Starting phenix.real_space_refine
on Sun May 11 12:49:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8flt_29286/05_2025/8flt_29286_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8flt_29286/05_2025/8flt_29286.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8flt_29286/05_2025/8flt_29286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8flt_29286/05_2025/8flt_29286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8flt_29286/05_2025/8flt_29286_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8flt_29286/05_2025/8flt_29286_neut.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.101
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      49      5.16       5
     C    5154      2.51       5
     N    1404      2.21       5
     O    1479      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8086
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1874
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 2574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2574
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "G"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 396
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "N"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 948
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "P"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 120
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'HRG:plan-2': 1, 'AIB:plan-1': 2}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 2174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2174
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 261}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 5.04, per 1000 atoms: 0.62
  Number of scatterers: 8086
  At special positions: 0
  Unit cell: (81.6, 96.9, 130.9, 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      49     16.00
     O    1479      8.00
     N    1404      7.00
     C    5154      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 281 " - pdb=" SG  CYS R 351 " 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: 2.11
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      44.1% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.596A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 3.618A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.548A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.339A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.674A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.703A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 9 through 25
      removed outlier: 3.505A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.502A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 14
    Processing helix  chain 'R' and resid 178 through 212
    Processing helix  chain 'R' and resid 217 through 246
      removed outlier: 3.797A  pdb=" N   SER R 246 " --> pdb=" O   ALA R 242 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 311
      removed outlier: 3.735A  pdb=" N   ASN R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE R 310 " --> pdb=" O   LEU R 306 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 347
      removed outlier: 3.807A  pdb=" N   TYR R 320 " --> pdb=" O   SER R 316 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   TRP R 322 " --> pdb=" O   LYS R 318 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   GLY R 323 " --> pdb=" O   LYS R 319 " (cutoff:3.500A)
      Proline residue:  R 332  - end of helix
    Processing helix  chain 'R' and resid 360 through 391
      Proline residue:  R 366  - end of helix
    Processing helix  chain 'R' and resid 400 through 418
      Proline residue:  R 415  - end of helix
    Processing helix  chain 'R' and resid 419 through 424
      removed outlier: 3.560A  pdb=" N   VAL R 423 " --> pdb=" O   HIS R 420 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 434 through 460
      removed outlier: 4.273A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 478
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.604A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.556A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.563A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.216A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.546A  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: 6.048A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.907A  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: 7.015A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.275A  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: 5.977A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.692A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.548A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1293 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: 2.20

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1305
        1.32 -     1.44: 2356
        1.44 -     1.56: 4529
        1.56 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8260
  Sorted by residual:
  bond pdb=" CZ  HRG P  11 "
       pdb=" NH1 HRG P  11 "
    ideal  model  delta    sigma   weight residual
    1.282  1.435 -0.153 2.00e-02 2.50e+03 5.85e+01
  bond pdb=" NE  HRG P  11 "
       pdb=" CZ  HRG P  11 "
    ideal  model  delta    sigma   weight residual
    1.371  1.451 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" CZ  HRG P  11 "
       pdb=" NH2 HRG P  11 "
    ideal  model  delta    sigma   weight residual
    1.380  1.311  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" C   PRO N 100 "
       pdb=" O   PRO N 100 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.36e-02 5.41e+03 1.03e+01
  bond pdb=" CA  ALA N 101 "
       pdb=" CB  ALA N 101 "
    ideal  model  delta    sigma   weight residual
    1.536  1.493  0.043 1.48e-02 4.57e+03 8.52e+00
  ... (remaining 8255 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 10866
        1.64 -     3.28: 273
        3.28 -     4.92: 44
        4.92 -     6.57: 17
        6.57 -     8.21: 4
  Bond angle restraints: 11204
  Sorted by residual:
  angle pdb=" N   PRO N 100 "
        pdb=" CA  PRO N 100 "
        pdb=" CB  PRO N 100 "
      ideal   model   delta    sigma   weight residual
     103.19   98.21    4.98 1.00e+00 1.00e+00 2.48e+01
  angle pdb=" CA  PHE N 108 "
        pdb=" CB  PHE N 108 "
        pdb=" CG  PHE N 108 "
      ideal   model   delta    sigma   weight residual
     113.80  118.50   -4.70 1.00e+00 1.00e+00 2.21e+01
  angle pdb=" C   ILE R 190 "
        pdb=" N   TYR R 191 "
        pdb=" CA  TYR R 191 "
      ideal   model   delta    sigma   weight residual
     121.14  114.06    7.08 1.75e+00 3.27e-01 1.64e+01
  angle pdb=" N   VAL A 224 "
        pdb=" CA  VAL A 224 "
        pdb=" C   VAL A 224 "
      ideal   model   delta    sigma   weight residual
     106.55  111.71   -5.16 1.45e+00 4.76e-01 1.26e+01
  angle pdb=" CA  ASN N  35 "
        pdb=" C   ASN N  35 "
        pdb=" O   ASN N  35 "
      ideal   model   delta    sigma   weight residual
     120.99  117.02    3.97 1.12e+00 7.97e-01 1.26e+01
  ... (remaining 11199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4436
       17.86 -    35.73: 331
       35.73 -    53.59: 65
       53.59 -    71.45: 14
       71.45 -    89.32: 5
  Dihedral angle restraints: 4851
    sinusoidal: 1859
      harmonic: 2992
  Sorted by residual:
  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  160.00   20.00     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  LEU A 291 "
           pdb=" C   LEU A 291 "
           pdb=" N   ASN A 292 "
           pdb=" CA  ASN A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.24  -19.76     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.57   19.43     0      5.00e+00 4.00e-02 1.51e+01
  ... (remaining 4848 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 963
       0.049 -    0.097: 244
       0.097 -    0.146: 43
       0.146 -    0.195: 6
       0.195 -    0.244: 1
  Chirality restraints: 1257
  Sorted by residual:
  chirality pdb=" CA  ARG N  98 "
            pdb=" N   ARG N  98 "
            pdb=" C   ARG N  98 "
            pdb=" CB  ARG N  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  PHE R 335 "
            pdb=" N   PHE R 335 "
            pdb=" C   PHE R 335 "
            pdb=" CB  PHE R 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.56e-01
  chirality pdb=" CA  ASN N  35 "
            pdb=" N   ASN N  35 "
            pdb=" C   ASN N  35 "
            pdb=" CB  ASN N  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.36e-01
  ... (remaining 1254 not shown)

  Planarity restraints: 1422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN N  35 "   -0.014 2.00e-02 2.50e+03   2.93e-02 8.60e+00
        pdb=" C   ASN N  35 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ASN N  35 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   TRP N  36 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG N 105 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.06e+00
        pdb=" C   ARG N 105 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ARG N 105 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASP N 106 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN N  31 "    0.011 2.00e-02 2.50e+03   2.12e-02 4.51e+00
        pdb=" C   ASN N  31 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ASN N  31 "    0.014 2.00e-02 2.50e+03
        pdb=" N   TYR N  32 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1419 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 534
        2.74 -     3.28: 8260
        3.28 -     3.82: 13888
        3.82 -     4.36: 17350
        4.36 -     4.90: 29676
  Nonbonded interactions: 69708
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 227 "
            pdb=" O   PRO N 100 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" N   AIB P   1 "
            pdb=" O   THR R 427 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" NE2 HIS B 311 "
            pdb=" OG1 THR B 329 "
     model   vdw
     2.267 3.120
  ... (remaining 69703 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  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:          0.370
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.220
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.153   8263  Z= 0.226
  Angle     :  0.667   8.208  11210  Z= 0.399
  Chirality :  0.044   0.244   1257
  Planarity :  0.004   0.049   1422
  Dihedral  : 13.483  89.317   2910
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.83 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 1005
  helix:  1.84 (0.27), residues: 399
  sheet: -0.56 (0.33), residues: 217
  loop : -0.33 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 298 
 HIS   0.008   0.002   HIS A 357 
 PHE   0.026   0.002   PHE R 335 
 TYR   0.012   0.002   TYR B  59 
 ARG   0.005   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14119 (  454)
  hydrogen bonds       : angle       6.35044 ( 1293)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       1.67729 (    6)
  covalent geometry    : bond        0.00441 ( 8260)
  covalent geometry    : angle       0.66582 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.838 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 129
  average time/residue: 0.2363
  time to fit residues: 40.0054
Evaluate side-chains
  114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  108 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.1980
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 440 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.159424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.135661 restraints weight = 8887.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.33
r_work: 0.3325 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.0938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8263  Z= 0.131
  Angle     :  0.515   5.528  11210  Z= 0.288
  Chirality :  0.042   0.178   1257
  Planarity :  0.004   0.039   1422
  Dihedral  :  5.218  58.096   1128
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  5.31 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.27), residues: 1005
  helix:  2.45 (0.26), residues: 397
  sheet: -0.58 (0.33), residues: 219
  loop : -0.21 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 298 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.030   0.002   PHE R 335 
 TYR   0.024   0.001   TYR R 191 
 ARG   0.004   0.000   ARG A 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04449 (  454)
  hydrogen bonds       : angle       4.74011 ( 1293)
  SS BOND              : bond        0.00526 (    3)
  SS BOND              : angle       1.73004 (    6)
  covalent geometry    : bond        0.00283 ( 8260)
  covalent geometry    : angle       0.51374 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.877 
Fit side-chains
REVERT: B  138 GLU cc_start: 0.7278 (tt0) cc_final: 0.6984 (pm20)
REVERT: N   95 TYR cc_start: 0.7812 (m-80) cc_final: 0.7599 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 125
  average time/residue: 0.2425
  time to fit residues: 39.8814
Evaluate side-chains
  118 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0980
   chunk 30 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 53 optimal weight:    0.1980
   chunk 32 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B 110 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.162141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.138218 restraints weight = 9007.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.39
r_work: 0.3340 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8263  Z= 0.109
  Angle     :  0.477   5.621  11210  Z= 0.267
  Chirality :  0.041   0.171   1257
  Planarity :  0.003   0.040   1422
  Dihedral  :  4.968  58.360   1128
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  7.32 %
    Favored  : 91.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.27), residues: 1005
  helix:  2.73 (0.26), residues: 389
  sheet: -0.46 (0.34), residues: 206
  loop : -0.05 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 298 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.028   0.001   PHE R 335 
 TYR   0.026   0.001   TYR R 191 
 ARG   0.006   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  454)
  hydrogen bonds       : angle       4.48839 ( 1293)
  SS BOND              : bond        0.00482 (    3)
  SS BOND              : angle       1.80744 (    6)
  covalent geometry    : bond        0.00227 ( 8260)
  covalent geometry    : angle       0.47490 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A  374 ARG cc_start: 0.6705 (mtm-85) cc_final: 0.6356 (ttm170)
REVERT: A  378 ASP cc_start: 0.7031 (m-30) cc_final: 0.6773 (m-30)
REVERT: B  135 VAL cc_start: 0.7429 (t) cc_final: 0.7155 (p)
REVERT: B  138 GLU cc_start: 0.7334 (tt0) cc_final: 0.6857 (pm20)
  outliers start: 8
  outliers final: 5
  residues processed: 127
  average time/residue: 0.2302
  time to fit residues: 38.5622
Evaluate side-chains
  116 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.0164

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 377 ASN
B  75 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.157913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.132854 restraints weight = 8991.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.43
r_work: 0.3264 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8263  Z= 0.157
  Angle     :  0.526   5.525  11210  Z= 0.291
  Chirality :  0.042   0.180   1257
  Planarity :  0.004   0.042   1422
  Dihedral  :  5.112  58.267   1128
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  7.79 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.27), residues: 1005
  helix:  2.49 (0.26), residues: 395
  sheet: -0.48 (0.33), residues: 219
  loop : -0.14 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 298 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.029   0.002   PHE R 335 
 TYR   0.025   0.001   TYR R 191 
 ARG   0.005   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04337 (  454)
  hydrogen bonds       : angle       4.56217 ( 1293)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       1.78725 (    6)
  covalent geometry    : bond        0.00358 ( 8260)
  covalent geometry    : angle       0.52440 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A  374 ARG cc_start: 0.7005 (mtm-85) cc_final: 0.6558 (ttm170)
REVERT: A  378 ASP cc_start: 0.7083 (m-30) cc_final: 0.6855 (m-30)
REVERT: B  135 VAL cc_start: 0.7701 (t) cc_final: 0.7388 (p)
REVERT: B  138 GLU cc_start: 0.7499 (tt0) cc_final: 0.7050 (pm20)
REVERT: N   19 ARG cc_start: 0.7458 (ttt90) cc_final: 0.7221 (ttm170)
REVERT: N   95 TYR cc_start: 0.7859 (m-80) cc_final: 0.7598 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 129
  average time/residue: 0.2372
  time to fit residues: 40.1304
Evaluate side-chains
  124 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0870
   chunk 9 optimal weight:    0.1980
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.160374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.135798 restraints weight = 8964.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.41
r_work: 0.3311 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8263  Z= 0.114
  Angle     :  0.482   5.522  11210  Z= 0.269
  Chirality :  0.041   0.172   1257
  Planarity :  0.003   0.041   1422
  Dihedral  :  4.924  59.151   1128
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.38 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.27), residues: 1005
  helix:  2.80 (0.26), residues: 389
  sheet: -0.41 (0.33), residues: 219
  loop :  0.00 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 298 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.029   0.001   PHE R 335 
 TYR   0.025   0.001   TYR R 191 
 ARG   0.005   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  454)
  hydrogen bonds       : angle       4.40083 ( 1293)
  SS BOND              : bond        0.00588 (    3)
  SS BOND              : angle       2.09811 (    6)
  covalent geometry    : bond        0.00246 ( 8260)
  covalent geometry    : angle       0.47931 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  374 ARG cc_start: 0.6834 (mtm-85) cc_final: 0.6446 (ttm170)
REVERT: A  378 ASP cc_start: 0.7019 (m-30) cc_final: 0.6779 (m-30)
REVERT: B  135 VAL cc_start: 0.7652 (t) cc_final: 0.7419 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 126
  average time/residue: 0.2339
  time to fit residues: 38.5426
Evaluate side-chains
  120 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0070
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.159769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.134959 restraints weight = 8930.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.43
r_work: 0.3297 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8263  Z= 0.123
  Angle     :  0.487   5.477  11210  Z= 0.271
  Chirality :  0.041   0.174   1257
  Planarity :  0.003   0.045   1422
  Dihedral  :  4.885  58.453   1128
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.68 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.27), residues: 1005
  helix:  2.92 (0.26), residues: 383
  sheet: -0.50 (0.33), residues: 223
  loop :  0.04 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 298 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.029   0.001   PHE R 335 
 TYR   0.024   0.001   TYR R 191 
 ARG   0.003   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  454)
  hydrogen bonds       : angle       4.42693 ( 1293)
  SS BOND              : bond        0.00419 (    3)
  SS BOND              : angle       1.56934 (    6)
  covalent geometry    : bond        0.00272 ( 8260)
  covalent geometry    : angle       0.48558 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A  374 ARG cc_start: 0.6871 (mtm-85) cc_final: 0.6476 (ttm170)
REVERT: A  378 ASP cc_start: 0.7085 (m-30) cc_final: 0.6836 (m-30)
REVERT: B  135 VAL cc_start: 0.7746 (t) cc_final: 0.7513 (p)
REVERT: B  197 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7797 (mmm160)
  outliers start: 11
  outliers final: 10
  residues processed: 122
  average time/residue: 0.2416
  time to fit residues: 38.5487
Evaluate side-chains
  124 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  384 VAL
Chi-restraints excluded: chain R residue  392 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0020
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.160828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.136107 restraints weight = 8960.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.42
r_work: 0.3311 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8263  Z= 0.111
  Angle     :  0.477   6.661  11210  Z= 0.266
  Chirality :  0.040   0.171   1257
  Planarity :  0.003   0.045   1422
  Dihedral  :  4.788  58.332   1128
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  9.80 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.27), residues: 1005
  helix:  3.03 (0.26), residues: 383
  sheet: -0.49 (0.32), residues: 223
  loop :  0.07 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.028   0.001   PHE R 335 
 TYR   0.023   0.001   TYR R 191 
 ARG   0.007   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  454)
  hydrogen bonds       : angle       4.34201 ( 1293)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       1.49041 (    6)
  covalent geometry    : bond        0.00240 ( 8260)
  covalent geometry    : angle       0.47598 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A  378 ASP cc_start: 0.6919 (m-30) cc_final: 0.6685 (m-30)
REVERT: B  135 VAL cc_start: 0.7698 (t) cc_final: 0.7487 (p)
REVERT: B  197 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7760 (mmm160)
REVERT: R  189 MET cc_start: 0.6783 (mpp) cc_final: 0.6238 (ppp)
  outliers start: 14
  outliers final: 10
  residues processed: 127
  average time/residue: 0.2367
  time to fit residues: 39.2968
Evaluate side-chains
  130 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  384 VAL
Chi-restraints excluded: chain R residue  392 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 82 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.157023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.131574 restraints weight = 9042.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.35
r_work: 0.3257 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8263  Z= 0.182
  Angle     :  0.543   5.669  11210  Z= 0.301
  Chirality :  0.043   0.181   1257
  Planarity :  0.004   0.044   1422
  Dihedral  :  5.026  58.017   1128
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.39 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.27), residues: 1005
  helix:  2.55 (0.26), residues: 395
  sheet: -0.61 (0.32), residues: 224
  loop : -0.12 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 298 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.030   0.002   PHE R 335 
 TYR   0.021   0.002   TYR R 191 
 ARG   0.006   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04381 (  454)
  hydrogen bonds       : angle       4.57784 ( 1293)
  SS BOND              : bond        0.00302 (    3)
  SS BOND              : angle       1.71108 (    6)
  covalent geometry    : bond        0.00425 ( 8260)
  covalent geometry    : angle       0.54186 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A  374 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.7052 (mtm-85)
REVERT: A  378 ASP cc_start: 0.7093 (m-30) cc_final: 0.6849 (m-30)
REVERT: A  392 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6584 (mt-10)
REVERT: N   20 LEU cc_start: 0.7797 (mt) cc_final: 0.7568 (mp)
REVERT: N   95 TYR cc_start: 0.7853 (m-80) cc_final: 0.7544 (m-80)
REVERT: R  189 MET cc_start: 0.6796 (mpp) cc_final: 0.6255 (ppp)
REVERT: R  321 LEU cc_start: 0.7807 (tp) cc_final: 0.7588 (tp)
  outliers start: 14
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2382
  time to fit residues: 38.3664
Evaluate side-chains
  127 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  384 VAL
Chi-restraints excluded: chain R residue  392 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 26 optimal weight:    0.4980
   chunk 76 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0670
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.158904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.132418 restraints weight = 9138.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 1.40
r_work: 0.3283 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8263  Z= 0.130
  Angle     :  0.499   5.845  11210  Z= 0.278
  Chirality :  0.041   0.174   1257
  Planarity :  0.003   0.042   1422
  Dihedral  :  4.918  58.833   1128
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.63 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.27), residues: 1005
  helix:  2.77 (0.26), residues: 389
  sheet: -0.56 (0.33), residues: 223
  loop :  0.01 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 298 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.029   0.002   PHE R 335 
 TYR   0.022   0.001   TYR R 191 
 ARG   0.004   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  454)
  hydrogen bonds       : angle       4.47511 ( 1293)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       1.39213 (    6)
  covalent geometry    : bond        0.00288 ( 8260)
  covalent geometry    : angle       0.49768 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A  374 ARG cc_start: 0.7252 (mtm-85) cc_final: 0.7017 (mtm-85)
REVERT: A  378 ASP cc_start: 0.7087 (m-30) cc_final: 0.6834 (m-30)
REVERT: A  392 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6468 (mt-10)
REVERT: B   44 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8185 (mm-40)
REVERT: N   20 LEU cc_start: 0.7653 (mt) cc_final: 0.7336 (mt)
REVERT: R  321 LEU cc_start: 0.7797 (tp) cc_final: 0.7572 (tp)
  outliers start: 14
  outliers final: 12
  residues processed: 123
  average time/residue: 0.2403
  time to fit residues: 38.9091
Evaluate side-chains
  129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  384 VAL
Chi-restraints excluded: chain R residue  392 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 60 optimal weight:    0.1980
   chunk 18 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.160897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.137062 restraints weight = 8923.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.34
r_work: 0.3312 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8263  Z= 0.116
  Angle     :  0.483   6.041  11210  Z= 0.270
  Chirality :  0.041   0.172   1257
  Planarity :  0.003   0.042   1422
  Dihedral  :  4.776  58.819   1128
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.51 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.27), residues: 1005
  helix:  2.99 (0.26), residues: 383
  sheet: -0.52 (0.33), residues: 223
  loop :  0.06 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 298 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.029   0.001   PHE R 335 
 TYR   0.023   0.001   TYR R 191 
 ARG   0.004   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  454)
  hydrogen bonds       : angle       4.40030 ( 1293)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       1.31772 (    6)
  covalent geometry    : bond        0.00251 ( 8260)
  covalent geometry    : angle       0.48173 (11204)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  374 ARG cc_start: 0.7256 (mtm-85) cc_final: 0.7022 (mtm-85)
REVERT: A  378 ASP cc_start: 0.7022 (m-30) cc_final: 0.6770 (m-30)
REVERT: A  392 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6450 (mt-10)
REVERT: B   44 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8158 (mm-40)
REVERT: N   20 LEU cc_start: 0.7635 (mt) cc_final: 0.7311 (mt)
REVERT: R  321 LEU cc_start: 0.7805 (tp) cc_final: 0.7585 (tp)
  outliers start: 12
  outliers final: 11
  residues processed: 126
  average time/residue: 0.2521
  time to fit residues: 41.6317
Evaluate side-chains
  128 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0070
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.2004

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.157457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.130550 restraints weight = 9060.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.40
r_work: 0.3257 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8263  Z= 0.173
  Angle     :  0.545   6.291  11210  Z= 0.301
  Chirality :  0.043   0.181   1257
  Planarity :  0.004   0.043   1422
  Dihedral  :  5.026  58.697   1128
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.10 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.27), residues: 1005
  helix:  2.66 (0.26), residues: 389
  sheet: -0.61 (0.33), residues: 224
  loop : -0.05 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 298 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.030   0.002   PHE R 335 
 TYR   0.022   0.002   TYR R 191 
 ARG   0.004   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04343 (  454)
  hydrogen bonds       : angle       4.57543 ( 1293)
  SS BOND              : bond        0.00272 (    3)
  SS BOND              : angle       1.57591 (    6)
  covalent geometry    : bond        0.00400 ( 8260)
  covalent geometry    : angle       0.54405 (11204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4734.00 seconds
wall clock time: 82 minutes 29.80 seconds (4949.80 seconds total)