   0.008   0.001   PHE A 360 
 TRP   0.010   0.001   TRP A 127 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 6282)
  covalent geometry    : angle       0.66898 ( 8569)
  SS BOND              : bond        0.00410 (    3)
  SS BOND              : angle       1.29858 (    6)
  hydrogen bonds       : bond        0.06906 (  410)
  hydrogen bonds       : angle       4.54567 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  132 CYS cc_start: 0.9161 (m) cc_final: 0.8855 (m)
REVERT: C   51 THR cc_start: 0.9577 (OUTLIER) cc_final: 0.9321 (m)
REVERT: D   29 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7607 (mm-30)
REVERT: D   59 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8632 (tpp80)
REVERT: D  108 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8394 (tm-30)
  outliers start: 19
  outliers final: 8
  residues processed: 57
  average time/residue: 0.5824
  time to fit residues: 34.7805
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain D residue   59 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 59 optimal weight:   50.0000
   chunk 60 optimal weight:   30.0000
   chunk 6 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:   30.0000
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.065557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.047869 restraints weight = 55605.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 5.27
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6285  Z= 0.226
  Angle     :  0.690  11.432   8575  Z= 0.357
  Chirality :  0.043   0.160   1025
  Planarity :  0.004   0.054   1088
  Dihedral  :  4.373  47.959    927
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.79 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.33 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.64 (0.30), residues: 867
  helix:  2.72 (0.25), residues: 388
  sheet:  0.89 (0.39), residues: 185
  loop : -1.10 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  40 
 TYR   0.014   0.001   TYR A 501 
 PHE   0.008   0.001   PHE A 360 
 TRP   0.011   0.001   TRP A  37 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 6282)
  covalent geometry    : angle       0.68740 ( 8569)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       2.50951 (    6)
  hydrogen bonds       : bond        0.06986 (  410)
  hydrogen bonds       : angle       4.59400 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  123 MET cc_start: 0.8828 (mtp) cc_final: 0.8291 (mmm)
REVERT: A  132 CYS cc_start: 0.9098 (m) cc_final: 0.8859 (m)
REVERT: C   51 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9297 (m)
REVERT: D   29 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7620 (mm-30)
REVERT: D   59 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8643 (tpp80)
REVERT: D   65 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8007 (mp0)
REVERT: D  108 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8337 (tm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 52
  average time/residue: 0.6168
  time to fit residues: 33.4922
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain D residue   59 ARG
Chi-restraints excluded: chain D residue  106 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3488 r_free = 0.3488 target = 0.070211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.052505 restraints weight = 74803.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 6.14
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6285  Z= 0.125
  Angle     :  0.649  13.270   8575  Z= 0.325
  Chirality :  0.041   0.176   1025
  Planarity :  0.004   0.056   1088
  Dihedral  :  4.089  46.489    927
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.86 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 25.04 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.98 (0.30), residues: 867
  helix:  3.05 (0.26), residues: 387
  sheet:  1.16 (0.40), residues: 179
  loop : -1.04 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  59 
 TYR   0.008   0.001   TYR A 501 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.012   0.001   TRP D  69 
 HIS   0.002   0.000   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6282)
  covalent geometry    : angle       0.64607 ( 8569)
  SS BOND              : bond        0.00321 (    3)
  SS BOND              : angle       2.32537 (    6)
  hydrogen bonds       : bond        0.04422 (  410)
  hydrogen bonds       : angle       4.13879 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: C   51 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9247 (m)
REVERT: D   29 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7590 (mm-30)
REVERT: D  108 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8473 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 55
  average time/residue: 0.5463
  time to fit residues: 31.6065
Evaluate side-chains
  45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 77 optimal weight:   40.0000
   chunk 17 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 70 optimal weight:    0.0170
   overall best weight:    1.7224

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

Flipped N/Q/H residues before XYZ refinement:
C  57 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.067925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.049421 restraints weight = 77446.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 6.26
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2900
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2900 r_free = 0.2900    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2900 r_free = 0.2900    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2900
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6285  Z= 0.147
  Angle     :  0.661  13.058   8575  Z= 0.334
  Chirality :  0.042   0.188   1025
  Planarity :  0.004   0.056   1088
  Dihedral  :  4.073  46.292    927
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 25.58 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.96 (0.30), residues: 867
  helix:  3.00 (0.25), residues: 387
  sheet:  1.05 (0.40), residues: 181
  loop : -0.94 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  59 
 TYR   0.010   0.001   TYR A 501 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.011   0.001   TRP A  37 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6282)
  covalent geometry    : angle       0.65892 ( 8569)
  SS BOND              : bond        0.00359 (    3)
  SS BOND              : angle       2.25458 (    6)
  hydrogen bonds       : bond        0.05169 (  410)
  hydrogen bonds       : angle       4.23460 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.273 
Fit side-chains
REVERT: C   51 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9273 (m)
REVERT: D   29 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7621 (mm-30)
REVERT: D   59 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8684 (tpp80)
REVERT: D  108 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8494 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 54
  average time/residue: 0.6478
  time to fit residues: 36.6518
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain D residue   59 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    0.0170
   chunk 84 optimal weight:    0.0370
   chunk 37 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 83 optimal weight:   50.0000
   chunk 57 optimal weight:    6.9990
   chunk 5 optimal weight:    0.1980
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 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 = 0.3499 r_free = 0.3499 target = 0.070755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.053043 restraints weight = 74258.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 6.19
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2969
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2969
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6285  Z= 0.126
  Angle     :  0.685  13.022   8575  Z= 0.339
  Chirality :  0.041   0.176   1025
  Planarity :  0.004   0.054   1088
  Dihedral  :  4.021  45.690    927
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.63 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 25.94 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.04 (0.30), residues: 867
  helix:  3.04 (0.25), residues: 387
  sheet:  1.23 (0.40), residues: 179
  loop : -0.94 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  59 
 TYR   0.011   0.001   TYR A 501 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.013   0.001   TRP D  69 
 HIS   0.002   0.000   HIS A 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6282)
  covalent geometry    : angle       0.68308 ( 8569)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       2.18765 (    6)
  hydrogen bonds       : bond        0.04377 (  410)
  hydrogen bonds       : angle       4.11336 ( 1165)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1692.94 seconds
wall clock time: 29 minutes 34.86 seconds (1774.86 seconds total)