Starting phenix.real_space_refine
on Sun Apr  5 02:46:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p85_71365/04_2026/9p85_71365.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p85_71365/04_2026/9p85_71365.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p85_71365/04_2026/9p85_71365.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p85_71365/04_2026/9p85_71365.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p85_71365/04_2026/9p85_71365.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p85_71365/04_2026/9p85_71365.map"
  }
  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=  -0.000 sd=   0.028
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      49      5.16       5
     C    4751      2.51       5
     N    1294      2.21       5
     O    1306      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7404
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2224
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 288}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 154
          Unresolved non-hydrogen angles: 198
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 95
    Chain: "L"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "B"
      Number of atoms: 2329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2329
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 273
          Unresolved non-hydrogen angles: 342
          Unresolved non-hydrogen dihedrals: 206
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 16, 'GLN:plan1': 8, 'ARG:plan': 8, 'ASN:plan1': 9, 'HIS:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 183
    Chain: "C"
      Number of atoms: 340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 340
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "A"
      Number of atoms: 2420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 345, 2420
          Classifications: {'peptide': 345}
          Incomplete info: {'truncation_to_alanine': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 340}
          Unresolved non-hydrogen bonds: 352
          Unresolved non-hydrogen angles: 426
          Unresolved non-hydrogen dihedrals: 284
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLU:plan': 24, 'ASP:plan': 15, 'ARG:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 226
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.74, per 1000 atoms: 0.24
  Number of scatterers: 7404
  At special positions: 0
  Unit cell: (100.672, 97.344, 124.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      49     16.00
     P       3     15.00
     Mg      1     11.99
     O    1306      8.00
     N    1294      7.00
     C    4751      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " 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: 0.69
  Conformation dependent library (CDL) restraints added in 205.6 milliseconds
  

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1970

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      51.2% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'R' and resid 51 through 55
    Processing helix  chain 'R' and resid 59 through 90
      removed outlier: 3.513A  pdb=" N   ARG R  90 " --> pdb=" O   PHE R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 127
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 136 through 172
    Processing helix  chain 'R' and resid 172 through 179
    Processing helix  chain 'R' and resid 181 through 200
      removed outlier: 3.644A  pdb=" N   ALA R 200 " --> pdb=" O   SER R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 202 through 207
    Processing helix  chain 'R' and resid 218 through 220
      No H-bonds generated for 'chain 'R' and resid 218 through 220'
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 273
    Processing helix  chain 'R' and resid 292 through 329
      removed outlier: 3.677A  pdb=" N   VAL R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 4.077A  pdb=" N   CYS R 327 " --> pdb=" O   ARG R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 330 through 334
    Processing helix  chain 'R' and resid 335 through 366
      removed outlier: 3.735A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR R 358 " --> pdb=" O   TYR R 354 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 367 through 369
      No H-bonds generated for 'chain 'R' and resid 367 through 369'
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 11 through 24
    Processing helix  chain 'C' and resid 29 through 45
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.995A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 62 through 68
    Processing helix  chain 'A' and resid 69 through 91
    Processing helix  chain 'A' and resid 98 through 111
      removed outlier: 4.077A  pdb=" N   ASP A 102 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 133 through 141
      removed outlier: 3.542A  pdb=" N   GLN A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 158
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 4.199A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.657A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.175A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 328 through 350
      removed outlier: 3.594A  pdb=" N   ASN A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ASN A 347 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.558A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.646A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.810A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.615A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.511A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.547A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.722A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.201A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 0.89 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: 1824
        1.33 -     1.45: 1507
        1.45 -     1.57: 4154
        1.57 -     1.69: 5
        1.69 -     1.81: 70
  Bond restraints: 7560
  Sorted by residual:
  bond pdb=" N   ILE A 285 "
       pdb=" CA  ILE A 285 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.35e+00
  bond pdb=" N   TYR A 287 "
       pdb=" CA  TYR A 287 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.21e-02 6.83e+03 6.98e+00
  bond pdb=" N   SER A 293 "
       pdb=" CA  SER A 293 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.31e-02 5.83e+03 6.67e+00
  bond pdb=" N   GLY A 292 "
       pdb=" CA  GLY A 292 "
    ideal  model  delta    sigma   weight residual
    1.446  1.476 -0.031 1.23e-02 6.61e+03 6.16e+00
  bond pdb=" N   TYR L  11 "
       pdb=" CA  TYR L  11 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.28e-02 6.10e+03 6.15e+00
  ... (remaining 7555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 9979
        1.39 -     2.78: 304
        2.78 -     4.18: 46
        4.18 -     5.57: 12
        5.57 -     6.96: 5
  Bond angle restraints: 10346
  Sorted by residual:
  angle pdb=" CA  GLY A 292 "
        pdb=" C   GLY A 292 "
        pdb=" O   GLY A 292 "
      ideal   model   delta    sigma   weight residual
     122.47  118.22    4.25 1.08e+00 8.57e-01 1.55e+01
  angle pdb=" N   TYR L  11 "
        pdb=" CA  TYR L  11 "
        pdb=" C   TYR L  11 "
      ideal   model   delta    sigma   weight residual
     113.88  109.21    4.67 1.23e+00 6.61e-01 1.44e+01
  angle pdb=" N   LEU A 283 "
        pdb=" CA  LEU A 283 "
        pdb=" C   LEU A 283 "
      ideal   model   delta    sigma   weight residual
     113.01  108.89    4.12 1.20e+00 6.94e-01 1.18e+01
  angle pdb=" N   GLU A 239 "
        pdb=" CA  GLU A 239 "
        pdb=" C   GLU A 239 "
      ideal   model   delta    sigma   weight residual
     114.56  110.74    3.82 1.27e+00 6.20e-01 9.03e+00
  angle pdb=" CA  SER A 293 "
        pdb=" C   SER A 293 "
        pdb=" O   SER A 293 "
      ideal   model   delta    sigma   weight residual
     121.81  118.30    3.51 1.18e+00 7.18e-01 8.84e+00
  ... (remaining 10341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.83: 4231
       30.83 -    61.66: 145
       61.66 -    92.50: 5
       92.50 -   123.33: 0
      123.33 -   154.16: 2
  Dihedral angle restraints: 4383
    sinusoidal: 1341
      harmonic: 3042
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.90  -88.10     1      1.00e+01 1.00e-02 9.28e+01
  dihedral pdb=" C8  GTP A 402 "
           pdb=" C1' GTP A 402 "
           pdb=" N9  GTP A 402 "
           pdb=" O4' GTP A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -49.57  154.16     1      2.00e+01 2.50e-03 4.56e+01
  dihedral pdb=" C5' GTP A 402 "
           pdb=" O5' GTP A 402 "
           pdb=" PA  GTP A 402 "
           pdb=" O3A GTP A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -137.07 -153.66     1      2.00e+01 2.50e-03 4.55e+01
  ... (remaining 4380 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 881
       0.038 -    0.076: 267
       0.076 -    0.113: 74
       0.113 -    0.151: 19
       0.151 -    0.189: 1
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  ILE A 285 "
            pdb=" N   ILE A 285 "
            pdb=" C   ILE A 285 "
            pdb=" CB  ILE A 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.94e-01
  chirality pdb=" CA  ARG L   9 "
            pdb=" N   ARG L   9 "
            pdb=" C   ARG L   9 "
            pdb=" CB  ARG L   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  ILE A 221 "
            pdb=" N   ILE A 221 "
            pdb=" C   ILE A 221 "
            pdb=" CB  ILE A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 1239 not shown)

  Planarity restraints: 1304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 201 "   -0.039 5.00e-02 4.00e+02   5.91e-02 5.59e+00
        pdb=" N   PRO R 202 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO R 202 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 202 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 168 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO A 169 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 169 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 169 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 225 "    0.029 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO R 226 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO R 226 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 226 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1301 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 68
        2.64 -     3.20: 6662
        3.20 -     3.77: 11542
        3.77 -     4.33: 15091
        4.33 -     4.90: 26164
  Nonbonded interactions: 59527
  Sorted by model distance:
  nonbonded pdb="MG    MG A 401 "
            pdb=" O2G GTP A 402 "
     model   vdw
     2.075 2.170
  nonbonded pdb=" OG  SER A  47 "
            pdb="MG    MG A 401 "
     model   vdw
     2.269 2.170
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" O   GLN A 137 "
            pdb=" ND2 ASN A 141 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OH  TYR A 167 "
            pdb=" OD2 ASP A 173 "
     model   vdw
     2.310 3.040
  ... (remaining 59522 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=1.00 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:             2.440
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.930
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
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      :  0.003   0.034   7561  Z= 0.181
  Angle     :  0.582   6.961  10348  Z= 0.352
  Chirality :  0.041   0.189   1242
  Planarity :  0.004   0.059   1304
  Dihedral  : 15.085 154.160   2410
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 21.68 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.38 (0.27), residues: 1027
  helix:  2.33 (0.24), residues: 489
  sheet:  0.75 (0.42), residues: 156
  loop : -0.95 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 306 
 TYR   0.013   0.001   TYR A 167 
 PHE   0.009   0.001   PHE B 292 
 TRP   0.020   0.001   TRP B 297 
 HIS   0.005   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7560)
  covalent geometry    : angle       0.58222 (10346)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.39791 (    2)
  hydrogen bonds       : bond        0.13001 (  472)
  hydrogen bonds       : angle       5.51704 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.281 
Fit side-chains
REVERT: R  180 MET cc_start: 0.7913 (ttp) cc_final: 0.7667 (ttt)
REVERT: B   46 ARG cc_start: 0.6246 (mtp-110) cc_final: 0.5586 (mtp180)
REVERT: B  142 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7633 (t-90)
REVERT: B  234 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7022 (t80)
  outliers start: 6
  outliers final: 1
  residues processed: 93
  average time/residue: 0.4433
  time to fit residues: 44.1613
Evaluate side-chains
  82 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 97 optimal weight:    0.3980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0470
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
C  44 HIS
A  52 GLN
A 141 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.176348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.140780 restraints weight = 9568.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.61
r_work: 0.3459 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.0735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7561  Z= 0.108
  Angle     :  0.483   6.678  10348  Z= 0.255
  Chirality :  0.040   0.143   1242
  Planarity :  0.004   0.055   1304
  Dihedral  :  8.575 155.042   1133
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.88 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.67 (0.27), residues: 1027
  helix:  2.56 (0.24), residues: 493
  sheet:  1.00 (0.42), residues: 155
  loop : -0.87 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 144 
 TYR   0.011   0.001   TYR B 111 
 PHE   0.010   0.001   PHE B 253 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 7560)
  covalent geometry    : angle       0.48306 (10346)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       0.34227 (    2)
  hydrogen bonds       : bond        0.03911 (  472)
  hydrogen bonds       : angle       4.50105 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.275 
Fit side-chains
REVERT: R  180 MET cc_start: 0.8097 (ttp) cc_final: 0.7854 (ttt)
REVERT: B   46 ARG cc_start: 0.6252 (mtp-110) cc_final: 0.5531 (mtp180)
REVERT: B  234 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7289 (t80)
REVERT: A  158 ASP cc_start: 0.7132 (m-30) cc_final: 0.6854 (m-30)
  outliers start: 20
  outliers final: 5
  residues processed: 96
  average time/residue: 0.4235
  time to fit residues: 43.6768
Evaluate side-chains
  85 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 99 optimal weight:    0.3980
   chunk 2 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 78 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
A 141 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.173245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.136394 restraints weight = 9551.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.60
r_work: 0.3424 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7561  Z= 0.121
  Angle     :  0.489   6.875  10348  Z= 0.257
  Chirality :  0.041   0.143   1242
  Planarity :  0.004   0.055   1304
  Dihedral  :  8.606 154.977   1131
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 19.46 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.73 (0.27), residues: 1027
  helix:  2.65 (0.24), residues: 490
  sheet:  0.92 (0.42), residues: 160
  loop : -0.84 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 306 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.010   0.001   PHE B 335 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7560)
  covalent geometry    : angle       0.48889 (10346)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       0.40828 (    2)
  hydrogen bonds       : bond        0.03987 (  472)
  hydrogen bonds       : angle       4.34194 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: R  180 MET cc_start: 0.8020 (ttp) cc_final: 0.7750 (ttt)
REVERT: B   46 ARG cc_start: 0.6361 (mtp-110) cc_final: 0.5637 (mtp180)
REVERT: B  234 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7313 (t80)
  outliers start: 20
  outliers final: 8
  residues processed: 96
  average time/residue: 0.3869
  time to fit residues: 40.1146
Evaluate side-chains
  85 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0010
   chunk 3 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 97 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
B 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.175081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.139214 restraints weight = 9759.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.52
r_work: 0.3442 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7561  Z= 0.099
  Angle     :  0.457   6.667  10348  Z= 0.240
  Chirality :  0.040   0.136   1242
  Planarity :  0.003   0.053   1304
  Dihedral  :  8.539 153.636   1131
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.57 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.89 (0.27), residues: 1027
  helix:  2.76 (0.24), residues: 491
  sheet:  1.11 (0.43), residues: 157
  loop : -0.77 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 306 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.010   0.001   PHE B 253 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 7560)
  covalent geometry    : angle       0.45728 (10346)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.47607 (    2)
  hydrogen bonds       : bond        0.03477 (  472)
  hydrogen bonds       : angle       4.19709 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.291 
Fit side-chains
REVERT: R  180 MET cc_start: 0.8028 (ttp) cc_final: 0.7815 (ttt)
REVERT: B   46 ARG cc_start: 0.6431 (mtp-110) cc_final: 0.5712 (mtp180)
REVERT: B  165 THR cc_start: 0.8512 (p) cc_final: 0.8256 (t)
REVERT: B  234 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7410 (t80)
  outliers start: 17
  outliers final: 8
  residues processed: 97
  average time/residue: 0.4095
  time to fit residues: 42.8752
Evaluate side-chains
  86 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 76 optimal weight:   20.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
A  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.167959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.127528 restraints weight = 9727.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.52
r_work: 0.3351 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7561  Z= 0.195
  Angle     :  0.569   9.207  10348  Z= 0.298
  Chirality :  0.044   0.176   1242
  Planarity :  0.004   0.053   1304
  Dihedral  :  9.094 160.260   1131
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 20.73 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.40 (0.27), residues: 1027
  helix:  2.38 (0.24), residues: 488
  sheet:  0.81 (0.41), residues: 156
  loop : -0.99 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 306 
 TYR   0.016   0.002   TYR R 339 
 PHE   0.015   0.002   PHE B 335 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.006   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 7560)
  covalent geometry    : angle       0.56892 (10346)
  SS BOND              : bond        0.00365 (    1)
  SS BOND              : angle       0.61812 (    2)
  hydrogen bonds       : bond        0.04897 (  472)
  hydrogen bonds       : angle       4.51017 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.275 
Fit side-chains
REVERT: R  125 TYR cc_start: 0.7932 (t80) cc_final: 0.7515 (t80)
REVERT: B   46 ARG cc_start: 0.6871 (mtp-110) cc_final: 0.6123 (mtp180)
REVERT: B  165 THR cc_start: 0.8470 (p) cc_final: 0.8197 (t)
REVERT: B  234 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.7813 (t80)
  outliers start: 25
  outliers final: 7
  residues processed: 100
  average time/residue: 0.4137
  time to fit residues: 44.4064
Evaluate side-chains
  85 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
R 365 ASN
A  52 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.170478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.130065 restraints weight = 9650.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.55
r_work: 0.3399 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7561  Z= 0.121
  Angle     :  0.490   6.982  10348  Z= 0.258
  Chirality :  0.041   0.130   1242
  Planarity :  0.003   0.053   1304
  Dihedral  :  8.818 159.196   1131
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.84 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.57 (0.27), residues: 1027
  helix:  2.59 (0.24), residues: 487
  sheet:  0.75 (0.42), residues: 160
  loop : -0.97 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 306 
 TYR   0.013   0.001   TYR R 339 
 PHE   0.010   0.001   PHE B 253 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7560)
  covalent geometry    : angle       0.48983 (10346)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.65781 (    2)
  hydrogen bonds       : bond        0.03976 (  472)
  hydrogen bonds       : angle       4.33346 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.281 
Fit side-chains
REVERT: R  267 VAL cc_start: 0.5654 (t) cc_final: 0.5271 (m)
REVERT: B   46 ARG cc_start: 0.6704 (mtp-110) cc_final: 0.6045 (mtp180)
REVERT: B  165 THR cc_start: 0.8529 (p) cc_final: 0.8318 (t)
REVERT: B  234 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7704 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 89
  average time/residue: 0.4260
  time to fit residues: 40.5693
Evaluate side-chains
  86 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 76 optimal weight:    0.0470
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    1.1682

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
A  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.169382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.128769 restraints weight = 9650.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.55
r_work: 0.3383 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7561  Z= 0.147
  Angle     :  0.513   7.662  10348  Z= 0.269
  Chirality :  0.042   0.151   1242
  Planarity :  0.003   0.053   1304
  Dihedral  :  8.901 159.015   1131
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.20 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 (0.27), residues: 1027
  helix:  2.50 (0.24), residues: 486
  sheet:  0.81 (0.41), residues: 163
  loop : -1.01 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 306 
 TYR   0.014   0.001   TYR R 339 
 PHE   0.011   0.001   PHE B 253 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7560)
  covalent geometry    : angle       0.51280 (10346)
  SS BOND              : bond        0.00310 (    1)
  SS BOND              : angle       0.67121 (    2)
  hydrogen bonds       : bond        0.04257 (  472)
  hydrogen bonds       : angle       4.34753 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.270 
Fit side-chains
REVERT: R   71 LEU cc_start: 0.8010 (mm) cc_final: 0.7773 (mm)
REVERT: R  125 TYR cc_start: 0.7944 (t80) cc_final: 0.7555 (t80)
REVERT: R  267 VAL cc_start: 0.5917 (t) cc_final: 0.5509 (m)
REVERT: B   46 ARG cc_start: 0.6727 (mtp-110) cc_final: 0.6063 (mtp180)
REVERT: B  165 THR cc_start: 0.8507 (p) cc_final: 0.8296 (t)
REVERT: B  234 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.7732 (t80)
REVERT: B  286 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7559 (mp)
REVERT: C   25 ILE cc_start: 0.7028 (mt) cc_final: 0.6805 (mp)
  outliers start: 19
  outliers final: 9
  residues processed: 92
  average time/residue: 0.4388
  time to fit residues: 43.2769
Evaluate side-chains
  89 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  180 MET
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 96 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
A  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.169966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.129218 restraints weight = 9796.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.57
r_work: 0.3393 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7561  Z= 0.133
  Angle     :  0.499   6.991  10348  Z= 0.262
  Chirality :  0.041   0.135   1242
  Planarity :  0.003   0.053   1304
  Dihedral  :  8.833 159.105   1131
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 22.15 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.57 (0.27), residues: 1027
  helix:  2.55 (0.24), residues: 488
  sheet:  0.76 (0.41), residues: 165
  loop : -0.93 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 306 
 TYR   0.014   0.001   TYR R 339 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7560)
  covalent geometry    : angle       0.49913 (10346)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       0.68697 (    2)
  hydrogen bonds       : bond        0.04048 (  472)
  hydrogen bonds       : angle       4.30983 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.261 
Fit side-chains
REVERT: R  267 VAL cc_start: 0.5868 (t) cc_final: 0.5463 (m)
REVERT: B   46 ARG cc_start: 0.6734 (mtp-110) cc_final: 0.6062 (mtp180)
REVERT: B  101 MET cc_start: 0.7585 (mtt) cc_final: 0.7281 (OUTLIER)
REVERT: B  165 THR cc_start: 0.8492 (p) cc_final: 0.8289 (t)
REVERT: B  234 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7744 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 93
  average time/residue: 0.4626
  time to fit residues: 46.0072
Evaluate side-chains
  87 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0060
   chunk 5 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 80 optimal weight:    6.9990
   chunk 38 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
B 239 ASN
A  52 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.174300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.133724 restraints weight = 9576.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.56
r_work: 0.3470 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7561  Z= 0.109
  Angle     :  0.480   6.052  10348  Z= 0.252
  Chirality :  0.040   0.130   1242
  Planarity :  0.003   0.053   1304
  Dihedral  :  8.700 157.268   1131
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 23.10 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.69 (0.27), residues: 1027
  helix:  2.62 (0.24), residues: 490
  sheet:  0.83 (0.42), residues: 165
  loop : -0.87 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 306 
 TYR   0.013   0.001   TYR B 111 
 PHE   0.011   0.001   PHE B 253 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7560)
  covalent geometry    : angle       0.48025 (10346)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.62229 (    2)
  hydrogen bonds       : bond        0.03678 (  472)
  hydrogen bonds       : angle       4.22017 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.283 
Fit side-chains
REVERT: R   71 LEU cc_start: 0.7977 (mm) cc_final: 0.7745 (mm)
REVERT: R  180 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7834 (ttt)
REVERT: B   46 ARG cc_start: 0.6715 (mtp-110) cc_final: 0.6058 (mtp180)
REVERT: B  101 MET cc_start: 0.7491 (mtt) cc_final: 0.7175 (OUTLIER)
REVERT: B  234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7755 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 88
  average time/residue: 0.4523
  time to fit residues: 42.5317
Evaluate side-chains
  82 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  180 MET
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0270
   overall best weight:    1.3644

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
A  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.171452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.130611 restraints weight = 9653.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.54
r_work: 0.3432 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7561  Z= 0.165
  Angle     :  0.536   7.431  10348  Z= 0.281
  Chirality :  0.042   0.154   1242
  Planarity :  0.003   0.053   1304
  Dihedral  :  8.913 158.910   1131
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 23.10 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.47 (0.27), residues: 1027
  helix:  2.43 (0.24), residues: 489
  sheet:  0.80 (0.41), residues: 163
  loop : -0.96 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 306 
 TYR   0.015   0.001   TYR R 339 
 PHE   0.012   0.002   PHE B 241 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 7560)
  covalent geometry    : angle       0.53556 (10346)
  SS BOND              : bond        0.00309 (    1)
  SS BOND              : angle       0.67859 (    2)
  hydrogen bonds       : bond        0.04333 (  472)
  hydrogen bonds       : angle       4.35119 ( 1368)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.263 
Fit side-chains
REVERT: R  125 TYR cc_start: 0.7977 (t80) cc_final: 0.7561 (t80)
REVERT: B   46 ARG cc_start: 0.6775 (mtp-110) cc_final: 0.6071 (mtp180)
REVERT: B  101 MET cc_start: 0.7526 (mtt) cc_final: 0.7205 (OUTLIER)
REVERT: B  234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7770 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 84
  average time/residue: 0.4590
  time to fit residues: 41.1965
Evaluate side-chains
  85 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  196 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0770
   chunk 98 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0370
   chunk 74 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.5216

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
R 365 ASN
A  52 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.171906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131038 restraints weight = 9586.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.55
r_work: 0.3436 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.160   7561  Z= 0.209
  Angle     :  0.979  59.081  10348  Z= 0.565
  Chirality :  0.049   0.911   1242
  Planarity :  0.003   0.053   1304
  Dihedral  :  8.915 158.963   1131
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 23.26 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.49 (0.27), residues: 1027
  helix:  2.46 (0.24), residues: 489
  sheet:  0.79 (0.41), residues: 163
  loop : -0.96 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 306 
 TYR   0.016   0.001   TYR R 339 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 7560)
  covalent geometry    : angle       0.97912 (10346)
  SS BOND              : bond        0.00309 (    1)
  SS BOND              : angle       0.68567 (    2)
  hydrogen bonds       : bond        0.04275 (  472)
  hydrogen bonds       : angle       4.35108 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2239.09 seconds
wall clock time: 38 minutes 56.10 seconds (2336.10 seconds total)