Starting phenix.real_space_refine
on Wed Sep 17 07:54:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t2g_25612/09_2025/7t2g_25612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t2g_25612/09_2025/7t2g_25612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t2g_25612/09_2025/7t2g_25612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t2g_25612/09_2025/7t2g_25612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t2g_25612/09_2025/7t2g_25612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t2g_25612/09_2025/7t2g_25612.cif"
  }
  resolution = 2.5
  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=   0.028 sd=   0.242
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    4461      2.51       5
     N    1154      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6922
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1690
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 112
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 59
    Chain: "B"
      Number of atoms: 2481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2481
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 8, 'GLU:plan': 5, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 90
    Chain: "C"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 348
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2279
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 288, 2270
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 25
      Conformer: "B"
        Number of residues, atoms: 288, 2270
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 25
          bond proxies already assigned to first conformer: 2317
    Chain: "R"
      Number of atoms: 124
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 11, 94
          Unusual residues: {'CLR': 2, 'EIG': 1}
          Classifications: {'undetermined': 3, 'water': 8}
          Link IDs: {None: 10}
      Conformer: "B"
        Number of residues, atoms: 11, 94
          Unusual residues: {'CLR': 2, 'EIG': 1}
          Classifications: {'undetermined': 3, 'water': 8}
          Link IDs: {None: 10}
          bond proxies already assigned to first conformer: 62
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C01AEIG R 501 " occ=0.50
      ... (58 atoms not shown)
      pdb=" O05BEIG R 501 " occ=0.50
  Time building chain proxies: 2.18, per 1000 atoms: 0.31
  Number of scatterers: 6922
  At special positions: 0
  Unit cell: (91.84, 98.4, 114.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    1248      8.00
     N    1154      7.00
     C    4461      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 140 " - pdb=" SG  CYS R 217 " 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: 0.49
  Conformation dependent library (CDL) restraints added in 390.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      47.8% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.630A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.061A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.722A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.691A  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 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 46
      removed outlier: 4.638A  pdb=" N   LYS C  46 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 96
    Processing helix  chain 'R' and resid 101 through 120
      removed outlier: 3.630A  pdb=" N   THR R 120 " --> pdb=" O   LEU R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 120 through 130
    Processing helix  chain 'R' and resid 135 through 171
      removed outlier: 4.173A  pdb=" N   LEU R 139 " --> pdb=" O   PHE R 135 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 179
      removed outlier: 4.142A  pdb=" N   ASP R 177 " --> pdb=" O   VAL R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 195
    Processing helix  chain 'R' and resid 195 through 206
      Proline residue:  R 201  - end of helix
    Processing helix  chain 'R' and resid 224 through 241
      removed outlier: 3.598A  pdb=" N   TRP R 228 " --> pdb=" O   PRO R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 241 through 260
    Processing helix  chain 'R' and resid 268 through 306
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 311 through 337
      removed outlier: 3.852A  pdb=" N   VAL R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN R 328 " --> pdb=" O   LEU R 324 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   SER R 329 " --> pdb=" O   GLY R 325 " (cutoff:3.500A)
      Proline residue:  R 333  - end of helix
    Processing helix  chain 'R' and resid 340 through 348
      removed outlier: 3.610A  pdb=" N   ARG R 345 " --> pdb=" O   GLU R 341 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   CYS R 346 " --> pdb=" O   ASN R 342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.189A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.524A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.826A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.680A  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: 3.987A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.524A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.696A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.172A  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: 3.526A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.690A  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: 5.826A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 208 through 211

    398 hydrogen bonds defined for protein.
    1158 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: 0.99

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1094
        1.30 -     1.43: 1855
        1.43 -     1.56: 4029
        1.56 -     1.69: 6
        1.69 -     1.82: 83
  Bond restraints: 7067
  Sorted by residual:
  bond pdb=" C08BEIG R 501 "
       pdb=" N01BEIG R 501 "
    ideal  model  delta    sigma   weight residual
    1.448  1.271  0.177 2.00e-02 2.50e+03 7.83e+01
  bond pdb=" C17BEIG R 501 "
       pdb=" C19BEIG R 501 "
    ideal  model  delta    sigma   weight residual
    1.470  1.611 -0.141 2.00e-02 2.50e+03 4.98e+01
  bond pdb=" C08BEIG R 501 "
       pdb=" C09BEIG R 501 "
    ideal  model  delta    sigma   weight residual
    1.529  1.404  0.125 2.00e-02 2.50e+03 3.89e+01
  bond pdb=" C   LEU B 252 "
       pdb=" O   LEU B 252 "
    ideal  model  delta    sigma   weight residual
    1.235  1.169  0.066 1.22e-02 6.72e+03 2.97e+01
  bond pdb=" C17AEIG R 501 "
       pdb=" C20AEIG R 501 "
    ideal  model  delta    sigma   weight residual
    1.348  1.445 -0.097 2.00e-02 2.50e+03 2.35e+01
  ... (remaining 7062 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.04: 9565
        4.04 -     8.08: 60
        8.08 -    12.12: 6
       12.12 -    16.16: 0
       16.16 -    20.20: 1
  Bond angle restraints: 9632
  Sorted by residual:
  angle pdb=" C09BEIG R 501 "
        pdb=" C08BEIG R 501 "
        pdb=" C12BEIG R 501 "
      ideal   model   delta    sigma   weight residual
     114.95   94.75   20.20 3.00e+00 1.11e-01 4.53e+01
  angle pdb=" N   GLY B  64 "
        pdb=" CA  GLY B  64 "
        pdb=" C   GLY B  64 "
      ideal   model   delta    sigma   weight residual
     112.82  105.38    7.44 1.38e+00 5.25e-01 2.90e+01
  angle pdb=" N   ASN R 328 "
        pdb=" CA  ASN R 328 "
        pdb=" C   ASN R 328 "
      ideal   model   delta    sigma   weight residual
     112.54  106.25    6.29 1.22e+00 6.72e-01 2.66e+01
  angle pdb=" N   SER R 329 "
        pdb=" CA  SER R 329 "
        pdb=" C   SER R 329 "
      ideal   model   delta    sigma   weight residual
     112.23  105.84    6.39 1.26e+00 6.30e-01 2.57e+01
  angle pdb=" N   LYS C  32 "
        pdb=" CA  LYS C  32 "
        pdb=" C   LYS C  32 "
      ideal   model   delta    sigma   weight residual
     112.90  106.27    6.63 1.31e+00 5.83e-01 2.56e+01
  ... (remaining 9627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 4044
       17.02 -    34.03: 238
       34.03 -    51.05: 35
       51.05 -    68.07: 18
       68.07 -    85.09: 4
  Dihedral angle restraints: 4339
    sinusoidal: 1710
      harmonic: 2629
  Sorted by residual:
  dihedral pdb=" CA  PHE B 151 "
           pdb=" C   PHE B 151 "
           pdb=" N   LEU B 152 "
           pdb=" CA  LEU B 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.17   18.83     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  ASN B 293 "
           pdb=" C   ASN B 293 "
           pdb=" N   CYS B 294 "
           pdb=" CA  CYS B 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.67   16.33     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4336 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1069
       0.096 -    0.192: 68
       0.192 -    0.288: 1
       0.288 -    0.383: 1
       0.383 -    0.479: 1
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" C08BEIG R 501 "
            pdb=" C09BEIG R 501 "
            pdb=" C10BEIG R 501 "
            pdb=" C12BEIG R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.77   -2.29   -0.48 2.00e-01 2.50e+01 5.74e+00
  chirality pdb=" C14BEIG R 501 "
            pdb=" C13BEIG R 501 "
            pdb=" C15BEIG R 501 "
            pdb=" C17BEIG R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.26   -2.58    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C10AEIG R 501 "
            pdb=" C08AEIG R 501 "
            pdb=" C13AEIG R 501 "
            pdb=" N02AEIG R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1137 not shown)

  Planarity restraints: 1190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C14BEIG R 501 "   -0.022 2.00e-02 2.50e+03   4.86e-02 2.95e+01
        pdb=" C17BEIG R 501 "    0.016 2.00e-02 2.50e+03
        pdb=" C19BEIG R 501 "    0.029 2.00e-02 2.50e+03
        pdb=" C20BEIG R 501 "   -0.082 2.00e-02 2.50e+03
        pdb=" O03BEIG R 501 "    0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 251 "    0.413 9.50e-02 1.11e+02   1.85e-01 2.10e+01
        pdb=" NE  ARG B 251 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 251 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 251 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 251 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 252 "   -0.020 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   LEU B 252 "    0.071 2.00e-02 2.50e+03
        pdb=" O   LEU B 252 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   PHE B 253 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1187 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1007
        2.75 -     3.29: 7286
        3.29 -     3.83: 12842
        3.83 -     4.36: 16022
        4.36 -     4.90: 25912
  Nonbonded interactions: 63069
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASN B 110 "
            pdb=" NZ  LYS B 127 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OD2 ASP R 147 "
            pdb=" OH  TYR R 326 "
     model   vdw
     2.314 3.040
  ... (remaining 63064 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=0.43 max=1.00 mean=0.99
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:             0.660
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.940
  Find NCS groups from input model:        0.040
  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:7.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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      :  0.007   0.177   7068  Z= 0.421
  Angle     :  0.880  20.195   9634  Z= 0.534
  Chirality :  0.049   0.479   1140
  Planarity :  0.008   0.185   1190
  Dihedral  : 12.032  85.085   2630
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.30 %
    Favored  : 91.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.28), residues: 890
  helix:  1.29 (0.27), residues: 376
  sheet:  0.19 (0.37), residues: 175
  loop : -0.38 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 251 
 TYR   0.019   0.002   TYR R 326 
 PHE   0.015   0.002   PHE B 151 
 TRP   0.024   0.002   TRP R 192 
 HIS   0.010   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00719 ( 7067)
  covalent geometry    : angle       0.87975 ( 9632)
  SS BOND              : bond        0.00223 (    1)
  SS BOND              : angle       0.54843 (    2)
  hydrogen bonds       : bond        0.20224 (  398)
  hydrogen bonds       : angle       8.00504 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 165
  time to evaluate  : 0.283 
Fit side-chains
REVERT: B   75 GLN cc_start: 0.7678 (mm110) cc_final: 0.7038 (mm110)
REVERT: B   83 ASP cc_start: 0.8110 (t0) cc_final: 0.7830 (t0)
  outliers start: 7
  outliers final: 2
  residues processed: 168
  average time/residue: 0.5535
  time to fit residues: 97.7787
Evaluate side-chains
  155 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain R residue  160 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 259 GLN
B 293 ASN
B 340 ASN
R 109 ASN
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.126322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.111171 restraints weight = 19640.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.56
r_work: 0.3308 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7068  Z= 0.157
  Angle     :  0.575   5.566   9634  Z= 0.311
  Chirality :  0.042   0.158   1140
  Planarity :  0.004   0.037   1190
  Dihedral  :  6.368  54.979   1208
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 12.02 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.28), residues: 890
  helix:  1.92 (0.26), residues: 390
  sheet:  0.29 (0.38), residues: 165
  loop : -0.69 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 251 
 TYR   0.009   0.001   TYR B 124 
 PHE   0.015   0.002   PHE R 237 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7067)
  covalent geometry    : angle       0.57510 ( 9632)
  SS BOND              : bond        0.00314 (    1)
  SS BOND              : angle       0.66407 (    2)
  hydrogen bonds       : bond        0.04962 (  398)
  hydrogen bonds       : angle       5.51309 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  285 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7144 (mt)
REVERT: A  308 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6991 (mm-30)
REVERT: B   32 GLN cc_start: 0.7704 (mt0) cc_final: 0.7487 (mt0)
REVERT: B   75 GLN cc_start: 0.7686 (mm110) cc_final: 0.7113 (mm110)
REVERT: B   83 ASP cc_start: 0.8231 (t0) cc_final: 0.7970 (t0)
REVERT: R  230 ASN cc_start: 0.7857 (m-40) cc_final: 0.7569 (m-40)
REVERT: R  280 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7832 (mtt-85)
  outliers start: 17
  outliers final: 6
  residues processed: 173
  average time/residue: 0.5573
  time to fit residues: 101.1942
Evaluate side-chains
  159 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain R residue  160 THR
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  280 ARG
Chi-restraints excluded: chain R residue  316 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 195 HIS
A 269 ASN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 104 ASN
R 109 ASN
R 150 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.126504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.110426 restraints weight = 28112.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.27
r_work: 0.3239 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7068  Z= 0.149
  Angle     :  0.541   5.589   9634  Z= 0.291
  Chirality :  0.041   0.159   1140
  Planarity :  0.004   0.037   1190
  Dihedral  :  5.981  58.891   1208
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.02 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.28), residues: 890
  helix:  1.92 (0.26), residues: 392
  sheet:  0.04 (0.37), residues: 167
  loop : -0.75 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  15 
 TYR   0.011   0.001   TYR R 149 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7067)
  covalent geometry    : angle       0.54094 ( 9632)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       0.18569 (    2)
  hydrogen bonds       : bond        0.04642 (  398)
  hydrogen bonds       : angle       5.28422 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7253 (pt)
REVERT: A   53 MET cc_start: 0.4673 (mtm) cc_final: 0.3934 (mpp)
REVERT: A  207 GLU cc_start: 0.7212 (tp30) cc_final: 0.6768 (mm-30)
REVERT: A  285 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7090 (mt)
REVERT: A  308 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7005 (mm-30)
REVERT: B   75 GLN cc_start: 0.7645 (mm110) cc_final: 0.6762 (mm-40)
REVERT: B  228 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6859 (m-30)
REVERT: R  276 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7581 (ttp80)
REVERT: R  280 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7802 (mtt-85)
  outliers start: 16
  outliers final: 4
  residues processed: 164
  average time/residue: 0.5643
  time to fit residues: 97.2874
Evaluate side-chains
  157 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  160 THR
Chi-restraints excluded: chain R residue  276 ARG
Chi-restraints excluded: chain R residue  280 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 78 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0470
   chunk 9 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.6482

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
A 311 ASN
B 220 GLN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 109 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.127432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.111658 restraints weight = 30549.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.58
r_work: 0.3239 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3236
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3236
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7068  Z= 0.139
  Angle     :  0.529   5.818   9634  Z= 0.282
  Chirality :  0.041   0.159   1140
  Planarity :  0.004   0.036   1190
  Dihedral  :  5.610  54.615   1208
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.45 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.27), residues: 890
  helix:  1.82 (0.25), residues: 402
  sheet:  0.06 (0.37), residues: 165
  loop : -0.95 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.010   0.001   TYR R 326 
 PHE   0.011   0.001   PHE R 237 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7067)
  covalent geometry    : angle       0.52912 ( 9632)
  SS BOND              : bond        0.00227 (    1)
  SS BOND              : angle       0.06761 (    2)
  hydrogen bonds       : bond        0.04361 (  398)
  hydrogen bonds       : angle       5.15244 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7257 (pt)
REVERT: A   52 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6926 (mm110)
REVERT: A   53 MET cc_start: 0.4652 (mtm) cc_final: 0.3854 (mpp)
REVERT: A  285 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7032 (mt)
REVERT: B   44 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7495 (mp10)
REVERT: B   75 GLN cc_start: 0.7699 (mm110) cc_final: 0.6797 (mm-40)
REVERT: B   83 ASP cc_start: 0.8137 (t0) cc_final: 0.7899 (t0)
REVERT: B  228 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6812 (m-30)
REVERT: R  276 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7567 (ttp80)
  outliers start: 19
  outliers final: 6
  residues processed: 164
  average time/residue: 0.5376
  time to fit residues: 92.7457
Evaluate side-chains
  161 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  276 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0170
   chunk 72 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.5022

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 104 ASN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.124264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.107613 restraints weight = 29927.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.10
r_work: 0.3238 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3106
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7068  Z= 0.211
  Angle     :  0.611   6.450   9634  Z= 0.323
  Chirality :  0.044   0.167   1140
  Planarity :  0.004   0.034   1190
  Dihedral  :  5.958  58.323   1207
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.60 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.27), residues: 890
  helix:  1.64 (0.25), residues: 398
  sheet: -0.20 (0.36), residues: 177
  loop : -0.92 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 280 
 TYR   0.015   0.002   TYR R 149 
 PHE   0.016   0.002   PHE R 241 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.007   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 7067)
  covalent geometry    : angle       0.61061 ( 9632)
  SS BOND              : bond        0.00194 (    1)
  SS BOND              : angle       0.22049 (    2)
  hydrogen bonds       : bond        0.04933 (  398)
  hydrogen bonds       : angle       5.34734 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7282 (pt)
REVERT: A   53 MET cc_start: 0.4991 (mtm) cc_final: 0.4105 (mpp)
REVERT: A  207 GLU cc_start: 0.7363 (tp30) cc_final: 0.6897 (mm-30)
REVERT: A  285 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7088 (mt)
REVERT: A  308 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7046 (mm-30)
REVERT: B   44 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7717 (mt0)
REVERT: B   75 GLN cc_start: 0.7841 (mm110) cc_final: 0.6954 (mm-40)
REVERT: B   83 ASP cc_start: 0.8243 (t0) cc_final: 0.7939 (t0)
REVERT: R  243 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7944 (mpm)
  outliers start: 21
  outliers final: 6
  residues processed: 158
  average time/residue: 0.5945
  time to fit residues: 98.6386
Evaluate side-chains
  158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  316 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 195 HIS
A 269 ASN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.126567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.109873 restraints weight = 29416.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.09
r_work: 0.3289 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7068  Z= 0.150
  Angle     :  0.551   6.852   9634  Z= 0.294
  Chirality :  0.042   0.153   1140
  Planarity :  0.004   0.035   1190
  Dihedral  :  5.557  54.629   1207
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.03 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.27), residues: 890
  helix:  1.67 (0.25), residues: 401
  sheet: -0.20 (0.36), residues: 177
  loop : -0.96 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 280 
 TYR   0.010   0.001   TYR R 326 
 PHE   0.012   0.002   PHE R 237 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7067)
  covalent geometry    : angle       0.55126 ( 9632)
  SS BOND              : bond        0.00191 (    1)
  SS BOND              : angle       0.13686 (    2)
  hydrogen bonds       : bond        0.04374 (  398)
  hydrogen bonds       : angle       5.18773 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7268 (pt)
REVERT: A   52 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6945 (mm110)
REVERT: A   53 MET cc_start: 0.4944 (mtm) cc_final: 0.4097 (mpp)
REVERT: A  207 GLU cc_start: 0.7440 (tp30) cc_final: 0.6996 (mm-30)
REVERT: A  285 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7038 (mt)
REVERT: A  308 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6960 (mm-30)
REVERT: B   44 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7701 (mp10)
REVERT: B   75 GLN cc_start: 0.7830 (mm110) cc_final: 0.6939 (mm-40)
REVERT: B   83 ASP cc_start: 0.8241 (t0) cc_final: 0.7949 (t0)
REVERT: B  220 GLN cc_start: 0.8370 (mt0) cc_final: 0.8160 (mt0)
REVERT: R  343 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6962 (m-80)
  outliers start: 14
  outliers final: 4
  residues processed: 153
  average time/residue: 0.6050
  time to fit residues: 97.2299
Evaluate side-chains
  154 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  343 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.0570
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 86 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.128425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.112411 restraints weight = 20997.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.78
r_work: 0.3328 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7068  Z= 0.129
  Angle     :  0.522   6.840   9634  Z= 0.278
  Chirality :  0.041   0.155   1140
  Planarity :  0.003   0.036   1190
  Dihedral  :  5.331  55.057   1207
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.88 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.27), residues: 890
  helix:  1.79 (0.25), residues: 401
  sheet: -0.09 (0.37), residues: 175
  loop : -0.91 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 208 
 TYR   0.014   0.001   TYR R 149 
 PHE   0.012   0.001   PHE R 237 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7067)
  covalent geometry    : angle       0.52176 ( 9632)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       0.12824 (    2)
  hydrogen bonds       : bond        0.04148 (  398)
  hydrogen bonds       : angle       5.04504 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7646 (tp30)
REVERT: A   19 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7228 (pt)
REVERT: A   52 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6974 (mm110)
REVERT: A   53 MET cc_start: 0.4846 (mtm) cc_final: 0.4065 (mpp)
REVERT: A  207 GLU cc_start: 0.7430 (tp30) cc_final: 0.6920 (mm-30)
REVERT: A  285 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7042 (mt)
REVERT: A  308 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6957 (mm-30)
REVERT: B   75 GLN cc_start: 0.7786 (mm110) cc_final: 0.6862 (mm-40)
REVERT: B   83 ASP cc_start: 0.8199 (t0) cc_final: 0.7933 (t0)
REVERT: B  220 GLN cc_start: 0.8349 (mt0) cc_final: 0.8133 (mt0)
REVERT: R  243 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7583 (mpm)
REVERT: R  276 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7640 (ttp80)
REVERT: R  343 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6944 (m-80)
  outliers start: 13
  outliers final: 5
  residues processed: 159
  average time/residue: 0.6051
  time to fit residues: 101.0173
Evaluate side-chains
  157 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  282 VAL
Chi-restraints excluded: chain R residue  343 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 69 optimal weight:    0.5980
   chunk 12 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B  32 GLN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.128705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.112927 restraints weight = 25007.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.10
r_work: 0.3300 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7068  Z= 0.131
  Angle     :  0.528   6.914   9634  Z= 0.282
  Chirality :  0.041   0.173   1140
  Planarity :  0.003   0.037   1190
  Dihedral  :  5.353  54.419   1207
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 20.60 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.27), residues: 890
  helix:  1.76 (0.25), residues: 401
  sheet: -0.05 (0.38), residues: 170
  loop : -0.96 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 280 
 TYR   0.008   0.001   TYR R 128 
 PHE   0.012   0.001   PHE R 237 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7067)
  covalent geometry    : angle       0.52852 ( 9632)
  SS BOND              : bond        0.00144 (    1)
  SS BOND              : angle       0.04504 (    2)
  hydrogen bonds       : bond        0.04127 (  398)
  hydrogen bonds       : angle       5.04125 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7724 (tp30)
REVERT: A   52 GLN cc_start: 0.7243 (mm-40) cc_final: 0.7021 (mm110)
REVERT: A   53 MET cc_start: 0.4781 (mtm) cc_final: 0.3991 (mpp)
REVERT: A  207 GLU cc_start: 0.7409 (tp30) cc_final: 0.6872 (mm-30)
REVERT: A  285 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7052 (mt)
REVERT: A  308 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6974 (mm-30)
REVERT: B   44 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7777 (mt0)
REVERT: B   75 GLN cc_start: 0.7857 (mm110) cc_final: 0.6931 (mm-40)
REVERT: B   83 ASP cc_start: 0.8247 (t0) cc_final: 0.7913 (t0)
REVERT: B  220 GLN cc_start: 0.8360 (mt0) cc_final: 0.8080 (mt0)
REVERT: R  276 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7705 (ttp80)
REVERT: R  343 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6918 (m-80)
  outliers start: 12
  outliers final: 5
  residues processed: 154
  average time/residue: 0.6030
  time to fit residues: 97.5932
Evaluate side-chains
  156 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  267 PHE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  343 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0770
   chunk 47 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B  17 GLN
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.128878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.113178 restraints weight = 26221.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.25
r_work: 0.3288 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7068  Z= 0.132
  Angle     :  0.534   6.836   9634  Z= 0.284
  Chirality :  0.041   0.166   1140
  Planarity :  0.003   0.037   1190
  Dihedral  :  5.349  55.425   1205
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.89 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.27), residues: 890
  helix:  1.70 (0.25), residues: 402
  sheet: -0.03 (0.37), residues: 175
  loop : -0.90 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 208 
 TYR   0.017   0.001   TYR R 149 
 PHE   0.012   0.001   PHE R 237 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7067)
  covalent geometry    : angle       0.53447 ( 9632)
  SS BOND              : bond        0.00145 (    1)
  SS BOND              : angle       0.02849 (    2)
  hydrogen bonds       : bond        0.04174 (  398)
  hydrogen bonds       : angle       5.03556 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7447 (tp30)
REVERT: A   52 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6876 (mm110)
REVERT: A   53 MET cc_start: 0.4684 (mtm) cc_final: 0.3958 (mpp)
REVERT: A  207 GLU cc_start: 0.7316 (tp30) cc_final: 0.6812 (mm-30)
REVERT: A  285 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7000 (mt)
REVERT: A  308 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6846 (mm-30)
REVERT: B   44 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7497 (mt0)
REVERT: B   75 GLN cc_start: 0.7650 (mm110) cc_final: 0.7238 (mm110)
REVERT: R  243 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7290 (mpm)
REVERT: R  276 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7573 (ttp80)
REVERT: R  343 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6847 (m-80)
  outliers start: 13
  outliers final: 6
  residues processed: 157
  average time/residue: 0.5821
  time to fit residues: 95.9805
Evaluate side-chains
  158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  267 PHE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  343 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B  17 GLN
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.127252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.111793 restraints weight = 20066.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.64
r_work: 0.3314 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7068  Z= 0.161
  Angle     :  0.576   7.614   9634  Z= 0.307
  Chirality :  0.042   0.177   1140
  Planarity :  0.004   0.037   1190
  Dihedral  :  5.546  55.624   1205
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.60 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.27), residues: 890
  helix:  1.55 (0.25), residues: 402
  sheet: -0.14 (0.37), residues: 179
  loop : -0.90 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 280 
 TYR   0.010   0.001   TYR R 326 
 PHE   0.013   0.002   PHE A 189 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7067)
  covalent geometry    : angle       0.57647 ( 9632)
  SS BOND              : bond        0.00168 (    1)
  SS BOND              : angle       0.12868 (    2)
  hydrogen bonds       : bond        0.04453 (  398)
  hydrogen bonds       : angle       5.14931 ( 1158)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7659 (tp30)
REVERT: A   52 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6938 (mm110)
REVERT: A   53 MET cc_start: 0.4914 (mtm) cc_final: 0.4114 (mpp)
REVERT: A  207 GLU cc_start: 0.7376 (tp30) cc_final: 0.6976 (mm-30)
REVERT: A  285 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.6992 (mt)
REVERT: A  308 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6973 (mm-30)
REVERT: B   44 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7694 (mt0)
REVERT: B   75 GLN cc_start: 0.7770 (mm110) cc_final: 0.6840 (mm-40)
REVERT: B   83 ASP cc_start: 0.8243 (t0) cc_final: 0.7949 (t0)
REVERT: R  243 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7656 (mpm)
REVERT: R  276 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7640 (ttp80)
REVERT: R  343 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6890 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 156
  average time/residue: 0.5828
  time to fit residues: 95.4869
Evaluate side-chains
  164 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  267 PHE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  255 MET
Chi-restraints excluded: chain R residue  343 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0970
   chunk 27 optimal weight:    7.9990
   chunk 76 optimal weight:    0.0770
   chunk 54 optimal weight:    0.5980
   chunk 10 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.1540

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 188 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.125953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.109182 restraints weight = 29075.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.10
r_work: 0.3262 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7068  Z= 0.184
  Angle     :  0.601   6.950   9634  Z= 0.319
  Chirality :  0.043   0.176   1140
  Planarity :  0.004   0.037   1190
  Dihedral  :  5.732  56.285   1205
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.89 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.27), residues: 890
  helix:  1.45 (0.25), residues: 400
  sheet: -0.17 (0.37), residues: 178
  loop : -0.87 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 280 
 TYR   0.017   0.002   TYR R 149 
 PHE   0.014   0.002   PHE A 189 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7067)
  covalent geometry    : angle       0.60155 ( 9632)
  SS BOND              : bond        0.00159 (    1)
  SS BOND              : angle       0.18886 (    2)
  hydrogen bonds       : bond        0.04666 (  398)
  hydrogen bonds       : angle       5.24450 ( 1158)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3278.31 seconds
wall clock time: 56 minutes 42.92 seconds (3402.92 seconds total)