Starting phenix.real_space_refine
on Sat Aug 23 01:12:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yn9_39419/08_2025/8yn9_39419.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yn9_39419/08_2025/8yn9_39419.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yn9_39419/08_2025/8yn9_39419.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yn9_39419/08_2025/8yn9_39419.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yn9_39419/08_2025/8yn9_39419.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yn9_39419/08_2025/8yn9_39419.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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      58      5.16       5
     C    5853      2.51       5
     N    1490      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9048
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1770
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'GLU:plan': 6}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1779
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2235
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 9, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 6}
          Unresolved non-hydrogen planarities: 24
    Chain: "R"
      Number of atoms: 206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 206
          Unusual residues: {'CLR': 7, 'HSM': 1}
          Classifications: {'undetermined': 8, 'water': 2}
          Link IDs: {None: 9}
  Time building chain proxies: 2.46, per 1000 atoms: 0.27
  Number of scatterers: 9048
  At special positions: 0
  Unit cell: (100.58, 118.77, 111.28, 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      58     16.00
     O    1647      8.00
     N    1490      7.00
     C    5853      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  87 " - pdb=" SG  CYS R 164 " 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: 0.77
  Conformation dependent library (CDL) restraints added in 277.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      39.1% alpha, 24.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.539A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.374A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.746A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.625A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
      removed outlier: 3.525A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'R' and resid 12 through 43
      removed outlier: 4.019A  pdb=" N   VAL R  36 " --> pdb=" O   GLY R  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 63
    Processing helix  chain 'R' and resid 67 through 78
      Proline residue:  R  74  - end of helix
    Processing helix  chain 'R' and resid 83 through 118
      removed outlier: 3.731A  pdb=" N   VAL R  88 " --> pdb=" O   LYS R  84 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 118 through 125
    Processing helix  chain 'R' and resid 128 through 155
      removed outlier: 3.531A  pdb=" N   TRP R 140 " --> pdb=" O   MET R 136 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ASN R 147 " --> pdb=" O   ALA R 143 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
    Processing helix  chain 'R' and resid 156 through 158
      No H-bonds generated for 'chain 'R' and resid 156 through 158'
    Processing helix  chain 'R' and resid 166 through 170
      removed outlier: 3.772A  pdb=" N   SER R 170 " --> pdb=" O   GLY R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 183
      removed outlier: 3.564A  pdb=" N   LEU R 175 " --> pdb=" O   GLU R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 200
    Processing helix  chain 'R' and resid 292 through 329
      removed outlier: 3.518A  pdb=" N   PHE R 312 " --> pdb=" O   LEU R 308 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 3.856A  pdb=" N   ILE R 324 " --> pdb=" O   SER R 320 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 337 through 358
      removed outlier: 3.594A  pdb=" N   GLN R 347 " --> pdb=" O   ALA R 343 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   TRP R 348 " --> pdb=" O   PHE R 344 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN R 350 " --> pdb=" O   LEU R 346 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   SER R 351 " --> pdb=" O   GLN R 347 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   PHE R 352 " --> pdb=" O   TRP R 348 " (cutoff:3.500A)
      Proline residue:  R 355  - end of helix
    Processing helix  chain 'R' and resid 362 through 374
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.226A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.573A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.737A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.860A  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: 5.986A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.090A  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: 6.261A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.651A  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: 6.784A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.295A  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: 3.514A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.844A  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: 3.604A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 5.936A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.352A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.499A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148
      removed outlier: 4.015A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1314 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2829
        1.34 -     1.46: 2014
        1.46 -     1.58: 4341
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 9268
  Sorted by residual:
  bond pdb=" CG  HSM R 701 "
       pdb=" ND1 HSM R 701 "
    ideal  model  delta    sigma   weight residual
    1.383  1.336  0.047 2.00e-02 2.50e+03 5.63e+00
  bond pdb=" C5  CLR R 703 "
       pdb=" C6  CLR R 703 "
    ideal  model  delta    sigma   weight residual
    1.332  1.297  0.035 2.00e-02 2.50e+03 3.08e+00
  bond pdb=" C5  CLR R 704 "
       pdb=" C6  CLR R 704 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.034 2.00e-02 2.50e+03 2.93e+00
  bond pdb=" C5  CLR R 705 "
       pdb=" C6  CLR R 705 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.034 2.00e-02 2.50e+03 2.85e+00
  bond pdb=" C5  CLR R 707 "
       pdb=" C6  CLR R 707 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.034 2.00e-02 2.50e+03 2.82e+00
  ... (remaining 9263 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 12320
        1.78 -     3.57: 220
        3.57 -     5.35: 54
        5.35 -     7.13: 13
        7.13 -     8.92: 4
  Bond angle restraints: 12611
  Sorted by residual:
  angle pdb=" C13 CLR R 702 "
        pdb=" C17 CLR R 702 "
        pdb=" C20 CLR R 702 "
      ideal   model   delta    sigma   weight residual
     119.60  110.68    8.92 3.00e+00 1.11e-01 8.84e+00
  angle pdb=" C13 CLR R 707 "
        pdb=" C17 CLR R 707 "
        pdb=" C20 CLR R 707 "
      ideal   model   delta    sigma   weight residual
     119.60  111.81    7.79 3.00e+00 1.11e-01 6.74e+00
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  126.49   -4.95 1.91e+00 2.74e-01 6.71e+00
  angle pdb=" C13 CLR R 705 "
        pdb=" C17 CLR R 705 "
        pdb=" C20 CLR R 705 "
      ideal   model   delta    sigma   weight residual
     119.60  111.90    7.70 3.00e+00 1.11e-01 6.59e+00
  angle pdb=" C13 CLR R 703 "
        pdb=" C17 CLR R 703 "
        pdb=" C20 CLR R 703 "
      ideal   model   delta    sigma   weight residual
     119.60  112.03    7.57 3.00e+00 1.11e-01 6.36e+00
  ... (remaining 12606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 5479
       16.92 -    33.85: 210
       33.85 -    50.77: 63
       50.77 -    67.70: 15
       67.70 -    84.62: 3
  Dihedral angle restraints: 5770
    sinusoidal: 2485
      harmonic: 3285
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.36   21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  TRP B 339 "
           pdb=" C   TRP B 339 "
           pdb=" N   ASN B 340 "
           pdb=" CA  ASN B 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.74   19.26     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 5767 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1340
       0.098 -    0.195: 82
       0.195 -    0.293: 7
       0.293 -    0.390: 7
       0.390 -    0.487: 7
  Chirality restraints: 1443
  Sorted by residual:
  chirality pdb=" C14 CLR R 702 "
            pdb=" C13 CLR R 702 "
            pdb=" C15 CLR R 702 "
            pdb=" C8  CLR R 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.80    0.49 2.00e-01 2.50e+01 5.94e+00
  chirality pdb=" C14 CLR R 705 "
            pdb=" C13 CLR R 705 "
            pdb=" C15 CLR R 705 "
            pdb=" C8  CLR R 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.78    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" C14 CLR R 707 "
            pdb=" C13 CLR R 707 "
            pdb=" C15 CLR R 707 "
            pdb=" C8  CLR R 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.78    0.46 2.00e-01 2.50e+01 5.39e+00
  ... (remaining 1440 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.030 5.00e-02 4.00e+02   4.46e-02 3.19e+00
        pdb=" N   PRO B 236 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.32e+00
        pdb=" N   PRO B 194 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 106 "   -0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        pdb=" N   PRO B 107 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1622
        2.77 -     3.30: 8501
        3.30 -     3.83: 15452
        3.83 -     4.37: 19349
        4.37 -     4.90: 32359
  Nonbonded interactions: 77283
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OE1 GLN A  52 "
            pdb=" ND2 ASN A 331 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" O   SER A 281 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASN A 269 "
            pdb=" OG1 THR A 324 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   ALA R 332 "
            pdb=" NZ  LYS R 336 "
     model   vdw
     2.317 3.120
  ... (remaining 77278 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.380
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
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   0.047   9271  Z= 0.165
  Angle     :  0.627   8.918  12617  Z= 0.280
  Chirality :  0.062   0.487   1443
  Planarity :  0.003   0.045   1543
  Dihedral  : 10.628  84.622   3641
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  3.03 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.12 (0.24), residues: 1114
  helix:  1.37 (0.24), residues: 415
  sheet:  0.84 (0.29), residues: 293
  loop :  0.17 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  72 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9268)
  covalent geometry    : angle       0.62652 (12611)
  SS BOND              : bond        0.00258 (    3)
  SS BOND              : angle       0.83934 (    6)
  hydrogen bonds       : bond        0.22349 (  465)
  hydrogen bonds       : angle       6.79330 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 162
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8385 (mttt) cc_final: 0.8025 (mppt)
REVERT: A  261 ASP cc_start: 0.7774 (m-30) cc_final: 0.7523 (m-30)
REVERT: B   79 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8952 (mt)
REVERT: B  137 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.8012 (tpt90)
REVERT: C   21 MET cc_start: 0.8182 (mmm) cc_final: 0.7739 (mpp)
REVERT: R   20 PHE cc_start: 0.8190 (t80) cc_final: 0.7744 (t80)
REVERT: R   24 LEU cc_start: 0.8775 (tp) cc_final: 0.8451 (mm)
REVERT: R   50 SER cc_start: 0.8879 (m) cc_final: 0.8581 (p)
  outliers start: 7
  outliers final: 2
  residues processed: 169
  average time/residue: 0.6907
  time to fit residues: 123.3983
Evaluate side-chains
  134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  275 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.1980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   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  22 ASN
B 259 GLN
B 266 HIS
E 171 ASN
E 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.149014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.104984 restraints weight = 9938.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.88
r_work: 0.3070 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9271  Z= 0.123
  Angle     :  0.525   6.777  12617  Z= 0.283
  Chirality :  0.042   0.171   1443
  Planarity :  0.004   0.043   1543
  Dihedral  :  7.156  59.564   1683
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  8.68 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.59 (0.25), residues: 1114
  helix:  2.12 (0.25), residues: 419
  sheet:  0.93 (0.29), residues: 285
  loop :  0.12 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  19 
 TYR   0.016   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9268)
  covalent geometry    : angle       0.52456 (12611)
  SS BOND              : bond        0.00446 (    3)
  SS BOND              : angle       0.72038 (    6)
  hydrogen bonds       : bond        0.04889 (  465)
  hydrogen bonds       : angle       4.85795 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8449 (mttt) cc_final: 0.7993 (mppt)
REVERT: A  275 GLU cc_start: 0.7678 (pt0) cc_final: 0.7230 (pp20)
REVERT: A  276 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: A  328 ASP cc_start: 0.7351 (m-30) cc_final: 0.7034 (m-30)
REVERT: B   23 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7728 (tptt)
REVERT: B  266 HIS cc_start: 0.8249 (t-90) cc_final: 0.7993 (t-90)
REVERT: C   21 MET cc_start: 0.8270 (mmm) cc_final: 0.7156 (ttp)
REVERT: C   42 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7308 (mp0)
REVERT: E  194 ASN cc_start: 0.8911 (m-40) cc_final: 0.8455 (m110)
REVERT: R   20 PHE cc_start: 0.8231 (t80) cc_final: 0.8021 (t80)
REVERT: R   93 THR cc_start: 0.8885 (t) cc_final: 0.8626 (p)
REVERT: R  342 ILE cc_start: 0.8586 (mm) cc_final: 0.8383 (mm)
  outliers start: 14
  outliers final: 8
  residues processed: 146
  average time/residue: 0.7148
  time to fit residues: 110.3092
Evaluate side-chains
  136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 176 GLN
B 259 GLN
E 186 GLN
R 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.147049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.102519 restraints weight = 9897.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.88
r_work: 0.3032 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9271  Z= 0.167
  Angle     :  0.542   5.723  12617  Z= 0.292
  Chirality :  0.043   0.177   1443
  Planarity :  0.004   0.046   1543
  Dihedral  :  6.790  55.985   1678
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  9.94 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.53 (0.25), residues: 1114
  helix:  2.28 (0.25), residues: 412
  sheet:  0.74 (0.29), residues: 288
  loop : -0.01 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.016   0.001   TYR R 358 
 PHE   0.015   0.002   PHE A 215 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.004   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 9268)
  covalent geometry    : angle       0.54103 (12611)
  SS BOND              : bond        0.00282 (    3)
  SS BOND              : angle       1.41294 (    6)
  hydrogen bonds       : bond        0.05041 (  465)
  hydrogen bonds       : angle       4.71100 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8505 (mttt) cc_final: 0.8005 (mppt)
REVERT: A  275 GLU cc_start: 0.7751 (pt0) cc_final: 0.7230 (pp20)
REVERT: A  276 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7924 (mt-10)
REVERT: A  328 ASP cc_start: 0.7340 (m-30) cc_final: 0.6983 (m-30)
REVERT: B   23 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7643 (tptt)
REVERT: B  266 HIS cc_start: 0.8265 (t-90) cc_final: 0.8029 (t-90)
REVERT: C   21 MET cc_start: 0.8284 (mmm) cc_final: 0.7142 (ttp)
REVERT: R   93 THR cc_start: 0.8899 (t) cc_final: 0.8487 (p)
REVERT: R  342 ILE cc_start: 0.8626 (mm) cc_final: 0.8407 (mm)
  outliers start: 19
  outliers final: 10
  residues processed: 138
  average time/residue: 0.7450
  time to fit residues: 108.4849
Evaluate side-chains
  132 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0770
   chunk 104 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0770
   chunk 100 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  91 HIS
E 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.150730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.106971 restraints weight = 10037.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.90
r_work: 0.3104 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9271  Z= 0.097
  Angle     :  0.464   5.549  12617  Z= 0.250
  Chirality :  0.040   0.169   1443
  Planarity :  0.003   0.044   1543
  Dihedral  :  6.399  59.358   1678
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 11.40 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.63 (0.25), residues: 1114
  helix:  2.48 (0.25), residues: 413
  sheet:  0.67 (0.29), residues: 274
  loop :  0.03 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.012   0.001   PHE R  20 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 9268)
  covalent geometry    : angle       0.46329 (12611)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       0.99565 (    6)
  hydrogen bonds       : bond        0.03865 (  465)
  hydrogen bonds       : angle       4.34239 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8402 (mttt) cc_final: 0.7954 (mppt)
REVERT: A  275 GLU cc_start: 0.7880 (pt0) cc_final: 0.7438 (pp20)
REVERT: A  276 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7883 (mt-10)
REVERT: A  328 ASP cc_start: 0.7353 (m-30) cc_final: 0.6994 (m-30)
REVERT: B   23 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7595 (tptt)
REVERT: B  137 ARG cc_start: 0.8090 (mmt-90) cc_final: 0.7719 (tpt90)
REVERT: B  266 HIS cc_start: 0.8116 (t-90) cc_final: 0.7908 (t-170)
REVERT: C   21 MET cc_start: 0.8249 (mmm) cc_final: 0.7159 (ttp)
REVERT: E  160 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7881 (ttp-110)
REVERT: E  194 ASN cc_start: 0.8870 (m-40) cc_final: 0.8475 (m110)
REVERT: R   24 LEU cc_start: 0.8744 (tp) cc_final: 0.8276 (mm)
REVERT: R   93 THR cc_start: 0.8756 (t) cc_final: 0.8482 (p)
REVERT: R  165 GLU cc_start: 0.8562 (pt0) cc_final: 0.7676 (pp20)
REVERT: R  342 ILE cc_start: 0.8587 (mm) cc_final: 0.8384 (mm)
  outliers start: 13
  outliers final: 9
  residues processed: 150
  average time/residue: 0.5418
  time to fit residues: 85.9986
Evaluate side-chains
  142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 103 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 155 ASN
B 259 GLN
E 171 ASN
E 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.149431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.110745 restraints weight = 9935.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.91
r_work: 0.3151 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9271  Z= 0.239
  Angle     :  0.593   6.219  12617  Z= 0.319
  Chirality :  0.045   0.181   1443
  Planarity :  0.004   0.052   1543
  Dihedral  :  6.683  57.594   1678
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 11.61 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.43 (0.25), residues: 1114
  helix:  2.27 (0.25), residues: 413
  sheet:  0.51 (0.28), residues: 294
  loop : -0.02 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.019   0.002   TYR R 358 
 PHE   0.019   0.002   PHE A 215 
 TRP   0.012   0.002   TRP B 169 
 HIS   0.005   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 9268)
  covalent geometry    : angle       0.59260 (12611)
  SS BOND              : bond        0.00277 (    3)
  SS BOND              : angle       1.46408 (    6)
  hydrogen bonds       : bond        0.05166 (  465)
  hydrogen bonds       : angle       4.67511 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8561 (mttt) cc_final: 0.8168 (mppt)
REVERT: A  275 GLU cc_start: 0.7886 (pt0) cc_final: 0.7492 (pp20)
REVERT: A  276 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: A  328 ASP cc_start: 0.7341 (m-30) cc_final: 0.6965 (m-30)
REVERT: A  330 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7918 (mtmt)
REVERT: B   23 LYS cc_start: 0.8511 (ttmm) cc_final: 0.7827 (tptt)
REVERT: B  172 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7918 (pt0)
REVERT: B  262 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8867 (tpp)
REVERT: C   21 MET cc_start: 0.8369 (mmm) cc_final: 0.7260 (ttp)
REVERT: R  165 GLU cc_start: 0.8653 (pt0) cc_final: 0.7881 (pp20)
  outliers start: 21
  outliers final: 10
  residues processed: 136
  average time/residue: 0.5535
  time to fit residues: 79.5957
Evaluate side-chains
  136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0970
   chunk 93 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0870
   chunk 65 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.5556

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
E 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.153731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.111331 restraints weight = 9913.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.80
r_work: 0.3215 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9271  Z= 0.102
  Angle     :  0.476   5.489  12617  Z= 0.256
  Chirality :  0.041   0.171   1443
  Planarity :  0.004   0.044   1543
  Dihedral  :  6.376  59.813   1678
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.76 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.57 (0.25), residues: 1114
  helix:  2.49 (0.25), residues: 413
  sheet:  0.56 (0.29), residues: 274
  loop : -0.01 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.010   0.001   PHE B 151 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 9268)
  covalent geometry    : angle       0.47529 (12611)
  SS BOND              : bond        0.00343 (    3)
  SS BOND              : angle       0.86569 (    6)
  hydrogen bonds       : bond        0.03906 (  465)
  hydrogen bonds       : angle       4.34298 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8448 (mttt) cc_final: 0.8098 (mppt)
REVERT: A  275 GLU cc_start: 0.7900 (pt0) cc_final: 0.7489 (pp20)
REVERT: A  276 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7906 (mt-10)
REVERT: B   23 LYS cc_start: 0.8448 (ttmm) cc_final: 0.7759 (tptt)
REVERT: B  137 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7804 (tpt90)
REVERT: B  172 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7801 (pt0)
REVERT: B  219 ARG cc_start: 0.8230 (mtt-85) cc_final: 0.7922 (mmt-90)
REVERT: C   21 MET cc_start: 0.8317 (mmm) cc_final: 0.7232 (ttp)
REVERT: E  160 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7967 (ttp-110)
REVERT: E  194 ASN cc_start: 0.8872 (m-40) cc_final: 0.8486 (m110)
REVERT: R  165 GLU cc_start: 0.8589 (pt0) cc_final: 0.7819 (pp20)
  outliers start: 13
  outliers final: 8
  residues processed: 135
  average time/residue: 0.6412
  time to fit residues: 91.3097
Evaluate side-chains
  132 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 41 optimal weight:    0.1980
   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  22 ASN
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.152882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.111530 restraints weight = 9895.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.75
r_work: 0.3209 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9271  Z= 0.110
  Angle     :  0.481   5.697  12617  Z= 0.259
  Chirality :  0.041   0.173   1443
  Planarity :  0.004   0.044   1543
  Dihedral  :  6.219  57.507   1678
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.66 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.59 (0.25), residues: 1114
  helix:  2.54 (0.25), residues: 414
  sheet:  0.52 (0.29), residues: 274
  loop : -0.01 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.014   0.001   TYR R 173 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9268)
  covalent geometry    : angle       0.48090 (12611)
  SS BOND              : bond        0.00120 (    3)
  SS BOND              : angle       0.91688 (    6)
  hydrogen bonds       : bond        0.03957 (  465)
  hydrogen bonds       : angle       4.28270 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8483 (mttt) cc_final: 0.8103 (mppt)
REVERT: A  275 GLU cc_start: 0.7890 (pt0) cc_final: 0.7425 (pp20)
REVERT: A  276 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7819 (mt-10)
REVERT: B   23 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7736 (tptt)
REVERT: B  172 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7871 (tp30)
REVERT: C   21 MET cc_start: 0.8303 (mmm) cc_final: 0.7205 (ttp)
REVERT: C   42 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7166 (tp30)
REVERT: E  160 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7954 (ttp-110)
REVERT: E  194 ASN cc_start: 0.8853 (m-40) cc_final: 0.8449 (m110)
REVERT: R  150 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8602 (tpt)
REVERT: R  165 GLU cc_start: 0.8627 (pt0) cc_final: 0.7755 (pp20)
  outliers start: 18
  outliers final: 10
  residues processed: 135
  average time/residue: 0.6074
  time to fit residues: 86.7351
Evaluate side-chains
  133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  150 MET
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.150348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.111496 restraints weight = 9906.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.98
r_work: 0.3162 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9271  Z= 0.204
  Angle     :  0.572   5.950  12617  Z= 0.308
  Chirality :  0.044   0.181   1443
  Planarity :  0.004   0.046   1543
  Dihedral  :  6.503  56.648   1678
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.34 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.40 (0.25), residues: 1114
  helix:  2.35 (0.25), residues: 413
  sheet:  0.42 (0.28), residues: 290
  loop : -0.09 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 219 
 TYR   0.018   0.002   TYR R 358 
 PHE   0.018   0.002   PHE A 215 
 TRP   0.011   0.002   TRP B 169 
 HIS   0.006   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 9268)
  covalent geometry    : angle       0.57189 (12611)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.26192 (    6)
  hydrogen bonds       : bond        0.04887 (  465)
  hydrogen bonds       : angle       4.59219 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8532 (mttt) cc_final: 0.8126 (mppt)
REVERT: A  275 GLU cc_start: 0.7872 (pt0) cc_final: 0.7364 (pp20)
REVERT: A  276 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7798 (mt-10)
REVERT: B   23 LYS cc_start: 0.8468 (ttmm) cc_final: 0.7770 (tptt)
REVERT: B  172 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7932 (pt0)
REVERT: B  219 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7887 (mmt-90)
REVERT: C   21 MET cc_start: 0.8246 (mmm) cc_final: 0.7175 (ttp)
REVERT: C   42 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7233 (tp30)
REVERT: R  165 GLU cc_start: 0.8620 (pt0) cc_final: 0.7868 (pp20)
  outliers start: 21
  outliers final: 14
  residues processed: 137
  average time/residue: 0.7184
  time to fit residues: 103.9701
Evaluate side-chains
  137 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 91 optimal weight:    0.1980
   chunk 90 optimal weight:    0.5980
   chunk 78 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 322 HIS
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.152860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.110783 restraints weight = 9910.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.79
r_work: 0.3208 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9271  Z= 0.108
  Angle     :  0.490   5.523  12617  Z= 0.264
  Chirality :  0.041   0.174   1443
  Planarity :  0.004   0.043   1543
  Dihedral  :  6.146  55.550   1678
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.97 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.50 (0.25), residues: 1114
  helix:  2.51 (0.25), residues: 414
  sheet:  0.43 (0.29), residues: 270
  loop : -0.08 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.015   0.001   TYR R 173 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 9268)
  covalent geometry    : angle       0.48957 (12611)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       0.76053 (    6)
  hydrogen bonds       : bond        0.03936 (  465)
  hydrogen bonds       : angle       4.33981 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8461 (mttt) cc_final: 0.8101 (mppt)
REVERT: A  275 GLU cc_start: 0.7927 (pt0) cc_final: 0.7399 (pp20)
REVERT: A  276 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7854 (mt-10)
REVERT: B   23 LYS cc_start: 0.8399 (ttmm) cc_final: 0.7697 (tptt)
REVERT: B  172 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7868 (tp30)
REVERT: B  219 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7878 (mmt-90)
REVERT: B  254 ASP cc_start: 0.8363 (t70) cc_final: 0.8033 (t70)
REVERT: C   21 MET cc_start: 0.8232 (mmm) cc_final: 0.7172 (ttp)
REVERT: C   42 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7168 (tp30)
REVERT: E  160 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7974 (ttp-110)
REVERT: R  165 GLU cc_start: 0.8629 (pt0) cc_final: 0.7755 (pp20)
  outliers start: 17
  outliers final: 12
  residues processed: 136
  average time/residue: 0.7582
  time to fit residues: 108.7559
Evaluate side-chains
  135 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 64 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 99 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 322 HIS
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.153460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.110878 restraints weight = 9845.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.80
r_work: 0.3208 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9271  Z= 0.110
  Angle     :  0.492   5.660  12617  Z= 0.264
  Chirality :  0.041   0.174   1443
  Planarity :  0.004   0.042   1543
  Dihedral  :  6.036  56.035   1678
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 13.39 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.55 (0.25), residues: 1114
  helix:  2.56 (0.25), residues: 414
  sheet:  0.43 (0.29), residues: 270
  loop : -0.03 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.016   0.001   TYR R 173 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9268)
  covalent geometry    : angle       0.49192 (12611)
  SS BOND              : bond        0.00144 (    3)
  SS BOND              : angle       0.81730 (    6)
  hydrogen bonds       : bond        0.03919 (  465)
  hydrogen bonds       : angle       4.30245 ( 1314)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8461 (mttt) cc_final: 0.8109 (mppt)
REVERT: A  275 GLU cc_start: 0.7924 (pt0) cc_final: 0.7397 (pp20)
REVERT: A  276 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7861 (mt-10)
REVERT: B   23 LYS cc_start: 0.8385 (ttmm) cc_final: 0.7686 (tptt)
REVERT: B  172 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7832 (tp30)
REVERT: B  219 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7890 (mmt-90)
REVERT: B  254 ASP cc_start: 0.8418 (t70) cc_final: 0.8114 (t70)
REVERT: C   21 MET cc_start: 0.8221 (mmm) cc_final: 0.7162 (ttp)
REVERT: C   42 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7191 (tp30)
REVERT: C   62 ARG cc_start: 0.6718 (mtt90) cc_final: 0.6462 (mtt90)
REVERT: E  160 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8005 (ttp-110)
REVERT: E  194 ASN cc_start: 0.8855 (m-40) cc_final: 0.8457 (m110)
REVERT: R  165 GLU cc_start: 0.8614 (pt0) cc_final: 0.7736 (pp20)
  outliers start: 13
  outliers final: 11
  residues processed: 131
  average time/residue: 0.7565
  time to fit residues: 104.5640
Evaluate side-chains
  135 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0370
   chunk 0 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   chunk 105 optimal weight:    0.1980
   chunk 78 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.5060

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 322 HIS
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.153921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.112738 restraints weight = 9808.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.75
r_work: 0.3228 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9271  Z= 0.100
  Angle     :  0.477   5.540  12617  Z= 0.256
  Chirality :  0.040   0.173   1443
  Planarity :  0.004   0.042   1543
  Dihedral  :  5.878  56.471   1678
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.28 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.60 (0.25), residues: 1114
  helix:  2.61 (0.25), residues: 414
  sheet:  0.44 (0.29), residues: 270
  loop : -0.01 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.016   0.001   TYR R 173 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 9268)
  covalent geometry    : angle       0.47733 (12611)
  SS BOND              : bond        0.00169 (    3)
  SS BOND              : angle       0.71411 (    6)
  hydrogen bonds       : bond        0.03740 (  465)
  hydrogen bonds       : angle       4.23234 ( 1314)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4635.27 seconds
wall clock time: 79 minutes 35.12 seconds (4775.12 seconds total)