Starting phenix.real_space_refine
on Wed Feb  4 05:50:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nk6_49494/02_2026/9nk6_49494.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nk6_49494/02_2026/9nk6_49494.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nk6_49494/02_2026/9nk6_49494.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nk6_49494/02_2026/9nk6_49494.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nk6_49494/02_2026/9nk6_49494.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nk6_49494/02_2026/9nk6_49494.map"
  }
  resolution = 2.88
  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=   0.013
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      15      5.16       5
     C    5710      2.51       5
     N    1505      2.21       5
     O    1583      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8813
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2430
          Classifications: {'peptide': 311}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 285}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 459, 3395
          Classifications: {'peptide': 459}
          Link IDs: {'PTRANS': 24, 'TRANS': 434}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2640
          Classifications: {'peptide': 351}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 323}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'ERG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 203
          Unusual residues: {'ERG': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "C"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 116
          Unusual residues: {'ERG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.98, per 1000 atoms: 0.22
  Number of scatterers: 8813
  At special positions: 0
  Unit cell: (79.104, 111.24, 131.016, 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      15     16.00
     O    1583      8.00
     N    1505      7.00
     C    5710      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.55
  Conformation dependent library (CDL) restraints added in 218.9 milliseconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2038

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      45.1% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 25
      removed outlier: 3.933A  pdb=" N   LEU A  23 " --> pdb=" O   PRO A  19 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 45
    Processing helix  chain 'A' and resid 57 through 64
      removed outlier: 3.689A  pdb=" N   LEU A  63 " --> pdb=" O   SER A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 82
      removed outlier: 3.827A  pdb=" N   TRP A  75 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 96
    Processing helix  chain 'A' and resid 122 through 130
    Processing helix  chain 'A' and resid 150 through 162
      removed outlier: 3.733A  pdb=" N   ALA A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE A 160 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 173
      removed outlier: 3.531A  pdb=" N   ALA A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 177
      No H-bonds generated for 'chain 'A' and resid 175 through 177'
    Processing helix  chain 'A' and resid 178 through 186
    Processing helix  chain 'A' and resid 186 through 191
      removed outlier: 3.793A  pdb=" N   ALA A 190 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A 191 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 186 through 191'
    Processing helix  chain 'A' and resid 193 through 214
    Processing helix  chain 'A' and resid 230 through 234
      removed outlier: 3.506A  pdb=" N   ILE A 234 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 257
      removed outlier: 3.774A  pdb=" N   SER A 257 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 265
      removed outlier: 3.807A  pdb=" N   GLY A 264 " --> pdb=" O   TRP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 286
      removed outlier: 4.047A  pdb=" N   TYR A 278 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   LEU A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 297
    Processing helix  chain 'A' and resid 300 through 308
    Processing helix  chain 'A' and resid 311 through 325
    Processing helix  chain 'B' and resid 58 through 73
      removed outlier: 3.629A  pdb=" N   LEU B  62 " --> pdb=" O   ARG B  58 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ILE B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.767A  pdb=" N   THR B  73 " --> pdb=" O   VAL B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 76
      No H-bonds generated for 'chain 'B' and resid 74 through 76'
    Processing helix  chain 'B' and resid 78 through 81
    Processing helix  chain 'B' and resid 82 through 96
      removed outlier: 3.619A  pdb=" N   GLY B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS B  92 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LYS B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA B  95 " --> pdb=" O   THR B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 151
    Processing helix  chain 'B' and resid 255 through 262
    Processing helix  chain 'B' and resid 446 through 463
      removed outlier: 3.658A  pdb=" N   LEU B 461 " --> pdb=" O   ALA B 457 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR B 462 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASN B 463 " --> pdb=" O   GLY B 459 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 32
    Processing helix  chain 'C' and resid 66 through 77
    Processing helix  chain 'C' and resid 105 through 132
      removed outlier: 4.920A  pdb=" N   ALA C 124 " --> pdb=" O   SER C 120 " (cutoff:3.500A)
      Proline residue:  C 125  - end of helix
    Processing helix  chain 'C' and resid 134 through 139
    Processing helix  chain 'C' and resid 141 through 148
    Processing helix  chain 'C' and resid 153 through 156
      removed outlier: 3.860A  pdb=" N   TRP C 156 " --> pdb=" O   PRO C 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 153 through 156'
    Processing helix  chain 'C' and resid 157 through 170
      removed outlier: 3.515A  pdb=" N   ALA C 161 " --> pdb=" O   THR C 157 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 171 through 174
    Processing helix  chain 'C' and resid 234 through 257
      removed outlier: 3.529A  pdb=" N   ARG C 239 " --> pdb=" O   GLU C 235 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ILE C 240 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL C 249 " --> pdb=" O   ALA C 245 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL C 252 " --> pdb=" O   GLU C 248 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU C 253 " --> pdb=" O   VAL C 249 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLU C 255 " --> pdb=" O   ASP C 251 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   VAL C 256 " --> pdb=" O   VAL C 252 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ASP C 257 " --> pdb=" O   LEU C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 284
      removed outlier: 3.773A  pdb=" N   LEU C 281 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   MET C 282 " --> pdb=" O   TYR C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 300
    Processing helix  chain 'C' and resid 300 through 315
    Processing helix  chain 'C' and resid 316 through 319
    Processing helix  chain 'C' and resid 324 through 327
    Processing helix  chain 'C' and resid 328 through 334
      removed outlier: 3.877A  pdb=" N   ALA C 333 " --> pdb=" O   ALA C 329 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   SER C 334 " --> pdb=" O   GLN C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 352
    Processing helix  chain 'C' and resid 357 through 378
      removed outlier: 3.679A  pdb=" N   ARG C 363 " --> pdb=" O   GLU C 359 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY C 378 " --> pdb=" O   LEU C 374 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 408
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 30 through 32
    current: chain 'B' and resid 153 through 162
      removed outlier: 3.915A  pdb=" N   ALA B 157 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   GLU B 167 " --> pdb=" O   ASN B 161 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 167 through 171
    current: chain 'B' and resid 179 through 191
      removed outlier: 5.838A  pdb=" N   THR B 179 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   GLN B 209 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER B 181 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   LEU B 197 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   ASP B 196 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 229 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY B 288 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 318 " --> pdb=" O   GLY B 337 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   VAL B 333 " --> pdb=" O   VAL B 322 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 395 through 400
    current: chain 'B' and resid 417 through 421
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 417 through 421
    current: chain 'B' and resid 467 through 476
      removed outlier: 6.470A  pdb=" N   LEU B 468 " --> pdb=" O   LEU B 491 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 109
      removed outlier: 4.637A  pdb=" N   LYS B 133 " --> pdb=" O   LYS B 101 " (cutoff:3.500A)
      removed outlier: 8.634A  pdb=" N   GLU B 103 " --> pdb=" O   ARG B 131 " (cutoff:3.500A)
      removed outlier: 10.191A  pdb=" N   ARG B 131 " --> pdb=" O   GLU B 103 " (cutoff:3.500A)
      removed outlier: 10.493A  pdb=" N   PHE B 105 " --> pdb=" O   SER B 129 " (cutoff:3.500A)
      removed outlier: 10.931A  pdb=" N   SER B 129 " --> pdb=" O   PHE B 105 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL B 132 " --> pdb=" O   HIS B  52 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B  49 " --> pdb=" O   TRP C 420 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLN C 418 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 37 through 41

    422 hydrogen bonds defined for protein.
    1215 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: 1.28

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2003
        1.33 -     1.45: 1809
        1.45 -     1.57: 5214
        1.57 -     1.69: 0
        1.69 -     1.81: 25
  Bond restraints: 9051
  Sorted by residual:
  bond pdb=" N   VAL B 158 "
       pdb=" CA  VAL B 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.19e-02 7.06e+03 9.45e+00
  bond pdb=" N   GLY B 143 "
       pdb=" CA  GLY B 143 "
    ideal  model  delta    sigma   weight residual
    1.447  1.475 -0.027 9.40e-03 1.13e+04 8.49e+00
  bond pdb=" N   THR B 144 "
       pdb=" CA  THR B 144 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.09e-02 8.42e+03 8.13e+00
  bond pdb=" N   GLU B 167 "
       pdb=" CA  GLU B 167 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.036 1.31e-02 5.83e+03 7.76e+00
  bond pdb=" N   VAL B 159 "
       pdb=" CA  VAL B 159 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.72e+00
  ... (remaining 9046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 12081
        2.03 -     4.06: 279
        4.06 -     6.09: 42
        6.09 -     8.12: 4
        8.12 -    10.15: 1
  Bond angle restraints: 12407
  Sorted by residual:
  angle pdb=" N   ALA A 260 "
        pdb=" CA  ALA A 260 "
        pdb=" C   ALA A 260 "
      ideal   model   delta    sigma   weight residual
     113.16  108.24    4.92 1.24e+00 6.50e-01 1.58e+01
  angle pdb=" CA  ALA B 166 "
        pdb=" C   ALA B 166 "
        pdb=" O   ALA B 166 "
      ideal   model   delta    sigma   weight residual
     122.44  117.61    4.83 1.34e+00 5.57e-01 1.30e+01
  angle pdb=" CA  ASN B 148 "
        pdb=" C   ASN B 148 "
        pdb=" O   ASN B 148 "
      ideal   model   delta    sigma   weight residual
     122.64  118.20    4.44 1.25e+00 6.40e-01 1.26e+01
  angle pdb=" CA  GLY B 143 "
        pdb=" C   GLY B 143 "
        pdb=" O   GLY B 143 "
      ideal   model   delta    sigma   weight residual
     121.47  118.28    3.19 9.10e-01 1.21e+00 1.23e+01
  angle pdb=" N   GLU A 258 "
        pdb=" CA  GLU A 258 "
        pdb=" C   GLU A 258 "
      ideal   model   delta    sigma   weight residual
     113.23  108.89    4.34 1.24e+00 6.50e-01 1.23e+01
  ... (remaining 12402 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 5431
       17.55 -    35.09: 381
       35.09 -    52.64: 120
       52.64 -    70.18: 19
       70.18 -    87.73: 6
  Dihedral angle restraints: 5957
    sinusoidal: 2777
      harmonic: 3180
  Sorted by residual:
  dihedral pdb=" CA  PRO C 151 "
           pdb=" C   PRO C 151 "
           pdb=" N   LEU C 152 "
           pdb=" CA  LEU C 152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.04  -19.96     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  ASP B  72 "
           pdb=" CB  ASP B  72 "
           pdb=" CG  ASP B  72 "
           pdb=" OD1 ASP B  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.45   59.45     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CB  GLU C 248 "
           pdb=" CG  GLU C 248 "
           pdb=" CD  GLU C 248 "
           pdb=" OE1 GLU C 248 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.73  -87.73     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 5954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1121
       0.047 -    0.094: 212
       0.094 -    0.141: 70
       0.141 -    0.188: 19
       0.188 -    0.234: 2
  Chirality restraints: 1424
  Sorted by residual:
  chirality pdb=" CA  ILE B 162 "
            pdb=" N   ILE B 162 "
            pdb=" C   ILE B 162 "
            pdb=" CB  ILE B 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  VAL B 159 "
            pdb=" N   VAL B 159 "
            pdb=" C   VAL B 159 "
            pdb=" CB  VAL B 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" CA  LEU A 101 "
            pdb=" N   LEU A 101 "
            pdb=" C   LEU A 101 "
            pdb=" CB  LEU A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.29e-01
  ... (remaining 1421 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 160 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.87e+00
        pdb=" C   ARG B 160 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ARG B 160 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASN B 161 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 478 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO B 479 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 479 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 479 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 159 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.30e+00
        pdb=" N   PRO C 160 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO C 160 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 160 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1473
        2.77 -     3.30: 8314
        3.30 -     3.83: 14172
        3.83 -     4.37: 17189
        4.37 -     4.90: 29889
  Nonbonded interactions: 71037
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C  36 "
            pdb=" OG1 THR C  81 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   HIS C  51 "
            pdb=" OG1 THR C  54 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   PHE A  55 "
            pdb=" OG  SER A  67 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   VAL B  87 "
            pdb=" OG1 THR B  91 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR B 421 "
            pdb=" OG  SER B 488 "
     model   vdw
     2.274 3.040
  ... (remaining 71032 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.350
  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:6.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
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   0.037   9051  Z= 0.255
  Angle     :  0.652  10.152  12407  Z= 0.396
  Chirality :  0.045   0.234   1424
  Planarity :  0.004   0.046   1552
  Dihedral  : 13.021  87.725   3919
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 15.37 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1107
  helix:  1.31 (0.26), residues: 404
  sheet:  0.14 (0.37), residues: 211
  loop : -0.21 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 180 
 TYR   0.005   0.001   TYR B 154 
 PHE   0.012   0.001   PHE A 103 
 TRP   0.008   0.001   TRP A 325 
 HIS   0.003   0.000   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 9051)
  covalent geometry    : angle       0.65218 (12407)
  hydrogen bonds       : bond        0.22713 (  422)
  hydrogen bonds       : angle       7.63887 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7610 (pmm150)
REVERT: A  206 ARG cc_start: 0.7204 (ttm170) cc_final: 0.6801 (mmt-90)
REVERT: A  221 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8382 (mtmt)
  outliers start: 5
  outliers final: 3
  residues processed: 76
  average time/residue: 0.5681
  time to fit residues: 46.0571
Evaluate side-chains
  54 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  314 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 211 GLN
B 161 ASN
B 223 ASN
B 286 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.123427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.089052 restraints weight = 14724.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.45
r_work: 0.3030 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9051  Z= 0.161
  Angle     :  0.580   7.287  12407  Z= 0.284
  Chirality :  0.042   0.168   1424
  Planarity :  0.005   0.043   1552
  Dihedral  :  7.151  86.100   2032
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.45 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.25), residues: 1107
  helix:  1.95 (0.26), residues: 415
  sheet:  0.03 (0.35), residues: 214
  loop : -0.15 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 417 
 TYR   0.009   0.001   TYR A  53 
 PHE   0.013   0.001   PHE A  68 
 TRP   0.008   0.001   TRP A 132 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 9051)
  covalent geometry    : angle       0.58020 (12407)
  hydrogen bonds       : bond        0.04423 (  422)
  hydrogen bonds       : angle       4.99730 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 52
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 ARG cc_start: 0.7622 (ttm170) cc_final: 0.7216 (mpt90)
REVERT: A  237 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7912 (tp30)
REVERT: B   58 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7007 (mtm-85)
REVERT: B  105 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8074 (t80)
  outliers start: 30
  outliers final: 9
  residues processed: 77
  average time/residue: 0.5575
  time to fit residues: 46.1039
Evaluate side-chains
  60 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 81 optimal weight:    0.5980
   chunk 84 optimal weight:    7.9990
   chunk 70 optimal weight:    0.7980
   chunk 97 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 161 ASN
B 286 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.123883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.089345 restraints weight = 14587.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.43
r_work: 0.3042 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9051  Z= 0.127
  Angle     :  0.540   7.920  12407  Z= 0.259
  Chirality :  0.041   0.162   1424
  Planarity :  0.004   0.042   1552
  Dihedral  :  7.037  86.038   2025
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 13.76 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.26), residues: 1107
  helix:  2.17 (0.26), residues: 413
  sheet:  0.07 (0.35), residues: 216
  loop : -0.13 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 180 
 TYR   0.008   0.001   TYR A  53 
 PHE   0.013   0.001   PHE A  68 
 TRP   0.007   0.001   TRP A 325 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9051)
  covalent geometry    : angle       0.53973 (12407)
  hydrogen bonds       : bond        0.03458 (  422)
  hydrogen bonds       : angle       4.58240 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 46
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  206 ARG cc_start: 0.7749 (ttm170) cc_final: 0.7351 (mpt90)
REVERT: A  237 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7982 (tp30)
REVERT: A  332 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.5037 (tpp-160)
REVERT: B   58 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7123 (mtm-85)
REVERT: B  105 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8020 (t80)
REVERT: B  154 TYR cc_start: 0.8226 (p90) cc_final: 0.7849 (p90)
  outliers start: 33
  outliers final: 12
  residues processed: 75
  average time/residue: 0.5533
  time to fit residues: 44.3930
Evaluate side-chains
  58 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  298 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  281 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0270
   chunk 9 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0070
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 161 ASN
B 286 GLN
** C 137 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 = 0.3732 r_free = 0.3732 target = 0.124489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.090115 restraints weight = 14689.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.45
r_work: 0.3058 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9051  Z= 0.101
  Angle     :  0.520   7.957  12407  Z= 0.246
  Chirality :  0.040   0.160   1424
  Planarity :  0.004   0.041   1552
  Dihedral  :  6.955  85.042   2025
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.02 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.26), residues: 1107
  helix:  2.24 (0.26), residues: 416
  sheet:  0.07 (0.35), residues: 217
  loop : -0.05 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 417 
 TYR   0.007   0.001   TYR A 240 
 PHE   0.011   0.001   PHE A  68 
 TRP   0.008   0.001   TRP A 325 
 HIS   0.003   0.000   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9051)
  covalent geometry    : angle       0.52049 (12407)
  hydrogen bonds       : bond        0.02904 (  422)
  hydrogen bonds       : angle       4.33916 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 49
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 ARG cc_start: 0.7550 (ttm170) cc_final: 0.7233 (mpt180)
REVERT: A  237 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7791 (tp30)
REVERT: A  332 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.4848 (tpp-160)
REVERT: B   58 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7259 (mtm-85)
REVERT: B  105 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8054 (t80)
  outliers start: 27
  outliers final: 10
  residues processed: 70
  average time/residue: 0.5859
  time to fit residues: 43.8619
Evaluate side-chains
  59 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain C residue  281 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 161 ASN
B 246 GLN
B 286 GLN
B 423 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.122761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.087811 restraints weight = 14738.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.46
r_work: 0.3015 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9051  Z= 0.163
  Angle     :  0.554   8.450  12407  Z= 0.263
  Chirality :  0.041   0.163   1424
  Planarity :  0.004   0.039   1552
  Dihedral  :  7.168  87.316   2025
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 14.45 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.26), residues: 1107
  helix:  2.19 (0.26), residues: 426
  sheet: -0.03 (0.35), residues: 216
  loop : -0.30 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.010   0.001   TYR A  53 
 PHE   0.013   0.001   PHE A  68 
 TRP   0.007   0.001   TRP C 258 
 HIS   0.005   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 9051)
  covalent geometry    : angle       0.55383 (12407)
  hydrogen bonds       : bond        0.03302 (  422)
  hydrogen bonds       : angle       4.35396 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 50
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  206 ARG cc_start: 0.7615 (ttm170) cc_final: 0.7280 (mpt180)
REVERT: A  237 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7826 (tp30)
REVERT: A  332 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5169 (tpp-160)
REVERT: B   58 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7208 (mtm-85)
REVERT: B  105 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7970 (t80)
REVERT: C  138 TYR cc_start: 0.8889 (t80) cc_final: 0.8684 (t80)
  outliers start: 34
  outliers final: 17
  residues processed: 79
  average time/residue: 0.6479
  time to fit residues: 54.5702
Evaluate side-chains
  68 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 47
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  298 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  161 ASN
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  281 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 34 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   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 211 GLN
B 161 ASN
B 223 ASN
B 286 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.123234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.088737 restraints weight = 14674.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.44
r_work: 0.3029 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9051  Z= 0.127
  Angle     :  0.538   8.706  12407  Z= 0.255
  Chirality :  0.040   0.162   1424
  Planarity :  0.004   0.039   1552
  Dihedral  :  7.114  87.177   2025
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 15.60 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.26), residues: 1107
  helix:  2.23 (0.26), residues: 426
  sheet: -0.09 (0.35), residues: 219
  loop : -0.25 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.009   0.001   TYR B 154 
 PHE   0.013   0.001   PHE A  68 
 TRP   0.008   0.001   TRP A 325 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9051)
  covalent geometry    : angle       0.53796 (12407)
  hydrogen bonds       : bond        0.02996 (  422)
  hydrogen bonds       : angle       4.28802 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 48
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  206 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7433 (mpt180)
REVERT: A  237 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7989 (tp30)
REVERT: A  332 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5092 (tpp-160)
REVERT: B   58 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7286 (mtm-85)
REVERT: B  105 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7964 (t80)
  outliers start: 31
  outliers final: 15
  residues processed: 75
  average time/residue: 0.5721
  time to fit residues: 45.9451
Evaluate side-chains
  66 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 47
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  298 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  281 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9980
   chunk 109 optimal weight:    4.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 161 ASN
B 223 ASN
B 286 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.119218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.086883 restraints weight = 15258.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 2.53
r_work: 0.2920 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9051  Z= 0.235
  Angle     :  0.619   9.047  12407  Z= 0.293
  Chirality :  0.044   0.164   1424
  Planarity :  0.005   0.038   1552
  Dihedral  :  7.428  89.458   2025
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 15.94 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.26), residues: 1107
  helix:  2.06 (0.26), residues: 426
  sheet: -0.12 (0.35), residues: 214
  loop : -0.39 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 180 
 TYR   0.023   0.002   TYR C 138 
 PHE   0.015   0.001   PHE A  68 
 TRP   0.009   0.001   TRP B 228 
 HIS   0.006   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 9051)
  covalent geometry    : angle       0.61868 (12407)
  hydrogen bonds       : bond        0.03587 (  422)
  hydrogen bonds       : angle       4.40815 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 49
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  206 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7325 (mpt180)
REVERT: A  237 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7831 (tp30)
REVERT: A  332 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6079 (tpp-160)
REVERT: B   58 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6797 (mtm-85)
REVERT: B  105 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7825 (t80)
  outliers start: 34
  outliers final: 20
  residues processed: 78
  average time/residue: 0.5809
  time to fit residues: 48.2852
Evaluate side-chains
  72 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  298 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  161 ASN
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  223 ASN
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain C residue  281 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 9 optimal weight:    0.0870
   chunk 35 optimal weight:    0.0980
   chunk 80 optimal weight:    0.2980
   chunk 103 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4160

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 161 ASN
B 286 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.120101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.089142 restraints weight = 14959.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.57
r_work: 0.2972 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9051  Z= 0.104
  Angle     :  0.550   9.030  12407  Z= 0.259
  Chirality :  0.040   0.159   1424
  Planarity :  0.004   0.039   1552
  Dihedral  :  7.166  88.634   2025
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.32 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.26), residues: 1107
  helix:  2.22 (0.26), residues: 430
  sheet: -0.15 (0.35), residues: 218
  loop : -0.30 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.019   0.001   TYR C 138 
 PHE   0.012   0.001   PHE A  68 
 TRP   0.010   0.001   TRP A 325 
 HIS   0.003   0.000   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9051)
  covalent geometry    : angle       0.54984 (12407)
  hydrogen bonds       : bond        0.02801 (  422)
  hydrogen bonds       : angle       4.25609 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 52
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  206 ARG cc_start: 0.7502 (ttm170) cc_final: 0.7215 (mpt180)
REVERT: A  237 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7754 (tp30)
REVERT: A  332 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5204 (tpp-160)
REVERT: B   58 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6841 (mtm-85)
REVERT: B  105 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7918 (t80)
REVERT: C  138 TYR cc_start: 0.8678 (t80) cc_final: 0.8051 (t80)
  outliers start: 24
  outliers final: 9
  residues processed: 72
  average time/residue: 0.5875
  time to fit residues: 44.9826
Evaluate side-chains
  64 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  161 ASN
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 161 ASN
B 223 ASN
B 286 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.119906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.088853 restraints weight = 14916.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.57
r_work: 0.2964 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9051  Z= 0.123
  Angle     :  0.562   9.500  12407  Z= 0.265
  Chirality :  0.041   0.161   1424
  Planarity :  0.004   0.039   1552
  Dihedral  :  7.152  88.563   2025
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.32 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.26), residues: 1107
  helix:  2.22 (0.26), residues: 430
  sheet: -0.16 (0.35), residues: 218
  loop : -0.29 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 180 
 TYR   0.015   0.001   TYR C 138 
 PHE   0.012   0.001   PHE A  68 
 TRP   0.009   0.001   TRP A 325 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9051)
  covalent geometry    : angle       0.56161 (12407)
  hydrogen bonds       : bond        0.02820 (  422)
  hydrogen bonds       : angle       4.21065 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 52
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  206 ARG cc_start: 0.7515 (ttm170) cc_final: 0.7223 (mpt180)
REVERT: A  237 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7781 (tp30)
REVERT: A  332 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5167 (tpp-160)
REVERT: B  105 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7989 (t80)
REVERT: C  138 TYR cc_start: 0.8664 (t80) cc_final: 0.8061 (t80)
  outliers start: 25
  outliers final: 15
  residues processed: 73
  average time/residue: 0.5538
  time to fit residues: 42.9870
Evaluate side-chains
  71 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  161 ASN
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  281 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 10 optimal weight:    0.0770
   chunk 35 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 161 ASN
B 223 ASN
B 286 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.120561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.089753 restraints weight = 15019.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.56
r_work: 0.2964 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9051  Z= 0.129
  Angle     :  0.562   9.636  12407  Z= 0.264
  Chirality :  0.041   0.161   1424
  Planarity :  0.004   0.040   1552
  Dihedral  :  7.147  88.596   2025
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.43 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.26), residues: 1107
  helix:  2.23 (0.26), residues: 430
  sheet: -0.16 (0.35), residues: 217
  loop : -0.28 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.014   0.001   TYR C 138 
 PHE   0.012   0.001   PHE A  68 
 TRP   0.008   0.001   TRP A 325 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9051)
  covalent geometry    : angle       0.56198 (12407)
  hydrogen bonds       : bond        0.02828 (  422)
  hydrogen bonds       : angle       4.19997 ( 1215)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 52
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  206 ARG cc_start: 0.7526 (ttm170) cc_final: 0.7229 (mpt180)
REVERT: A  237 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7784 (tp30)
REVERT: A  332 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.5168 (tpp-160)
REVERT: B  105 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7986 (t80)
REVERT: C  138 TYR cc_start: 0.8672 (t80) cc_final: 0.8079 (t80)
  outliers start: 23
  outliers final: 13
  residues processed: 71
  average time/residue: 0.6128
  time to fit residues: 46.2462
Evaluate side-chains
  68 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  105 PHE
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  281 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 161 ASN
B 223 ASN
B 286 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.120351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.089362 restraints weight = 14834.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.57
r_work: 0.2968 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9051  Z= 0.125
  Angle     :  0.563   9.831  12407  Z= 0.265
  Chirality :  0.041   0.161   1424
  Planarity :  0.004   0.047   1552
  Dihedral  :  7.129  88.472   2025
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.55 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.26), residues: 1107
  helix:  2.25 (0.26), residues: 430
  sheet: -0.11 (0.34), residues: 222
  loop : -0.34 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 180 
 TYR   0.013   0.001   TYR C 138 
 PHE   0.011   0.001   PHE A  68 
 TRP   0.009   0.001   TRP A 325 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9051)
  covalent geometry    : angle       0.56313 (12407)
  hydrogen bonds       : bond        0.02785 (  422)
  hydrogen bonds       : angle       4.17902 ( 1215)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2325.00 seconds
wall clock time: 40 minutes 33.67 seconds (2433.67 seconds total)