Starting phenix.real_space_refine
on Tue Mar  3 17:07:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9onj_70642/03_2026/9onj_70642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9onj_70642/03_2026/9onj_70642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9onj_70642/03_2026/9onj_70642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9onj_70642/03_2026/9onj_70642.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9onj_70642/03_2026/9onj_70642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9onj_70642/03_2026/9onj_70642.map"
  }
  resolution = 3.72
  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=   0.001 sd=   0.007
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      22      5.16       5
     C    4497      2.51       5
     N    1360      2.21       5
     O    1385      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7264
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 1766
          Classifications: {'peptide': 359}
          Incomplete info: {'truncation_to_alanine': 294}
          Link IDs: {'PTRANS': 17, 'TRANS': 341}
          Unresolved chain link angles: 17
          Unresolved non-hydrogen bonds: 1100
          Unresolved non-hydrogen angles: 1415
          Unresolved non-hydrogen dihedrals: 911
          Unresolved non-hydrogen chiralities: 104
          Planarities with less than four sites: {'ARG:plan': 29, 'PHE:plan': 10, 'HIS:plan': 4, 'GLN:plan1': 8, 'GLU:plan': 27, 'TYR:plan': 13, 'ASN:plan1': 10, 'ASP:plan': 23, 'TRP:plan': 6}
          Unresolved non-hydrogen planarities: 609
    Chain: "C"
      Number of atoms: 2665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2665
          Classifications: {'peptide': 379}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 357}
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 174
          Unresolved non-hydrogen angles: 226
          Unresolved non-hydrogen dihedrals: 138
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 108
    Chain: "B"
      Number of atoms: 2833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 2833
          Classifications: {'peptide': 395}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 373}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 139
          Unresolved non-hydrogen angles: 180
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 96
  Time building chain proxies: 2.09, per 1000 atoms: 0.29
  Number of scatterers: 7264
  At special positions: 0
  Unit cell: (80.987, 101.048, 123.338, 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      22     16.00
     O    1385      8.00
     N    1360      7.00
     C    4497      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: 0.78
  Conformation dependent library (CDL) restraints added in 323.3 milliseconds
  

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2074

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 4 sheets defined
      55.5% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 111
      removed outlier: 3.660A  pdb=" N   GLU A 111 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 133 through 144
    Processing helix  chain 'A' and resid 160 through 174
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.184A  pdb=" N   VAL A 213 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 220
      removed outlier: 3.535A  pdb=" N   LEU A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 240 through 242
      No H-bonds generated for 'chain 'A' and resid 240 through 242'
    Processing helix  chain 'A' and resid 255 through 265
    Processing helix  chain 'A' and resid 276 through 292
    Processing helix  chain 'A' and resid 293 through 322
      Proline residue:  A 317  - end of helix
      removed outlier: 3.992A  pdb=" N   ALA A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ARG A 321 " --> pdb=" O   PRO A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 346
      removed outlier: 3.561A  pdb=" N   TRP A 337 " --> pdb=" O   GLY A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 368
    Processing helix  chain 'A' and resid 383 through 392
    Processing helix  chain 'A' and resid 418 through 422
    Processing helix  chain 'A' and resid 426 through 444
    Processing helix  chain 'A' and resid 445 through 451
    Processing helix  chain 'C' and resid 19 through 29
      removed outlier: 3.828A  pdb=" N   GLY C  23 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 91
    Processing helix  chain 'C' and resid 111 through 117
    Processing helix  chain 'C' and resid 119 through 121
      No H-bonds generated for 'chain 'C' and resid 119 through 121'
    Processing helix  chain 'C' and resid 122 through 126
      removed outlier: 3.852A  pdb=" N   TYR C 125 " --> pdb=" O   TYR C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 158
      removed outlier: 3.671A  pdb=" N   GLY C 145 " --> pdb=" O   CYS C 141 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL C 158 " --> pdb=" O   VAL C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 194
    Processing helix  chain 'C' and resid 227 through 233
    Processing helix  chain 'C' and resid 234 through 237
    Processing helix  chain 'C' and resid 247 through 259
    Processing helix  chain 'C' and resid 270 through 286
      removed outlier: 3.713A  pdb=" N   ASP C 275 " --> pdb=" O   LEU C 271 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ALA C 276 " --> pdb=" O   ASP C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 312
      removed outlier: 3.549A  pdb=" N   LYS C 294 " --> pdb=" O   PRO C 290 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA C 298 " --> pdb=" O   LYS C 294 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   PHE C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   MET C 310 " --> pdb=" O   ASP C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 336
      removed outlier: 3.738A  pdb=" N   SER C 334 " --> pdb=" O   ALA C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 348 through 354
      removed outlier: 3.552A  pdb=" N   VAL C 352 " --> pdb=" O   ALA C 349 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 363 through 375
    Processing helix  chain 'C' and resid 382 through 384
      No H-bonds generated for 'chain 'C' and resid 382 through 384'
    Processing helix  chain 'C' and resid 385 through 392
    Processing helix  chain 'C' and resid 416 through 435
      removed outlier: 3.697A  pdb=" N   HIS C 434 " --> pdb=" O   LEU C 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 30
    Processing helix  chain 'B' and resid 43 through 57
    Processing helix  chain 'B' and resid 77 through 91
    Processing helix  chain 'B' and resid 102 through 108
    Processing helix  chain 'B' and resid 110 through 122
      removed outlier: 4.079A  pdb=" N   ALA B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 126
    Processing helix  chain 'B' and resid 141 through 158
    Processing helix  chain 'B' and resid 161 through 165
      removed outlier: 4.181A  pdb=" N   GLN B 164 " --> pdb=" O   ARG B 161 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   VAL B 165 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 161 through 165'
    Processing helix  chain 'B' and resid 181 through 195
      removed outlier: 4.012A  pdb=" N   PHE B 195 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
    Processing helix  chain 'B' and resid 233 through 236
    Processing helix  chain 'B' and resid 247 through 259
    Processing helix  chain 'B' and resid 269 through 286
      removed outlier: 4.391A  pdb=" N   ALA B 273 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 307
      removed outlier: 3.568A  pdb=" N   LYS B 294 " --> pdb=" O   PRO B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 3.871A  pdb=" N   LEU B 311 " --> pdb=" O   THR B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 334
    Processing helix  chain 'B' and resid 348 through 354
    Processing helix  chain 'B' and resid 363 through 375
    Processing helix  chain 'B' and resid 385 through 393
    Processing helix  chain 'B' and resid 417 through 435
      removed outlier: 3.680A  pdb=" N   HIS B 434 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 39
    Processing sheet with id=AA2, first strand: chain 'C' and resid 199 through 202
      removed outlier: 6.537A  pdb=" N   VAL C 172 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   ILE C 202 " --> pdb=" O   VAL C 172 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   VAL C 174 " --> pdb=" O   ILE C 202 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   ASN C 173 " --> pdb=" O   LEU C 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 38
      removed outlier: 3.755A  pdb=" N   GLY B  97 " --> pdb=" O   MET B  35 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 198 through 201
      removed outlier: 6.775A  pdb=" N   VAL B 172 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   GLN B 171 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   LEU B 241 " --> pdb=" O   GLN B 171 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ASN B 173 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    398 hydrogen bonds defined for protein.
    1155 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.93

  Time building geometry restraints manager: 0.98 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: 2589
        1.34 -     1.46: 707
        1.46 -     1.57: 4021
        1.57 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 7353
  Sorted by residual:
  bond pdb=" C   ASP B 323 "
       pdb=" N   LEU B 324 "
    ideal  model  delta    sigma   weight residual
    1.335  1.268  0.067 1.36e-02 5.41e+03 2.42e+01
  bond pdb=" N   VAL B 131 "
       pdb=" CA  VAL B 131 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 7.60e-03 1.73e+04 2.09e+01
  bond pdb=" C   LEU B 324 "
       pdb=" N   LEU B 325 "
    ideal  model  delta    sigma   weight residual
    1.334  1.387 -0.053 1.27e-02 6.20e+03 1.73e+01
  bond pdb=" C   ALA B 229 "
       pdb=" N   GLU B 230 "
    ideal  model  delta    sigma   weight residual
    1.334  1.275  0.059 1.46e-02 4.69e+03 1.64e+01
  bond pdb=" N   VAL C 131 "
       pdb=" CA  VAL C 131 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 9.10e-03 1.21e+04 1.34e+01
  ... (remaining 7348 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 9408
        1.61 -     3.23: 526
        3.23 -     4.84: 102
        4.84 -     6.45: 22
        6.45 -     8.06: 5
  Bond angle restraints: 10063
  Sorted by residual:
  angle pdb=" CA  ARG B 263 "
        pdb=" C   ARG B 263 "
        pdb=" O   ARG B 263 "
      ideal   model   delta    sigma   weight residual
     121.55  116.30    5.25 1.06e+00 8.90e-01 2.45e+01
  angle pdb=" C   PHE C 142 "
        pdb=" CA  PHE C 142 "
        pdb=" CB  PHE C 142 "
      ideal   model   delta    sigma   weight residual
     110.68  102.62    8.06 1.70e+00 3.46e-01 2.25e+01
  angle pdb=" CA  GLY B 244 "
        pdb=" C   GLY B 244 "
        pdb=" O   GLY B 244 "
      ideal   model   delta    sigma   weight residual
     120.94  117.43    3.51 7.80e-01 1.64e+00 2.03e+01
  angle pdb=" C   GLN B  42 "
        pdb=" CA  GLN B  42 "
        pdb=" CB  GLN B  42 "
      ideal   model   delta    sigma   weight residual
     115.79  110.49    5.30 1.19e+00 7.06e-01 1.99e+01
  angle pdb=" CA  GLY B 266 "
        pdb=" C   GLY B 266 "
        pdb=" O   GLY B 266 "
      ideal   model   delta    sigma   weight residual
     122.28  117.84    4.44 1.00e+00 1.00e+00 1.97e+01
  ... (remaining 10058 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.93: 3911
       14.93 -    29.86: 318
       29.86 -    44.78: 108
       44.78 -    59.71: 24
       59.71 -    74.64: 11
  Dihedral angle restraints: 4372
    sinusoidal: 1165
      harmonic: 3207
  Sorted by residual:
  dihedral pdb=" C   PHE C 142 "
           pdb=" N   PHE C 142 "
           pdb=" CA  PHE C 142 "
           pdb=" CB  PHE C 142 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.00   -9.60     0      2.50e+00 1.60e-01 1.47e+01
  dihedral pdb=" CA  GLU B 193 "
           pdb=" CB  GLU B 193 "
           pdb=" CG  GLU B 193 "
           pdb=" CD  GLU B 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.93   59.93     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   MET B 335 "
           pdb=" CA  MET B 335 "
           pdb=" CB  MET B 335 "
           pdb=" CG  MET B 335 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.20   53.20     3      1.50e+01 4.44e-03 9.18e+00
  ... (remaining 4369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 900
       0.046 -    0.091: 228
       0.091 -    0.137: 82
       0.137 -    0.183: 18
       0.183 -    0.228: 7
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" CA  PHE C 142 "
            pdb=" N   PHE C 142 "
            pdb=" C   PHE C 142 "
            pdb=" CB  PHE C 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  ILE B 130 "
            pdb=" N   ILE B 130 "
            pdb=" C   ILE B 130 "
            pdb=" CB  ILE B 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  GLU B 230 "
            pdb=" N   GLU B 230 "
            pdb=" C   GLU B 230 "
            pdb=" CB  GLU B 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1232 not shown)

  Planarity restraints: 1368
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 412 "    0.231 9.50e-02 1.11e+02   1.03e-01 6.58e+00
        pdb=" NE  ARG B 412 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 412 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 412 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 412 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 264 "    0.228 9.50e-02 1.11e+02   1.02e-01 6.39e+00
        pdb=" NE  ARG C 264 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 264 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 264 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 264 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 354 "    0.041 5.00e-02 4.00e+02   6.28e-02 6.32e+00
        pdb=" N   PRO C 355 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO C 355 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 355 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1365 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 3850
        3.00 -     3.47: 7725
        3.47 -     3.95: 10938
        3.95 -     4.42: 12062
        4.42 -     4.90: 19095
  Nonbonded interactions: 53670
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 339 "
            pdb=" O   ALA B 341 "
     model   vdw
     2.520 3.040
  nonbonded pdb=" O   ASN B  92 "
            pdb=" OD1 ASN B  92 "
     model   vdw
     2.522 3.040
  nonbonded pdb=" N   LEU B  37 "
            pdb=" O   LEU B  37 "
     model   vdw
     2.561 2.496
  nonbonded pdb=" N   ARG B 263 "
            pdb=" O   ARG B 263 "
     model   vdw
     2.572 2.496
  nonbonded pdb=" N   GLY C 266 "
            pdb=" O   GLY C 266 "
     model   vdw
     2.580 2.496
  ... (remaining 53665 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 19 through 40 or resid 45 through 46 or resid 48 or (resid \ 
 77 through 96 and (name N or name CA or name C or name O or name CB )) or resid \ 
 97 or (resid 98 through 101 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 102 or (resid 103 through 105 and (name N or name CA or name C or \ 
 name O or name CB )) or (resid 110 through 117 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 119 through 138 or (resid 139 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 140 through 162 or (resid 163  \ 
and (name N or name CA or name C or name O or name CB )) or resid 164 through 22 \ 
2 or resid 224 through 437))
  selection = (chain 'C' and (resid 19 through 40 or resid 65 through 66 or resid 76 through 2 \ 
90 or (resid 291 and (name N or name CA or name C or name O or name CB )) or res \ 
id 292 through 298 or (resid 299 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 300 through 437))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.720
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
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      :  0.006   0.067   7353  Z= 0.413
  Angle     :  0.834   8.065  10063  Z= 0.570
  Chirality :  0.050   0.228   1235
  Planarity :  0.007   0.103   1368
  Dihedral  : 13.987  74.641   2298
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.69 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.35 (0.26), residues: 1113
  helix:  1.49 (0.23), residues: 528
  sheet: -1.73 (0.57), residues: 80
  loop : -1.93 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 412 
 TYR   0.011   0.001   TYR B 269 
 PHE   0.031   0.002   PHE B 410 
 TRP   0.012   0.002   TRP C 414 
 HIS   0.009   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 7353)
  covalent geometry    : angle       0.83439 (10063)
  hydrogen bonds       : bond        0.15242 (  398)
  hydrogen bonds       : angle       6.00231 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0745
  time to fit residues: 19.5378
Evaluate side-chains
  130 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
B 134 ASN
B 236 GLN
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.082076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.057550 restraints weight = 34491.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.059271 restraints weight = 21537.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.060485 restraints weight = 15688.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.061302 restraints weight = 12702.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.061825 restraints weight = 10973.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7353  Z= 0.149
  Angle     :  0.626   7.906  10063  Z= 0.313
  Chirality :  0.041   0.206   1235
  Planarity :  0.004   0.047   1368
  Dihedral  :  3.562  14.160   1180
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 24.62 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.08 (0.26), residues: 1113
  helix:  1.72 (0.22), residues: 543
  sheet: -1.75 (0.56), residues: 80
  loop : -1.62 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 257 
 TYR   0.016   0.001   TYR B 187 
 PHE   0.026   0.002   PHE C 328 
 TRP   0.012   0.001   TRP B 277 
 HIS   0.004   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7353)
  covalent geometry    : angle       0.62646 (10063)
  hydrogen bonds       : bond        0.03716 (  398)
  hydrogen bonds       : angle       4.31219 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   22 MET cc_start: 0.9396 (mmm) cc_final: 0.9102 (mpp)
REVERT: C   39 HIS cc_start: 0.9187 (t70) cc_final: 0.8890 (t70)
REVERT: C  193 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9048 (mm-30)
REVERT: C  197 LEU cc_start: 0.9163 (mt) cc_final: 0.8669 (mt)
REVERT: C  279 MET cc_start: 0.8464 (mmp) cc_final: 0.8214 (mmt)
REVERT: C  426 ASP cc_start: 0.9157 (m-30) cc_final: 0.8930 (m-30)
REVERT: B  281 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9401 (mm)
REVERT: B  398 ARG cc_start: 0.8403 (mtt90) cc_final: 0.8077 (mtt90)
REVERT: B  403 GLN cc_start: 0.9236 (mt0) cc_final: 0.8714 (mp10)
REVERT: B  411 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7770 (tm-30)
  outliers start: 28
  outliers final: 15
  residues processed: 145
  average time/residue: 0.0624
  time to fit residues: 13.4051
Evaluate side-chains
  131 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  176 CYS
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  369 HIS
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  411 GLN
Chi-restraints excluded: chain B residue  433 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 8 optimal weight:   10.0000
   chunk 78 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 105 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 19 optimal weight:   40.0000
   chunk 98 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.081467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.056862 restraints weight = 33799.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.058480 restraints weight = 21742.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.059568 restraints weight = 16129.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.060334 restraints weight = 13171.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.060769 restraints weight = 11461.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7353  Z= 0.138
  Angle     :  0.593   8.652  10063  Z= 0.296
  Chirality :  0.041   0.241   1235
  Planarity :  0.004   0.049   1368
  Dihedral  :  3.469  13.642   1180
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 27.12 %
    Favored  : 68.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.26 (0.26), residues: 1113
  helix:  1.91 (0.22), residues: 543
  sheet: -1.64 (0.59), residues: 78
  loop : -1.59 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 263 
 TYR   0.012   0.001   TYR B 187 
 PHE   0.014   0.002   PHE C 425 
 TRP   0.011   0.001   TRP B 277 
 HIS   0.003   0.001   HIS B 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7353)
  covalent geometry    : angle       0.59301 (10063)
  hydrogen bonds       : bond        0.03304 (  398)
  hydrogen bonds       : angle       4.10157 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 MET cc_start: 0.6853 (tpt) cc_final: 0.6113 (tmm)
REVERT: C  193 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9073 (mm-30)
REVERT: C  279 MET cc_start: 0.8497 (mmp) cc_final: 0.8226 (mmt)
REVERT: C  426 ASP cc_start: 0.9170 (m-30) cc_final: 0.8929 (m-30)
REVERT: B  281 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9354 (mm)
REVERT: B  403 GLN cc_start: 0.9196 (mt0) cc_final: 0.8672 (mp10)
REVERT: B  410 PHE cc_start: 0.8790 (p90) cc_final: 0.8472 (p90)
  outliers start: 22
  outliers final: 16
  residues processed: 135
  average time/residue: 0.0637
  time to fit residues: 12.6357
Evaluate side-chains
  125 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  176 CYS
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  369 HIS
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  433 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:   30.0000
   chunk 86 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 80 optimal weight:   30.0000
   chunk 28 optimal weight:    0.0570
   chunk 51 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    0.3980
   chunk 44 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   overall best weight:    1.2904

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

Flipped N/Q/H residues before XYZ refinement:
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.081610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.056501 restraints weight = 34515.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.058123 restraints weight = 22373.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.059282 restraints weight = 16571.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.060017 restraints weight = 13480.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.060602 restraints weight = 11808.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7353  Z= 0.109
  Angle     :  0.591  12.055  10063  Z= 0.287
  Chirality :  0.041   0.241   1235
  Planarity :  0.004   0.048   1368
  Dihedral  :  3.386  15.987   1180
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 27.69 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.39 (0.26), residues: 1113
  helix:  2.02 (0.22), residues: 544
  sheet: -1.69 (0.64), residues: 66
  loop : -1.53 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 263 
 TYR   0.022   0.002   TYR C 404 
 PHE   0.009   0.001   PHE C 425 
 TRP   0.009   0.001   TRP B 277 
 HIS   0.002   0.001   HIS B 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7353)
  covalent geometry    : angle       0.59054 (10063)
  hydrogen bonds       : bond        0.02978 (  398)
  hydrogen bonds       : angle       3.94454 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 MET cc_start: 0.6992 (tpt) cc_final: 0.6180 (tmm)
REVERT: C   39 HIS cc_start: 0.9277 (t70) cc_final: 0.8948 (t70)
REVERT: C  193 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9093 (mm-30)
REVERT: C  279 MET cc_start: 0.8498 (mmp) cc_final: 0.8200 (mmt)
REVERT: C  426 ASP cc_start: 0.9172 (m-30) cc_final: 0.8925 (m-30)
REVERT: B  281 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9367 (mm)
REVERT: B  403 GLN cc_start: 0.9216 (mt0) cc_final: 0.8622 (mp10)
REVERT: B  407 LEU cc_start: 0.9508 (mm) cc_final: 0.9260 (mm)
REVERT: B  410 PHE cc_start: 0.8797 (p90) cc_final: 0.8339 (p90)
  outliers start: 21
  outliers final: 15
  residues processed: 131
  average time/residue: 0.0671
  time to fit residues: 12.6145
Evaluate side-chains
  126 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  173 ASN
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  369 HIS
Chi-restraints excluded: chain B residue  426 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 104 optimal weight:    6.9990
   chunk 100 optimal weight:    0.6980
   chunk 31 optimal weight:   30.0000
   chunk 17 optimal weight:   20.0000
   chunk 94 optimal weight:    0.2980
   chunk 79 optimal weight:   40.0000
   chunk 44 optimal weight:   10.0000
   chunk 3 optimal weight:   50.0000
   chunk 42 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0670
   overall best weight:    1.4122

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

Flipped N/Q/H residues before XYZ refinement:
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.080883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.056090 restraints weight = 34049.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.057699 restraints weight = 21918.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.058792 restraints weight = 16325.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.059487 restraints weight = 13354.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.060042 restraints weight = 11766.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7353  Z= 0.109
  Angle     :  0.587  13.217  10063  Z= 0.284
  Chirality :  0.040   0.233   1235
  Planarity :  0.004   0.039   1368
  Dihedral  :  3.367  16.391   1180
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 28.85 %
    Favored  : 67.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.54 (0.26), residues: 1113
  helix:  2.18 (0.22), residues: 545
  sheet: -1.57 (0.65), residues: 66
  loop : -1.51 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 257 
 TYR   0.011   0.001   TYR B 404 
 PHE   0.037   0.002   PHE B 328 
 TRP   0.009   0.001   TRP B 277 
 HIS   0.002   0.001   HIS B 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7353)
  covalent geometry    : angle       0.58742 (10063)
  hydrogen bonds       : bond        0.02845 (  398)
  hydrogen bonds       : angle       3.87827 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  193 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9125 (mm-30)
REVERT: C  279 MET cc_start: 0.8505 (mmp) cc_final: 0.8188 (mmt)
REVERT: C  426 ASP cc_start: 0.9185 (m-30) cc_final: 0.8930 (m-30)
REVERT: B  281 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9366 (mm)
REVERT: B  403 GLN cc_start: 0.9195 (mt0) cc_final: 0.8616 (mp10)
REVERT: B  407 LEU cc_start: 0.9502 (mm) cc_final: 0.9269 (mm)
REVERT: B  410 PHE cc_start: 0.8813 (p90) cc_final: 0.8337 (p90)
  outliers start: 21
  outliers final: 14
  residues processed: 129
  average time/residue: 0.0682
  time to fit residues: 12.7433
Evaluate side-chains
  126 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  173 ASN
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  388 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 6 optimal weight:   50.0000
   chunk 24 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   chunk 79 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0060
   chunk 97 optimal weight:    0.8980
   chunk 13 optimal weight:   50.0000
   overall best weight:    1.9200

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

Flipped N/Q/H residues before XYZ refinement:
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.079991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.055663 restraints weight = 34936.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.057252 restraints weight = 22504.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.058345 restraints weight = 16673.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.059088 restraints weight = 13643.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.059595 restraints weight = 11893.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7353  Z= 0.124
  Angle     :  0.602  14.797  10063  Z= 0.292
  Chirality :  0.041   0.220   1235
  Planarity :  0.004   0.039   1368
  Dihedral  :  3.348  16.670   1180
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 29.04 %
    Favored  : 66.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.65 (0.26), residues: 1113
  helix:  2.27 (0.22), residues: 543
  sheet: -1.45 (0.66), residues: 67
  loop : -1.45 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  54 
 TYR   0.015   0.001   TYR B 269 
 PHE   0.028   0.002   PHE B 328 
 TRP   0.008   0.001   TRP B 277 
 HIS   0.002   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7353)
  covalent geometry    : angle       0.60168 (10063)
  hydrogen bonds       : bond        0.02889 (  398)
  hydrogen bonds       : angle       3.91502 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  193 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9135 (mm-30)
REVERT: C  279 MET cc_start: 0.8522 (mmp) cc_final: 0.8194 (mmt)
REVERT: C  426 ASP cc_start: 0.9187 (m-30) cc_final: 0.8920 (m-30)
REVERT: B  281 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9369 (mm)
REVERT: B  398 ARG cc_start: 0.8544 (mtt90) cc_final: 0.8091 (mtt90)
REVERT: B  403 GLN cc_start: 0.9179 (mt0) cc_final: 0.8625 (mp10)
REVERT: B  407 LEU cc_start: 0.9509 (mm) cc_final: 0.9279 (mm)
REVERT: B  410 PHE cc_start: 0.8813 (p90) cc_final: 0.8332 (p90)
  outliers start: 23
  outliers final: 19
  residues processed: 123
  average time/residue: 0.0668
  time to fit residues: 12.0288
Evaluate side-chains
  126 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  173 ASN
Chi-restraints excluded: chain C residue  176 CYS
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  369 HIS
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  426 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:   70.0000
   chunk 110 optimal weight:    2.9990
   chunk 25 optimal weight:   20.0000
   chunk 11 optimal weight:   30.0000
   chunk 80 optimal weight:   30.0000
   chunk 9 optimal weight:    0.9980
   chunk 82 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B 179 ASN
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.079916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.055728 restraints weight = 34940.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.057318 restraints weight = 22560.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.058416 restraints weight = 16822.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.059171 restraints weight = 13790.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.059665 restraints weight = 12038.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7353  Z= 0.114
  Angle     :  0.610  14.681  10063  Z= 0.294
  Chirality :  0.040   0.208   1235
  Planarity :  0.004   0.046   1368
  Dihedral  :  3.360  22.781   1180
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 30.77 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.75 (0.26), residues: 1113
  helix:  2.32 (0.22), residues: 545
  sheet: -1.60 (0.61), residues: 74
  loop : -1.34 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 257 
 TYR   0.015   0.001   TYR B 269 
 PHE   0.027   0.002   PHE B 328 
 TRP   0.008   0.001   TRP B 277 
 HIS   0.003   0.001   HIS C 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7353)
  covalent geometry    : angle       0.61037 (10063)
  hydrogen bonds       : bond        0.02797 (  398)
  hydrogen bonds       : angle       3.90726 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  193 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9135 (mm-30)
REVERT: C  426 ASP cc_start: 0.9192 (m-30) cc_final: 0.8922 (m-30)
REVERT: B  186 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8868 (tm-30)
REVERT: B  281 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9357 (mm)
REVERT: B  398 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8110 (mtt90)
REVERT: B  403 GLN cc_start: 0.9161 (mt0) cc_final: 0.8574 (mp10)
REVERT: B  407 LEU cc_start: 0.9524 (mm) cc_final: 0.9287 (mm)
REVERT: B  410 PHE cc_start: 0.8815 (p90) cc_final: 0.8324 (p90)
  outliers start: 23
  outliers final: 17
  residues processed: 121
  average time/residue: 0.0676
  time to fit residues: 12.0403
Evaluate side-chains
  125 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  173 ASN
Chi-restraints excluded: chain C residue  176 CYS
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  179 ASN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  369 HIS
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  426 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 12 optimal weight:   50.0000
   chunk 15 optimal weight:   30.0000
   chunk 21 optimal weight:   50.0000
   chunk 50 optimal weight:    7.9990
   chunk 53 optimal weight:    0.5980
   chunk 29 optimal weight:   20.0000
   chunk 82 optimal weight:    0.5980
   chunk 94 optimal weight:    5.9990
   chunk 10 optimal weight:   50.0000
   chunk 81 optimal weight:    8.9990
   chunk 5 optimal weight:    0.2980
   overall best weight:    3.0984

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

Flipped N/Q/H residues before XYZ refinement:
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.078526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.054429 restraints weight = 35548.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.055978 restraints weight = 22927.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.057052 restraints weight = 17056.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.057783 restraints weight = 13946.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.058266 restraints weight = 12170.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7353  Z= 0.169
  Angle     :  0.641  14.115  10063  Z= 0.314
  Chirality :  0.041   0.190   1235
  Planarity :  0.004   0.041   1368
  Dihedral  :  3.512  18.903   1180
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 30.77 %
    Favored  : 64.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.68 (0.26), residues: 1113
  helix:  2.22 (0.22), residues: 547
  sheet: -1.56 (0.57), residues: 84
  loop : -1.33 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 257 
 TYR   0.013   0.001   TYR B 269 
 PHE   0.027   0.002   PHE C 425 
 TRP   0.010   0.001   TRP B 277 
 HIS   0.003   0.001   HIS C 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7353)
  covalent geometry    : angle       0.64145 (10063)
  hydrogen bonds       : bond        0.03055 (  398)
  hydrogen bonds       : angle       4.00983 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  193 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9113 (mm-30)
REVERT: C  426 ASP cc_start: 0.9192 (m-30) cc_final: 0.8927 (m-30)
REVERT: C  439 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8980 (pp30)
REVERT: B  186 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8849 (tm-30)
REVERT: B  281 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9359 (mm)
REVERT: B  368 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8617 (mt-10)
REVERT: B  398 ARG cc_start: 0.8583 (mtt90) cc_final: 0.8112 (mtt90)
REVERT: B  407 LEU cc_start: 0.9550 (mm) cc_final: 0.9310 (mm)
REVERT: B  410 PHE cc_start: 0.8839 (p90) cc_final: 0.8308 (p90)
  outliers start: 24
  outliers final: 20
  residues processed: 119
  average time/residue: 0.0665
  time to fit residues: 11.6026
Evaluate side-chains
  121 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  173 ASN
Chi-restraints excluded: chain C residue  176 CYS
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain C residue  439 GLN
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  369 HIS
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  426 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:   50.0000
   chunk 42 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 30 optimal weight:   40.0000
   chunk 39 optimal weight:   20.0000
   chunk 73 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 179 ASN
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.077659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.053648 restraints weight = 35554.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.055127 restraints weight = 23163.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.056153 restraints weight = 17406.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.056863 restraints weight = 14382.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.057196 restraints weight = 12610.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.4253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7353  Z= 0.172
  Angle     :  0.661  13.925  10063  Z= 0.325
  Chirality :  0.040   0.146   1235
  Planarity :  0.004   0.046   1368
  Dihedral  :  3.676  27.779   1180
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 30.58 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 (0.26), residues: 1113
  helix:  2.13 (0.22), residues: 548
  sheet: -1.83 (0.60), residues: 74
  loop : -1.37 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 257 
 TYR   0.015   0.002   TYR C 269 
 PHE   0.025   0.002   PHE C 309 
 TRP   0.009   0.001   TRP B 277 
 HIS   0.003   0.001   HIS B 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7353)
  covalent geometry    : angle       0.66091 (10063)
  hydrogen bonds       : bond        0.03242 (  398)
  hydrogen bonds       : angle       4.08527 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  190 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8890 (mm-30)
REVERT: C  193 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9104 (mm-30)
REVERT: C  426 ASP cc_start: 0.9150 (m-30) cc_final: 0.8879 (m-30)
REVERT: C  439 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8978 (pp30)
REVERT: B  186 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8856 (tm-30)
REVERT: B  281 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9334 (mm)
REVERT: B  368 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8743 (mm-30)
REVERT: B  407 LEU cc_start: 0.9525 (mm) cc_final: 0.9250 (mm)
REVERT: B  410 PHE cc_start: 0.8923 (p90) cc_final: 0.8362 (p90)
  outliers start: 24
  outliers final: 21
  residues processed: 116
  average time/residue: 0.0625
  time to fit residues: 10.7726
Evaluate side-chains
  118 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  173 ASN
Chi-restraints excluded: chain C residue  176 CYS
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain C residue  427 LEU
Chi-restraints excluded: chain C residue  439 GLN
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  179 ASN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  308 HIS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  369 HIS
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  426 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 92 optimal weight:    0.8980
   chunk 44 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 25 optimal weight:   30.0000
   chunk 40 optimal weight:   50.0000
   chunk 37 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    6.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 134 ASN
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 HIS
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.074909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.051348 restraints weight = 36597.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.052759 restraints weight = 23615.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.053770 restraints weight = 17747.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.054423 restraints weight = 14600.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.054866 restraints weight = 12801.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   7353  Z= 0.314
  Angle     :  0.788  12.889  10063  Z= 0.401
  Chirality :  0.043   0.148   1235
  Planarity :  0.005   0.055   1368
  Dihedral  :  4.248  25.491   1180
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 30.77 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.04 (0.26), residues: 1113
  helix:  1.62 (0.22), residues: 549
  sheet: -2.05 (0.56), residues: 85
  loop : -1.51 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 257 
 TYR   0.012   0.002   TYR B 404 
 PHE   0.025   0.003   PHE C 328 
 TRP   0.020   0.003   TRP C 414 
 HIS   0.006   0.002   HIS C 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 ( 7353)
  covalent geometry    : angle       0.78770 (10063)
  hydrogen bonds       : bond        0.04095 (  398)
  hydrogen bonds       : angle       4.56139 ( 1155)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 MET cc_start: 0.7597 (tpt) cc_final: 0.7396 (tpt)
REVERT: C  193 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9049 (mm-30)
REVERT: C  279 MET cc_start: 0.7803 (mmt) cc_final: 0.7200 (mmt)
REVERT: C  426 ASP cc_start: 0.9187 (m-30) cc_final: 0.8961 (m-30)
REVERT: B  171 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6347 (tm-30)
REVERT: B  186 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8873 (tm-30)
REVERT: B  281 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9332 (mm)
REVERT: B  410 PHE cc_start: 0.8960 (p90) cc_final: 0.8431 (p90)
  outliers start: 23
  outliers final: 18
  residues processed: 108
  average time/residue: 0.0614
  time to fit residues: 9.7781
Evaluate side-chains
  109 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue  173 ASN
Chi-restraints excluded: chain C residue  176 CYS
Chi-restraints excluded: chain C residue  359 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  171 GLN
Chi-restraints excluded: chain B residue  179 ASN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  308 HIS
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  369 HIS
Chi-restraints excluded: chain B residue  388 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0870
   chunk 3 optimal weight:   50.0000
   overall best weight:    0.9364

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

Flipped N/Q/H residues before XYZ refinement:
** B  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 179 ASN
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.078425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.054440 restraints weight = 34476.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.056056 restraints weight = 21824.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.057174 restraints weight = 16022.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.057953 restraints weight = 12979.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.058478 restraints weight = 11223.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.4573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7353  Z= 0.115
  Angle     :  0.671  15.540  10063  Z= 0.325
  Chirality :  0.041   0.145   1235
  Planarity :  0.004   0.054   1368
  Dihedral  :  3.763  29.085   1180
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 32.69 %
    Favored  : 64.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.61 (0.26), residues: 1113
  helix:  2.11 (0.22), residues: 548
  sheet: -1.86 (0.59), residues: 74
  loop : -1.25 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 168 
 TYR   0.017   0.002   TYR B 269 
 PHE   0.030   0.002   PHE B 328 
 TRP   0.008   0.001   TRP B 277 
 HIS   0.004   0.001   HIS B 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7353)
  covalent geometry    : angle       0.67059 (10063)
  hydrogen bonds       : bond        0.03143 (  398)
  hydrogen bonds       : angle       4.07887 ( 1155)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1564.92 seconds
wall clock time: 27 minutes 23.91 seconds (1643.91 seconds total)