Starting phenix.real_space_refine
on Fri Jul  3 20:24:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vjh_43281/07_2026/8vjh_43281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vjh_43281/07_2026/8vjh_43281.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vjh_43281/07_2026/8vjh_43281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vjh_43281/07_2026/8vjh_43281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vjh_43281/07_2026/8vjh_43281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vjh_43281/07_2026/8vjh_43281.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
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: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      66      5.16       5
     C    9861      2.51       5
     N    2860      2.21       5
     O    3179      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 15967
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 769, 4654
          Classifications: {'peptide': 769}
          Incomplete info: {'backbone_only': 331}
          Link IDs: {'PTRANS': 42, 'TRANS': 726}
          Unresolved chain link angles: 26
          Unresolved non-hydrogen bonds: 1464
          Unresolved non-hydrogen angles: 2145
          Unresolved non-hydrogen dihedrals: 956
          Unresolved non-hydrogen chiralities: 428
          Planarities with less than four sites: {'TYR:plan': 18, 'GLU:plan': 21, 'ASN:plan1': 15, 'ARG:plan': 19, 'ASP:plan': 29, 'GLN:plan1': 14, 'PHE:plan': 10, 'TRP:plan': 9, 'HIS:plan': 5}
          Unresolved non-hydrogen planarities: 745
    Chain: "B"
      Number of atoms: 4412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4412
          Classifications: {'peptide': 557}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 31, 'TRANS': 525}
    Chain: "D"
      Number of atoms: 2055
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2055
          Classifications: {'peptide': 271}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 252}
    Chain: "J"
      Number of atoms: 2147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2147
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 8, 'TRANS': 267}
    Chain: "K"
      Number of atoms: 2139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2139
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 8, 'TRANS': 266}
    Chain: "Q"
      Number of atoms: 243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 243
          Classifications: {'peptide': 32}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 28}
    Chain: "U"
      Number of atoms: 316
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 316
          Classifications: {'peptide': 39}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 38}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 0
          Ad-hoc single atom residues: {' FE': 1}
          Chain breaks: 1

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  10243  SG  CYS D 155      55.749  56.905 105.259  1.00115.21           S
  ATOM  10905  SG  CYS D 244      53.687  55.245 101.530  1.00111.87           S

  Time building chain proxies: 3.14, per 1000 atoms: 0.20
  Number of scatterers: 15967
  At special positions: 0
  Unit cell: (145.14, 110.7, 238.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      66     16.00
     O    3179      8.00
     N    2860      7.00
     C    9861      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: 1.21
  Conformation dependent library (CDL) restraints added in 582.9 milliseconds
  

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3398

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 31 sheets defined
      13.2% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 8
      removed outlier: 3.959A  pdb=" N   VAL A   8 " --> pdb=" O   SER A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 59
    Processing helix  chain 'A' and resid 84 through 92
      removed outlier: 3.934A  pdb=" N   LYS A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 140
      removed outlier: 3.621A  pdb=" N   LYS A 140 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 137 through 140'
    Processing helix  chain 'A' and resid 161 through 171
    Processing helix  chain 'A' and resid 180 through 184
    Processing helix  chain 'A' and resid 185 through 199
      removed outlier: 3.744A  pdb=" N   THR A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASN A 198 " --> pdb=" O   ASP A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 225
    Processing helix  chain 'A' and resid 297 through 305
      removed outlier: 3.706A  pdb=" N   ASN A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY A 305 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 336
      removed outlier: 3.527A  pdb=" N   THR A 336 " --> pdb=" O   ARG A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 438
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 4.058A  pdb=" N   ASN A 444 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 515
      removed outlier: 4.251A  pdb=" N   ASP A 514 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 677
    Processing helix  chain 'A' and resid 723 through 728
    Processing helix  chain 'B' and resid 15 through 21
    Processing helix  chain 'B' and resid 140 through 145
    Processing helix  chain 'B' and resid 153 through 158
      removed outlier: 3.643A  pdb=" N   LEU B 156 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 169
      removed outlier: 3.614A  pdb=" N   ASP B 169 " --> pdb=" O   ASN B 166 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 166 through 169'
    Processing helix  chain 'B' and resid 211 through 224
    Processing helix  chain 'B' and resid 233 through 236
    Processing helix  chain 'B' and resid 409 through 423
    Processing helix  chain 'B' and resid 458 through 463
    Processing helix  chain 'B' and resid 467 through 470
    Processing helix  chain 'D' and resid 3 through 8
    Processing helix  chain 'D' and resid 73 through 78
    Processing helix  chain 'D' and resid 128 through 132
    Processing helix  chain 'D' and resid 178 through 183
      removed outlier: 3.808A  pdb=" N   ALA D 182 " --> pdb=" O   ALA D 178 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR D 183 " --> pdb=" O   ALA D 179 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 178 through 183'
    Processing helix  chain 'D' and resid 240 through 247
    Processing helix  chain 'D' and resid 250 through 254
    Processing helix  chain 'J' and resid 81 through 90
    Processing helix  chain 'J' and resid 150 through 154
      removed outlier: 3.735A  pdb=" N   ILE J 153 " --> pdb=" O   SER J 150 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   THR J 154 " --> pdb=" O   GLY J 151 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 150 through 154'
    Processing helix  chain 'K' and resid 81 through 90
    Processing helix  chain 'Q' and resid 1401 through 1406
      removed outlier: 3.564A  pdb=" N   ALA Q1405 " --> pdb=" O   LYS Q1401 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 1409 through 1421
      removed outlier: 4.024A  pdb=" N   LYS Q1413 " --> pdb=" O   PRO Q1409 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 1422 through 1431
    Processing helix  chain 'U' and resid 2 through 7
    Processing helix  chain 'U' and resid 8 through 10
      No H-bonds generated for 'chain 'U' and resid 8 through 10'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 24
      removed outlier: 5.668A  pdb=" N   PHE A  19 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   PHE A 106 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   GLY A  21 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ALA A 104 " --> pdb=" O   GLY A  21 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   PHE A  23 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A  74 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 45
      removed outlier: 5.341A  pdb=" N   THR A  39 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   VAL A  35 " --> pdb=" O   THR A  39 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   THR A  31 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ILE A  45 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLU A  29 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ILE A  30 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   ARG A 125 " --> pdb=" O   ILE A  30 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLU A  32 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   THR U  66 " --> pdb=" O   TRP A 120 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   PHE A 122 " --> pdb=" O   THR U  66 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 146
    Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 230
    Processing sheet with id=AA5, first strand: chain 'A' and resid 253 through 254
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 253 through 254
    current: chain 'A' and resid 340 through 345
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 340 through 345
    current: chain 'A' and resid 368 through 379
      removed outlier: 5.364A  pdb=" N   VAL A 391 " --> pdb=" O   GLY A 376 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   VAL A 378 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LYS A 389 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 296
      removed outlier: 3.515A  pdb=" N   GLU A 289 " --> pdb=" O   ASN A 284 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428
    Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 451
    Processing sheet with id=AA9, first strand: chain 'A' and resid 464 through 472
      removed outlier: 6.839A  pdb=" N   TYR A 467 " --> pdb=" O   ASN A 484 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   ASN A 484 " --> pdb=" O   TYR A 467 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   MET A 469 " --> pdb=" O   ARG A 482 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 480 through 485
    current: chain 'A' and resid 605 through 606
    Processing sheet with id=AB1, first strand: chain 'A' and resid 503 through 504
      removed outlier: 7.300A  pdb=" N   VAL A 552 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   ILE A 548 " --> pdb=" O   VAL A 552 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   THR A 554 " --> pdb=" O   ASP A 546 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   MET A 572 " --> pdb=" O   ALA A 525 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 630 through 635
      removed outlier: 5.987A  pdb=" N   ASN A 631 " --> pdb=" O   ALA A 669 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   ALA A 669 " --> pdb=" O   ASN A 631 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 651
      removed outlier: 3.703A  pdb=" N   SER A 764 " --> pdb=" O   SER A 649 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   TYR A 696 " --> pdb=" O   GLY A 713 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY A 713 " --> pdb=" O   TYR A 696 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG A 709 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AB5, first strand: chain 'B' and resid 40 through 50
    Processing sheet with id=AB6, first strand: chain 'B' and resid 56 through 61
      removed outlier: 3.616A  pdb=" N   VAL B  58 " --> pdb=" O   GLN B 116 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 66 through 69
      removed outlier: 6.582A  pdb=" N   LEU B  67 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 171 through 176
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 199 through 208
    current: chain 'B' and resid 275 through 284
      removed outlier: 3.973A  pdb=" N   GLY B 282 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   HIS B 289 " --> pdb=" O   ASP B 284 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 289 through 292
    current: chain 'B' and resid 328 through 336
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 328 through 336
    current: chain 'B' and resid 541 through 543
    Processing sheet with id=AB9, first strand: chain 'B' and resid 179 through 183
    Processing sheet with id=AC1, first strand: chain 'B' and resid 399 through 402
    Processing sheet with id=AC2, first strand: chain 'B' and resid 451 through 455
      removed outlier: 3.579A  pdb=" N   SER B 489 " --> pdb=" O   PHE B 500 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   GLU B 476 " --> pdb=" O   ARG B 514 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 18 through 23
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 26 through 31
    current: chain 'D' and resid 42 through 46
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 42 through 46
    current: chain 'D' and resid 104 through 106
    Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 69
      removed outlier: 3.533A  pdb=" N   THR D 123 " --> pdb=" O   ASN D 114 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER D 112 " --> pdb=" O   THR D 125 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 164 through 167
      removed outlier: 7.642A  pdb=" N   ILE D 230 " --> pdb=" O   ILE D 197 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   ILE D 197 " --> pdb=" O   ILE D 230 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 170 through 172
      removed outlier: 3.583A  pdb=" N   THR D 175 " --> pdb=" O   GLY D 172 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'J' and resid 16 through 20
  WARNING: can't find start of bonding for strands!
    previous: chain 'J' and resid 16 through 20
    current: chain 'J' and resid 71 through 77
  WARNING: can't find start of bonding for strands!
    previous: chain 'J' and resid 71 through 77
    current: chain 'J' and resid 202 through 207
  WARNING: can't find start of bonding for strands!
    previous: chain 'J' and resid 202 through 207
    current: chain 'J' and resid 229 through 245
      removed outlier: 4.075A  pdb=" N   LYS J 235 " --> pdb=" O   MET J 261 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASP J 241 " --> pdb=" O   SER J 255 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   SER J 255 " --> pdb=" O   ASP J 241 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'J' and resid 254 through 261
    current: chain 'K' and resid 31 through 33
  WARNING: can't find start of bonding for strands!
    previous: chain 'K' and resid 31 through 33
    current: chain 'K' and resid 59 through 77
  WARNING: can't find start of bonding for strands!
    previous: chain 'K' and resid 59 through 77
    current: chain 'K' and resid 229 through 240
    Processing sheet with id=AC8, first strand: chain 'J' and resid 47 through 49
      removed outlier: 7.818A  pdb=" N   GLU J  47 " --> pdb=" O   LEU J  67 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU J  67 " --> pdb=" O   GLU J  47 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU J  49 " --> pdb=" O   VAL J  65 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL J  65 " --> pdb=" O   LEU J  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC8
    Processing sheet with id=AC9, first strand: chain 'J' and resid 105 through 107
      removed outlier: 3.936A  pdb=" N   THR J 160 " --> pdb=" O   LYS J 139 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'J' and resid 116 through 118
      removed outlier: 3.751A  pdb=" N   ARG J 176 " --> pdb=" O   ASP J 171 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'K' and resid 93 through 97
    Processing sheet with id=AD3, first strand: chain 'K' and resid 101 through 108
      removed outlier: 5.362A  pdb=" N   THR K 102 " --> pdb=" O   VAL K 198 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL K 198 " --> pdb=" O   THR K 102 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'K' and resid 115 through 118
      removed outlier: 3.853A  pdb=" N   ARG K 176 " --> pdb=" O   ASP K 171 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP K 171 " --> pdb=" O   ARG K 176 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    951 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.82

  Time building geometry restraints manager: 1.57 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: 5593
        1.34 -     1.46: 3487
        1.46 -     1.58: 7078
        1.58 -     1.70: 0
        1.70 -     1.81: 115
  Bond restraints: 16273
  Sorted by residual:
  bond pdb=" CA  THR B 378 "
       pdb=" C   THR B 378 "
    ideal  model  delta    sigma   weight residual
    1.523  1.489  0.034 1.34e-02 5.57e+03 6.42e+00
  bond pdb=" N   GLY A   2 "
       pdb=" CA  GLY A   2 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.13e+00
  bond pdb=" CA  TYR B 379 "
       pdb=" C   TYR B 379 "
    ideal  model  delta    sigma   weight residual
    1.523  1.499  0.025 1.24e-02 6.50e+03 3.93e+00
  bond pdb=" N   MET U   1 "
       pdb=" CA  MET U   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.90e-02 2.77e+03 3.49e+00
  bond pdb=" N   MET J   1 "
       pdb=" CA  MET J   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  ... (remaining 16268 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 21580
        1.92 -     3.83: 357
        3.83 -     5.75: 25
        5.75 -     7.66: 5
        7.66 -     9.58: 2
  Bond angle restraints: 21969
  Sorted by residual:
  angle pdb=" C   PRO A 384 "
        pdb=" N   ASP A 385 "
        pdb=" CA  ASP A 385 "
      ideal   model   delta    sigma   weight residual
     121.54  128.12   -6.58 1.91e+00 2.74e-01 1.19e+01
  angle pdb=" N   ASP J  50 "
        pdb=" CA  ASP J  50 "
        pdb=" C   ASP J  50 "
      ideal   model   delta    sigma   weight residual
     107.93  113.30   -5.37 1.65e+00 3.67e-01 1.06e+01
  angle pdb=" CB  ARG B 255 "
        pdb=" CG  ARG B 255 "
        pdb=" CD  ARG B 255 "
      ideal   model   delta    sigma   weight residual
     111.30  118.34   -7.04 2.30e+00 1.89e-01 9.36e+00
  angle pdb=" N   ASP D  98 "
        pdb=" CA  ASP D  98 "
        pdb=" C   ASP D  98 "
      ideal   model   delta    sigma   weight residual
     113.72  109.11    4.61 1.52e+00 4.33e-01 9.19e+00
  angle pdb=" C   SER B 347 "
        pdb=" N   ASP B 348 "
        pdb=" CA  ASP B 348 "
      ideal   model   delta    sigma   weight residual
     121.54  127.12   -5.58 1.91e+00 2.74e-01 8.55e+00
  ... (remaining 21964 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 8400
       17.57 -    35.15: 626
       35.15 -    52.72: 95
       52.72 -    70.30: 25
       70.30 -    87.87: 8
  Dihedral angle restraints: 9154
    sinusoidal: 3466
      harmonic: 5688
  Sorted by residual:
  dihedral pdb=" CA  PRO A 115 "
           pdb=" C   PRO A 115 "
           pdb=" N   TYR A 116 "
           pdb=" CA  TYR A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.59  -26.41     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  MET K 112 "
           pdb=" C   MET K 112 "
           pdb=" N   ARG K 113 "
           pdb=" CA  ARG K 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.46   25.54     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  VAL J 213 "
           pdb=" C   VAL J 213 "
           pdb=" N   TYR J 214 "
           pdb=" CA  TYR J 214 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.83  -24.17     0      5.00e+00 4.00e-02 2.34e+01
  ... (remaining 9151 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1476
       0.034 -    0.069: 484
       0.069 -    0.103: 158
       0.103 -    0.138: 111
       0.138 -    0.172: 10
  Chirality restraints: 2239
  Sorted by residual:
  chirality pdb=" CA  ILE B 372 "
            pdb=" N   ILE B 372 "
            pdb=" C   ILE B 372 "
            pdb=" CB  ILE B 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.39e-01
  chirality pdb=" CA  ILE K 156 "
            pdb=" N   ILE K 156 "
            pdb=" C   ILE K 156 "
            pdb=" CB  ILE K 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.95e-01
  chirality pdb=" CA  ILE B 101 "
            pdb=" N   ILE B 101 "
            pdb=" C   ILE B 101 "
            pdb=" CB  ILE B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.08e-01
  ... (remaining 2236 not shown)

  Planarity restraints: 3015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU K 180 "   -0.045 5.00e-02 4.00e+02   6.74e-02 7.27e+00
        pdb=" N   PRO K 181 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO K 181 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO K 181 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 392 "   -0.036 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO B 393 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 393 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 393 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 379 "    0.022 2.00e-02 2.50e+03   1.33e-02 3.54e+00
        pdb=" CG  TYR B 379 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 379 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 379 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 379 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 379 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 379 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 379 "    0.005 2.00e-02 2.50e+03
  ... (remaining 3012 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 343
        2.61 -     3.18: 15503
        3.18 -     3.75: 23949
        3.75 -     4.33: 33173
        4.33 -     4.90: 53050
  Nonbonded interactions: 126018
  Sorted by model distance:
  nonbonded pdb=" OH  TYR J 244 "
            pdb=" OE1 GLN J 252 "
     model   vdw
     2.036 3.040
  nonbonded pdb=" OD1 ASP K 123 "
            pdb=" N   ASP K 124 "
     model   vdw
     2.111 3.120
  nonbonded pdb=" O   GLY B 270 "
            pdb=" OG1 THR B 271 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OE1 GLU D  20 "
            pdb=" NH2 ARG D  93 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OG1 THR B  54 "
            pdb=" OD1 ASP B 120 "
     model   vdw
     2.202 3.040
  ... (remaining 126013 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 'J' and resid 2 through 276)
  selection = chain 'K'
}

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:             21.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     13.900
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
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      :  0.003   0.051  16273  Z= 0.131
  Angle     :  0.596   9.580  21969  Z= 0.327
  Chirality :  0.045   0.172   2239
  Planarity :  0.004   0.069   3015
  Dihedral  : 12.743  87.869   5756
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  0.19 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.73 (0.17), residues: 2203
  helix: -0.25 (0.37), residues: 197
  sheet: -1.55 (0.20), residues: 608
  loop : -2.27 (0.15), residues: 1398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG J 176 
 TYR   0.029   0.001   TYR B 379 
 PHE   0.030   0.001   PHE B 294 
 TRP   0.019   0.001   TRP B 177 
 HIS   0.004   0.001   HIS B 234 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.13 (16273)
  covalent geometry    : angle       0.59648 /  0.33 (21969)
  hydrogen bonds       : bond        0.23876 / 16.22 (  363)
  hydrogen bonds       : angle      10.59596 /  7.40 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  417 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 412
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.5460 (tpt) cc_final: 0.5143 (mmm)
REVERT: A  173 TYR cc_start: 0.8269 (t80) cc_final: 0.8060 (t80)
REVERT: A  196 LEU cc_start: 0.9446 (mt) cc_final: 0.9173 (mt)
REVERT: A  203 LEU cc_start: 0.8787 (tp) cc_final: 0.8490 (tp)
REVERT: B   13 PHE cc_start: 0.7647 (t80) cc_final: 0.7249 (t80)
REVERT: B  194 ILE cc_start: 0.8230 (mm) cc_final: 0.7997 (mm)
REVERT: B  524 LEU cc_start: 0.8805 (tp) cc_final: 0.8542 (tt)
REVERT: B  545 LEU cc_start: 0.8652 (mp) cc_final: 0.8428 (mp)
REVERT: B  550 PHE cc_start: 0.8213 (p90) cc_final: 0.7660 (p90)
REVERT: D    7 GLU cc_start: 0.9085 (tp30) cc_final: 0.8782 (tp30)
REVERT: D  118 ASN cc_start: 0.8664 (t0) cc_final: 0.8187 (p0)
REVERT: J    1 MET cc_start: 0.2617 (mtt) cc_final: 0.2252 (mtm)
REVERT: J  229 LYS cc_start: 0.7305 (ptpt) cc_final: 0.7019 (pttt)
REVERT: K   16 VAL cc_start: 0.9382 (t) cc_final: 0.9022 (p)
REVERT: K  112 MET cc_start: 0.7726 (pmm) cc_final: 0.7286 (ppp)
REVERT: K  192 ILE cc_start: 0.9284 (mm) cc_final: 0.9060 (tp)
REVERT: K  209 LYS cc_start: 0.6635 (tptt) cc_final: 0.5982 (mmtt)
REVERT: K  222 ASP cc_start: 0.8305 (t0) cc_final: 0.7998 (t0)
REVERT: K  261 MET cc_start: 0.7211 (ptp) cc_final: 0.6951 (ttt)
REVERT: Q 1421 ARG cc_start: 0.9020 (mtm-85) cc_final: 0.8387 (mtm-85)
REVERT: Q 1422 ASN cc_start: 0.8890 (m-40) cc_final: 0.7953 (p0)
REVERT: Q 1427 LYS cc_start: 0.6060 (mmtt) cc_final: 0.5721 (mttt)
REVERT: U    7 MET cc_start: 0.8798 (mmm) cc_final: 0.8436 (mmm)
REVERT: U   67 LYS cc_start: 0.6341 (mtpt) cc_final: 0.5620 (ttpt)
  outliers start: 5
  outliers final: 0
  residues processed: 416
  average time/residue: 0.1163
  time to fit residues: 71.3039
Evaluate side-chains
  237 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 216 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:   20.0000
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:   40.0000
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   chunk 200 optimal weight:    9.9990
   chunk 212 optimal weight:   10.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 328 GLN
B  14 ASN
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 HIS
B 225 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 503 GLN
** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  36 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.076476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.068796 restraints weight = 96916.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.070151 restraints weight = 62176.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.071093 restraints weight = 43745.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.071775 restraints weight = 32855.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.072277 restraints weight = 25975.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  16273  Z= 0.272
  Angle     :  0.790  10.909  21969  Z= 0.417
  Chirality :  0.052   0.214   2239
  Planarity :  0.006   0.046   3015
  Dihedral  :  6.142  39.989   2397
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.53 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  7.19 %
    Favored  : 92.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.86 (0.17), residues: 2203
  helix: -0.85 (0.33), residues: 221
  sheet: -1.70 (0.19), residues: 655
  loop : -2.26 (0.16), residues: 1327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 240 
 TYR   0.031   0.003   TYR B 379 
 PHE   0.025   0.003   PHE J 108 
 TRP   0.022   0.002   TRP D 142 
 HIS   0.007   0.002   HIS B 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00598 /  0.27 (16273)
  covalent geometry    : angle       0.79012 /  0.42 (21969)
  hydrogen bonds       : bond        0.04116 /  2.85 (  363)
  hydrogen bonds       : angle       7.83634 /  5.35 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 300
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 TYR cc_start: 0.8422 (t80) cc_final: 0.8076 (t80)
REVERT: A  196 LEU cc_start: 0.9526 (mt) cc_final: 0.9224 (mt)
REVERT: A  203 LEU cc_start: 0.8861 (tp) cc_final: 0.8560 (tp)
REVERT: A  277 GLU cc_start: 0.7904 (tp30) cc_final: 0.7675 (tp30)
REVERT: B   93 ASP cc_start: 0.8965 (m-30) cc_final: 0.8495 (t0)
REVERT: B  119 ARG cc_start: 0.8616 (tmm160) cc_final: 0.8192 (tmm160)
REVERT: B  524 LEU cc_start: 0.9064 (tp) cc_final: 0.8754 (tt)
REVERT: B  550 PHE cc_start: 0.8618 (p90) cc_final: 0.8137 (p90)
REVERT: D   11 ASP cc_start: 0.8250 (p0) cc_final: 0.7957 (p0)
REVERT: D  118 ASN cc_start: 0.8863 (t0) cc_final: 0.8395 (p0)
REVERT: D  230 ILE cc_start: 0.8388 (mt) cc_final: 0.8084 (tt)
REVERT: J    1 MET cc_start: 0.3120 (mtt) cc_final: 0.2667 (mtm)
REVERT: J   39 GLU cc_start: 0.8610 (mp0) cc_final: 0.8399 (mp0)
REVERT: J   61 MET cc_start: 0.7724 (tmm) cc_final: 0.7441 (tmm)
REVERT: J  173 GLU cc_start: 0.8769 (pp20) cc_final: 0.8468 (pp20)
REVERT: J  229 LYS cc_start: 0.7219 (ptpt) cc_final: 0.6919 (pttt)
REVERT: K  112 MET cc_start: 0.8080 (pmm) cc_final: 0.7495 (ppp)
REVERT: K  192 ILE cc_start: 0.9404 (mm) cc_final: 0.9136 (tp)
REVERT: K  209 LYS cc_start: 0.6524 (tptt) cc_final: 0.5357 (mmtt)
REVERT: K  212 MET cc_start: 0.8754 (ttt) cc_final: 0.8333 (ttt)
REVERT: Q 1406 MET cc_start: 0.9002 (tpp) cc_final: 0.8765 (tpp)
REVERT: Q 1421 ARG cc_start: 0.9044 (mtm-85) cc_final: 0.8101 (mmp-170)
REVERT: Q 1427 LYS cc_start: 0.6372 (mmtt) cc_final: 0.5896 (mttt)
REVERT: U   67 LYS cc_start: 0.6760 (mtpt) cc_final: 0.5653 (ttpt)
  outliers start: 2
  outliers final: 1
  residues processed: 302
  average time/residue: 0.1215
  time to fit residues: 55.2413
Evaluate side-chains
  216 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 113 optimal weight:   10.0000
   chunk 146 optimal weight:    3.9990
   chunk 164 optimal weight:    4.9990
   chunk 178 optimal weight:    0.0980
   chunk 82 optimal weight:    0.9980
   chunk 136 optimal weight:   10.0000
   chunk 135 optimal weight:    1.9990
   chunk 190 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0030
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7392

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 GLN
** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 291 GLN
** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 125 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 = 0.3691 r_free = 0.3691 target = 0.079905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.071949 restraints weight = 95065.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.073361 restraints weight = 60812.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.074354 restraints weight = 42743.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.075068 restraints weight = 32047.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.075592 restraints weight = 25234.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  16273  Z= 0.129
  Angle     :  0.648  10.585  21969  Z= 0.340
  Chirality :  0.048   0.186   2239
  Planarity :  0.005   0.076   3015
  Dihedral  :  5.657  44.955   2397
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.53 (0.17), residues: 2203
  helix: -0.32 (0.36), residues: 214
  sheet: -1.51 (0.19), residues: 662
  loop : -2.06 (0.16), residues: 1327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 240 
 TYR   0.022   0.002   TYR B 102 
 PHE   0.027   0.002   PHE J  89 
 TRP   0.047   0.002   TRP A 207 
 HIS   0.004   0.001   HIS D  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 (16273)
  covalent geometry    : angle       0.64773 /  0.34 (21969)
  hydrogen bonds       : bond        0.03552 /  2.53 (  363)
  hydrogen bonds       : angle       7.09608 /  4.84 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7662 (ttp) cc_final: 0.7210 (ttp)
REVERT: A  173 TYR cc_start: 0.8295 (t80) cc_final: 0.8017 (t80)
REVERT: A  196 LEU cc_start: 0.9449 (mt) cc_final: 0.9074 (mt)
REVERT: A  203 LEU cc_start: 0.8867 (tp) cc_final: 0.8543 (tp)
REVERT: B  102 TYR cc_start: 0.5462 (p90) cc_final: 0.5167 (p90)
REVERT: B  119 ARG cc_start: 0.8490 (tmm160) cc_final: 0.8153 (tmm160)
REVERT: B  333 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7567 (ttm-80)
REVERT: B  524 LEU cc_start: 0.8984 (tp) cc_final: 0.8757 (tt)
REVERT: B  550 PHE cc_start: 0.8121 (p90) cc_final: 0.7690 (p90)
REVERT: D   11 ASP cc_start: 0.8124 (p0) cc_final: 0.7877 (p0)
REVERT: D   18 MET cc_start: 0.8347 (mtm) cc_final: 0.8090 (ttm)
REVERT: D  115 GLN cc_start: 0.8183 (mp-120) cc_final: 0.5921 (tt0)
REVERT: D  118 ASN cc_start: 0.8795 (t0) cc_final: 0.8288 (p0)
REVERT: D  230 ILE cc_start: 0.8360 (mt) cc_final: 0.8019 (tt)
REVERT: J    1 MET cc_start: 0.3080 (mtt) cc_final: 0.2738 (mtt)
REVERT: J   61 MET cc_start: 0.7746 (tmm) cc_final: 0.7434 (tmm)
REVERT: J  229 LYS cc_start: 0.6922 (ptpt) cc_final: 0.6717 (pttt)
REVERT: K  112 MET cc_start: 0.7850 (pmm) cc_final: 0.7465 (ppp)
REVERT: K  180 GLU cc_start: 0.8338 (tp30) cc_final: 0.8078 (tp30)
REVERT: K  192 ILE cc_start: 0.9361 (mm) cc_final: 0.9141 (tp)
REVERT: K  209 LYS cc_start: 0.6445 (tptt) cc_final: 0.5207 (mmtt)
REVERT: K  212 MET cc_start: 0.8727 (ttt) cc_final: 0.8382 (ttt)
REVERT: Q 1406 MET cc_start: 0.8976 (tpp) cc_final: 0.8705 (tpp)
REVERT: Q 1421 ARG cc_start: 0.8946 (mtm-85) cc_final: 0.8012 (mmp-170)
REVERT: Q 1427 LYS cc_start: 0.6335 (mmtt) cc_final: 0.5884 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.1281
  time to fit residues: 56.7004
Evaluate side-chains
  212 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 214 optimal weight:    0.0370
   chunk 85 optimal weight:   10.0000
   chunk 165 optimal weight:    5.9990
   chunk 153 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 38 optimal weight:    0.3980
   chunk 73 optimal weight:    0.0770
   chunk 6 optimal weight:   30.0000
   chunk 68 optimal weight:   30.0000
   chunk 191 optimal weight:   20.0000
   overall best weight:    2.5020

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 GLN
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 125 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 = 0.3667 r_free = 0.3667 target = 0.078834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.071138 restraints weight = 95964.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.073303 restraints weight = 59189.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.074606 restraints weight = 33412.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.074883 restraints weight = 21945.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.075257 restraints weight = 19909.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16273  Z= 0.146
  Angle     :  0.641  10.540  21969  Z= 0.334
  Chirality :  0.048   0.182   2239
  Planarity :  0.005   0.064   3015
  Dihedral  :  5.456  41.429   2397
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  4.52 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.45 (0.17), residues: 2203
  helix: -0.32 (0.35), residues: 218
  sheet: -1.46 (0.19), residues: 677
  loop : -1.99 (0.16), residues: 1308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 191 
 TYR   0.016   0.001   TYR B  55 
 PHE   0.018   0.002   PHE J  89 
 TRP   0.036   0.002   TRP A 207 
 HIS   0.004   0.001   HIS D  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 (16273)
  covalent geometry    : angle       0.64073 /  0.33 (21969)
  hydrogen bonds       : bond        0.03237 /  2.30 (  363)
  hydrogen bonds       : angle       6.73468 /  4.59 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 284
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 TYR cc_start: 0.8446 (t80) cc_final: 0.8175 (t80)
REVERT: A  203 LEU cc_start: 0.8919 (tp) cc_final: 0.8592 (tp)
REVERT: A  208 ASN cc_start: 0.7737 (m-40) cc_final: 0.7150 (m-40)
REVERT: A  277 GLU cc_start: 0.7822 (tp30) cc_final: 0.7518 (tp30)
REVERT: A  279 VAL cc_start: 0.8692 (t) cc_final: 0.8343 (t)
REVERT: B   93 ASP cc_start: 0.8959 (m-30) cc_final: 0.8347 (t0)
REVERT: B  119 ARG cc_start: 0.8556 (tmm160) cc_final: 0.8169 (tmm160)
REVERT: B  333 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7600 (ttm-80)
REVERT: B  524 LEU cc_start: 0.9095 (tp) cc_final: 0.8861 (tt)
REVERT: D   45 GLU cc_start: 0.9053 (mp0) cc_final: 0.8740 (mp0)
REVERT: D  115 GLN cc_start: 0.8136 (mp-120) cc_final: 0.5853 (tt0)
REVERT: D  118 ASN cc_start: 0.8854 (t0) cc_final: 0.8291 (p0)
REVERT: D  163 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7961 (mmt-90)
REVERT: D  230 ILE cc_start: 0.8381 (mt) cc_final: 0.8008 (tt)
REVERT: J    1 MET cc_start: 0.3032 (mtt) cc_final: 0.2794 (mtt)
REVERT: J   61 MET cc_start: 0.7775 (tmm) cc_final: 0.7471 (tmm)
REVERT: K   16 VAL cc_start: 0.9309 (t) cc_final: 0.9060 (p)
REVERT: K   18 PHE cc_start: 0.8828 (t80) cc_final: 0.8577 (t80)
REVERT: K   20 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7435 (mtt180)
REVERT: K   32 MET cc_start: 0.7653 (tmm) cc_final: 0.7036 (tmm)
REVERT: K  112 MET cc_start: 0.7849 (pmm) cc_final: 0.7517 (ppp)
REVERT: K  163 ASN cc_start: 0.8469 (t0) cc_final: 0.8010 (t0)
REVERT: K  169 GLU cc_start: 0.5523 (pt0) cc_final: 0.5293 (pt0)
REVERT: K  178 TYR cc_start: 0.8794 (t80) cc_final: 0.8338 (t80)
REVERT: K  180 GLU cc_start: 0.8404 (tp30) cc_final: 0.8141 (tp30)
REVERT: K  192 ILE cc_start: 0.9300 (mm) cc_final: 0.9020 (tp)
REVERT: K  212 MET cc_start: 0.8793 (ttt) cc_final: 0.8397 (ttt)
REVERT: Q 1406 MET cc_start: 0.8968 (tpp) cc_final: 0.8702 (tpp)
REVERT: Q 1421 ARG cc_start: 0.8888 (mtm-85) cc_final: 0.8290 (mtm110)
REVERT: Q 1427 LYS cc_start: 0.6414 (mmtt) cc_final: 0.5912 (mttt)
REVERT: U   67 LYS cc_start: 0.5798 (mtpt) cc_final: 0.4559 (ttpt)
  outliers start: 1
  outliers final: 0
  residues processed: 285
  average time/residue: 0.1273
  time to fit residues: 53.7209
Evaluate side-chains
  212 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 192 optimal weight:    0.0060
   chunk 131 optimal weight:   10.0000
   chunk 198 optimal weight:    6.9990
   chunk 127 optimal weight:    6.9990
   chunk 15 optimal weight:   20.0000
   chunk 174 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 179 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   overall best weight:    6.4004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
B 380 ASN
** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J   7 ASN
K   8 ASN
** U  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.075779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.068276 restraints weight = 98636.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.069576 restraints weight = 63021.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.070496 restraints weight = 44588.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.071156 restraints weight = 33605.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.071624 restraints weight = 26642.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  16273  Z= 0.268
  Angle     :  0.755  10.381  21969  Z= 0.395
  Chirality :  0.050   0.254   2239
  Planarity :  0.006   0.144   3015
  Dihedral  :  5.959  39.795   2397
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.69 (0.17), residues: 2203
  helix: -0.65 (0.33), residues: 220
  sheet: -1.59 (0.19), residues: 693
  loop : -2.15 (0.16), residues: 1290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.001   ARG J  20 
 TYR   0.021   0.003   TYR J  17 
 PHE   0.021   0.002   PHE B 381 
 TRP   0.056   0.003   TRP A 207 
 HIS   0.005   0.002   HIS B 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00582 /  0.27 (16273)
  covalent geometry    : angle       0.75475 /  0.40 (21969)
  hydrogen bonds       : bond        0.03768 /  2.61 (  363)
  hydrogen bonds       : angle       7.00159 /  4.74 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8229 (tmm) cc_final: 0.7676 (tmm)
REVERT: A  203 LEU cc_start: 0.8861 (tp) cc_final: 0.8514 (tp)
REVERT: A  297 ASN cc_start: 0.8149 (t0) cc_final: 0.7830 (t0)
REVERT: B   44 MET cc_start: 0.6735 (pmm) cc_final: 0.6490 (pmm)
REVERT: B  119 ARG cc_start: 0.8652 (tmm160) cc_final: 0.8146 (tmm160)
REVERT: B  177 TRP cc_start: 0.7906 (m-90) cc_final: 0.7134 (m-90)
REVERT: B  290 MET cc_start: 0.8215 (ptp) cc_final: 0.7966 (ptp)
REVERT: B  362 LEU cc_start: 0.7581 (tp) cc_final: 0.6632 (tp)
REVERT: B  550 PHE cc_start: 0.8778 (p90) cc_final: 0.8221 (p90)
REVERT: D   11 ASP cc_start: 0.8183 (p0) cc_final: 0.7927 (p0)
REVERT: D   45 GLU cc_start: 0.9160 (mp0) cc_final: 0.8744 (mp0)
REVERT: D   47 MET cc_start: 0.7012 (tpp) cc_final: 0.6807 (tpp)
REVERT: D  118 ASN cc_start: 0.8922 (t0) cc_final: 0.8325 (p0)
REVERT: J    1 MET cc_start: 0.2955 (mtt) cc_final: 0.2609 (mtt)
REVERT: J   39 GLU cc_start: 0.8452 (mp0) cc_final: 0.8251 (mp0)
REVERT: K   16 VAL cc_start: 0.9408 (t) cc_final: 0.9140 (p)
REVERT: K   18 PHE cc_start: 0.8941 (t80) cc_final: 0.8716 (t80)
REVERT: K   61 MET cc_start: 0.9021 (ppp) cc_final: 0.8466 (ppp)
REVERT: K  106 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8036 (mt-10)
REVERT: K  112 MET cc_start: 0.7850 (pmm) cc_final: 0.7640 (ppp)
REVERT: K  163 ASN cc_start: 0.8617 (t0) cc_final: 0.7865 (t0)
REVERT: K  180 GLU cc_start: 0.8487 (tp30) cc_final: 0.8205 (tp30)
REVERT: K  212 MET cc_start: 0.8866 (ttt) cc_final: 0.8441 (ttt)
REVERT: Q 1421 ARG cc_start: 0.8956 (mtm-85) cc_final: 0.8302 (mtm110)
REVERT: U    1 MET cc_start: 0.7408 (ppp) cc_final: 0.7006 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.1268
  time to fit residues: 49.4186
Evaluate side-chains
  198 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 211 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 124 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 178 optimal weight:    0.5980
   chunk 141 optimal weight:    5.9990
   chunk 122 optimal weight:   10.0000
   chunk 206 optimal weight:    6.9990
   chunk 135 optimal weight:   10.0000
   overall best weight:    2.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 ASN
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 191 GLN
K 125 ASN
** U  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.077802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.070098 restraints weight = 95770.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.072275 restraints weight = 59884.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.073599 restraints weight = 33639.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.073943 restraints weight = 21711.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.074259 restraints weight = 19481.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16273  Z= 0.146
  Angle     :  0.657  11.391  21969  Z= 0.340
  Chirality :  0.048   0.209   2239
  Planarity :  0.005   0.102   3015
  Dihedral  :  5.626  48.413   2397
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.51 (0.17), residues: 2203
  helix: -0.41 (0.35), residues: 216
  sheet: -1.42 (0.19), residues: 671
  loop : -2.09 (0.16), residues: 1316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  29 
 TYR   0.023   0.002   TYR A  14 
 PHE   0.015   0.002   PHE B 294 
 TRP   0.048   0.002   TRP A 207 
 HIS   0.003   0.001   HIS A 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.15 (16273)
  covalent geometry    : angle       0.65718 /  0.34 (21969)
  hydrogen bonds       : bond        0.03165 /  2.21 (  363)
  hydrogen bonds       : angle       6.61221 /  4.52 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8176 (tmm) cc_final: 0.7648 (tmm)
REVERT: A  160 MET cc_start: 0.7751 (ttp) cc_final: 0.7332 (ttp)
REVERT: A  203 LEU cc_start: 0.8895 (tp) cc_final: 0.8560 (tp)
REVERT: A  208 ASN cc_start: 0.8058 (m-40) cc_final: 0.7536 (m-40)
REVERT: A  277 GLU cc_start: 0.7832 (tp30) cc_final: 0.7481 (tp30)
REVERT: A  279 VAL cc_start: 0.8684 (t) cc_final: 0.8292 (t)
REVERT: B   48 MET cc_start: 0.7700 (mtm) cc_final: 0.7136 (mtm)
REVERT: B   93 ASP cc_start: 0.8969 (m-30) cc_final: 0.8284 (t0)
REVERT: B  119 ARG cc_start: 0.8589 (tmm160) cc_final: 0.8048 (tmm160)
REVERT: B  333 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7633 (ttm-80)
REVERT: B  362 LEU cc_start: 0.7576 (tp) cc_final: 0.6631 (tp)
REVERT: B  550 PHE cc_start: 0.8429 (p90) cc_final: 0.8136 (p90)
REVERT: D   11 ASP cc_start: 0.8027 (p0) cc_final: 0.7803 (p0)
REVERT: D   45 GLU cc_start: 0.9168 (mp0) cc_final: 0.8688 (mp0)
REVERT: D   47 MET cc_start: 0.6727 (tpp) cc_final: 0.6510 (tpp)
REVERT: D  118 ASN cc_start: 0.8864 (t0) cc_final: 0.8241 (p0)
REVERT: D  189 PHE cc_start: 0.8065 (m-80) cc_final: 0.7695 (m-80)
REVERT: D  193 PHE cc_start: 0.8408 (p90) cc_final: 0.8000 (p90)
REVERT: D  195 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6673 (mm-30)
REVERT: J   61 MET cc_start: 0.7822 (tmm) cc_final: 0.7595 (tmm)
REVERT: K   16 VAL cc_start: 0.9391 (t) cc_final: 0.9112 (p)
REVERT: K   32 MET cc_start: 0.7656 (tmm) cc_final: 0.7373 (tmm)
REVERT: K   61 MET cc_start: 0.8846 (ppp) cc_final: 0.8485 (ppp)
REVERT: K  153 ILE cc_start: 0.7613 (pt) cc_final: 0.7383 (pt)
REVERT: K  163 ASN cc_start: 0.8547 (t0) cc_final: 0.7771 (t0)
REVERT: K  180 GLU cc_start: 0.8475 (tp30) cc_final: 0.8248 (tp30)
REVERT: K  212 MET cc_start: 0.8902 (ttt) cc_final: 0.8470 (ttt)
REVERT: Q 1427 LYS cc_start: 0.6347 (mmtt) cc_final: 0.5914 (mttt)
REVERT: U   75 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8862 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.1205
  time to fit residues: 47.8046
Evaluate side-chains
  193 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 44 optimal weight:   30.0000
   chunk 173 optimal weight:    3.9990
   chunk 144 optimal weight:    7.9990
   chunk 66 optimal weight:   50.0000
   chunk 154 optimal weight:    0.9990
   chunk 116 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 117 optimal weight:    6.9990
   chunk 133 optimal weight:   10.0000
   overall best weight:    5.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 125 ASN
K 230 ASN
** U  73 GLN ** 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 = 0.3587 r_free = 0.3587 target = 0.075659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.068120 restraints weight = 100092.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.069480 restraints weight = 63371.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.070405 restraints weight = 44370.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.071077 restraints weight = 33285.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.071559 restraints weight = 26291.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.4423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  16273  Z= 0.250
  Angle     :  0.747  11.151  21969  Z= 0.390
  Chirality :  0.049   0.187   2239
  Planarity :  0.005   0.090   3015
  Dihedral  :  5.932  41.400   2397
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.62 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.75 (0.17), residues: 2203
  helix: -0.68 (0.33), residues: 213
  sheet: -1.50 (0.20), residues: 642
  loop : -2.28 (0.16), residues: 1348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K  59 
 TYR   0.040   0.002   TYR A 137 
 PHE   0.023   0.002   PHE B 381 
 TRP   0.072   0.003   TRP A 207 
 HIS   0.005   0.002   HIS D 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00547 /  0.25 (16273)
  covalent geometry    : angle       0.74678 /  0.39 (21969)
  hydrogen bonds       : bond        0.03614 /  2.48 (  363)
  hydrogen bonds       : angle       6.84438 /  4.66 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8200 (tmm) cc_final: 0.7646 (tmm)
REVERT: A  190 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7805 (mtm-85)
REVERT: A  203 LEU cc_start: 0.8850 (tp) cc_final: 0.8513 (tp)
REVERT: A  208 ASN cc_start: 0.8059 (m-40) cc_final: 0.7693 (m-40)
REVERT: A  297 ASN cc_start: 0.8147 (t0) cc_final: 0.7816 (t0)
REVERT: B   48 MET cc_start: 0.7724 (mtm) cc_final: 0.7334 (mtm)
REVERT: B  119 ARG cc_start: 0.8641 (tmm160) cc_final: 0.8229 (tmm160)
REVERT: B  362 LEU cc_start: 0.7596 (tp) cc_final: 0.6691 (tp)
REVERT: B  550 PHE cc_start: 0.8845 (p90) cc_final: 0.8307 (p90)
REVERT: D   11 ASP cc_start: 0.8231 (p0) cc_final: 0.7961 (p0)
REVERT: D   45 GLU cc_start: 0.9239 (mp0) cc_final: 0.8764 (mp0)
REVERT: D   47 MET cc_start: 0.6985 (tpp) cc_final: 0.6737 (tpp)
REVERT: D  118 ASN cc_start: 0.8942 (t0) cc_final: 0.8291 (p0)
REVERT: K   32 MET cc_start: 0.7720 (tmm) cc_final: 0.7471 (tmm)
REVERT: K   61 MET cc_start: 0.8949 (ppp) cc_final: 0.8440 (ppp)
REVERT: K  156 ILE cc_start: 0.5569 (mt) cc_final: 0.5269 (mt)
REVERT: K  163 ASN cc_start: 0.8590 (t0) cc_final: 0.8318 (t0)
REVERT: K  180 GLU cc_start: 0.8513 (tp30) cc_final: 0.8249 (tp30)
REVERT: Q 1421 ARG cc_start: 0.8943 (mtm-85) cc_final: 0.8482 (mtm110)
REVERT: Q 1427 LYS cc_start: 0.6341 (mmtt) cc_final: 0.5910 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1069
  time to fit residues: 38.9240
Evaluate side-chains
  190 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 180 optimal weight:    9.9990
   chunk 63 optimal weight:   50.0000
   chunk 33 optimal weight:   10.0000
   chunk 74 optimal weight:   40.0000
   chunk 186 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 110 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 177 optimal weight:    6.9990
   chunk 201 optimal weight:    2.9990
   overall best weight:    6.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 154 GLN
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 191 GLN
K 125 ASN
** U  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.074988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.067355 restraints weight = 100398.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.068709 restraints weight = 63350.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.069652 restraints weight = 44357.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.070333 restraints weight = 33294.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.070835 restraints weight = 26344.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.4759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  16273  Z= 0.282
  Angle     :  0.783  11.369  21969  Z= 0.410
  Chirality :  0.050   0.268   2239
  Planarity :  0.006   0.073   3015
  Dihedral  :  6.227  45.265   2397
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.17 %
    Favored  : 88.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.95 (0.17), residues: 2203
  helix: -0.88 (0.33), residues: 217
  sheet: -1.60 (0.19), residues: 652
  loop : -2.43 (0.16), residues: 1334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 206 
 TYR   0.039   0.003   TYR A 137 
 PHE   0.024   0.002   PHE B 381 
 TRP   0.062   0.003   TRP A 207 
 HIS   0.006   0.002   HIS A 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00620 /  0.28 (16273)
  covalent geometry    : angle       0.78270 /  0.41 (21969)
  hydrogen bonds       : bond        0.03817 /  2.60 (  363)
  hydrogen bonds       : angle       7.05714 /  4.80 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LEU cc_start: 0.8977 (tp) cc_final: 0.8664 (tt)
REVERT: A   90 MET cc_start: 0.8231 (tmm) cc_final: 0.7668 (tmm)
REVERT: A  203 LEU cc_start: 0.8833 (tp) cc_final: 0.8463 (tp)
REVERT: A  279 VAL cc_start: 0.8590 (t) cc_final: 0.8125 (t)
REVERT: A  297 ASN cc_start: 0.8253 (t0) cc_final: 0.8014 (t0)
REVERT: B   13 PHE cc_start: 0.7518 (t80) cc_final: 0.6867 (t80)
REVERT: B   44 MET cc_start: 0.6951 (pmm) cc_final: 0.6738 (pmm)
REVERT: B   48 MET cc_start: 0.7710 (mtm) cc_final: 0.7305 (mtm)
REVERT: B  113 MET cc_start: 0.7564 (mmt) cc_final: 0.7148 (mmt)
REVERT: B  142 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8934 (mmmm)
REVERT: B  177 TRP cc_start: 0.7880 (m-90) cc_final: 0.7093 (m-90)
REVERT: B  362 LEU cc_start: 0.7589 (tp) cc_final: 0.6705 (tp)
REVERT: B  550 PHE cc_start: 0.8647 (p90) cc_final: 0.8402 (p90)
REVERT: D   11 ASP cc_start: 0.8173 (p0) cc_final: 0.7957 (p0)
REVERT: D   45 GLU cc_start: 0.9154 (mp0) cc_final: 0.8596 (mp0)
REVERT: D  118 ASN cc_start: 0.8935 (t0) cc_final: 0.8269 (p0)
REVERT: D  189 PHE cc_start: 0.8247 (m-80) cc_final: 0.8010 (m-80)
REVERT: D  193 PHE cc_start: 0.8477 (p90) cc_final: 0.7807 (p90)
REVERT: D  195 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6601 (mm-30)
REVERT: K   61 MET cc_start: 0.8999 (ppp) cc_final: 0.8583 (ppp)
REVERT: K  163 ASN cc_start: 0.8633 (t0) cc_final: 0.8321 (t0)
REVERT: K  180 GLU cc_start: 0.8503 (tp30) cc_final: 0.8245 (tp30)
REVERT: Q 1421 ARG cc_start: 0.8884 (mtm-85) cc_final: 0.8148 (mtm-85)
REVERT: Q 1427 LYS cc_start: 0.6325 (mmtt) cc_final: 0.5901 (mttt)
REVERT: U   75 LYS cc_start: 0.9270 (mmmm) cc_final: 0.8954 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1239
  time to fit residues: 45.8129
Evaluate side-chains
  194 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 177 optimal weight:    5.9990
   chunk 192 optimal weight:    6.9990
   chunk 110 optimal weight:   10.0000
   chunk 182 optimal weight:    7.9990
   chunk 123 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 113 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 184 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 GLN
** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 191 GLN
K 125 ASN
K 191 GLN
** U  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.074988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.067529 restraints weight = 100761.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.068846 restraints weight = 63857.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.069760 restraints weight = 44844.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.070425 restraints weight = 33772.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.070922 restraints weight = 26772.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.4975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  16273  Z= 0.246
  Angle     :  0.758  11.969  21969  Z= 0.394
  Chirality :  0.049   0.219   2239
  Planarity :  0.005   0.079   3015
  Dihedral  :  6.231  46.964   2397
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.30 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.99 (0.17), residues: 2203
  helix: -0.88 (0.33), residues: 211
  sheet: -1.65 (0.20), residues: 649
  loop : -2.44 (0.15), residues: 1343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 192 
 TYR   0.027   0.002   TYR A 137 
 PHE   0.024   0.002   PHE A 399 
 TRP   0.054   0.003   TRP A 207 
 HIS   0.005   0.002   HIS A 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00545 /  0.25 (16273)
  covalent geometry    : angle       0.75848 /  0.39 (21969)
  hydrogen bonds       : bond        0.03558 /  2.39 (  363)
  hydrogen bonds       : angle       7.03424 /  4.78 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LEU cc_start: 0.8954 (tp) cc_final: 0.8715 (tt)
REVERT: A   90 MET cc_start: 0.8164 (tmm) cc_final: 0.7651 (tmm)
REVERT: A  203 LEU cc_start: 0.8858 (tp) cc_final: 0.8495 (tp)
REVERT: A  208 ASN cc_start: 0.8302 (m-40) cc_final: 0.7987 (m-40)
REVERT: A  297 ASN cc_start: 0.8148 (t0) cc_final: 0.7920 (t0)
REVERT: B   44 MET cc_start: 0.6936 (pmm) cc_final: 0.6688 (pmm)
REVERT: B   48 MET cc_start: 0.7792 (mtm) cc_final: 0.7320 (mtm)
REVERT: B  142 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8901 (mmmm)
REVERT: B  177 TRP cc_start: 0.7906 (m-90) cc_final: 0.7224 (m-90)
REVERT: B  362 LEU cc_start: 0.7659 (tp) cc_final: 0.6824 (tp)
REVERT: B  550 PHE cc_start: 0.8860 (p90) cc_final: 0.8328 (p90)
REVERT: D   11 ASP cc_start: 0.8189 (p0) cc_final: 0.7975 (p0)
REVERT: D   45 GLU cc_start: 0.9212 (mp0) cc_final: 0.8710 (mp0)
REVERT: D   55 LYS cc_start: 0.8605 (mptt) cc_final: 0.8306 (mmtt)
REVERT: D  118 ASN cc_start: 0.8910 (t0) cc_final: 0.8237 (p0)
REVERT: J  261 MET cc_start: 0.7205 (mtm) cc_final: 0.6943 (mtm)
REVERT: K   61 MET cc_start: 0.9015 (ppp) cc_final: 0.7748 (ppp)
REVERT: K  163 ASN cc_start: 0.8618 (t0) cc_final: 0.8377 (t0)
REVERT: K  180 GLU cc_start: 0.8571 (tp30) cc_final: 0.8289 (tp30)
REVERT: Q 1421 ARG cc_start: 0.8855 (mtm-85) cc_final: 0.8160 (mtm-85)
REVERT: Q 1427 LYS cc_start: 0.6381 (mmtt) cc_final: 0.5961 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.1133
  time to fit residues: 41.3698
Evaluate side-chains
  192 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 127 optimal weight:    9.9990
   chunk 213 optimal weight:    0.6980
   chunk 194 optimal weight:    5.9990
   chunk 142 optimal weight:    8.9990
   chunk 217 optimal weight:    6.9990
   chunk 41 optimal weight:   40.0000
   chunk 144 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 63 optimal weight:   50.0000
   chunk 143 optimal weight:    8.9990
   chunk 149 optimal weight:   10.0000
   overall best weight:    5.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 191 GLN
K 125 ASN
K 191 GLN
** U  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.075271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.068105 restraints weight = 100235.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.069323 restraints weight = 65392.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.070189 restraints weight = 46629.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.070823 restraints weight = 35463.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.071280 restraints weight = 28341.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.5116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  16273  Z= 0.228
  Angle     :  0.757  12.282  21969  Z= 0.393
  Chirality :  0.049   0.224   2239
  Planarity :  0.006   0.105   3015
  Dihedral  :  6.205  49.551   2397
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.12 %
    Favored  : 88.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.97 (0.17), residues: 2203
  helix: -0.79 (0.33), residues: 212
  sheet: -1.65 (0.19), residues: 658
  loop : -2.43 (0.16), residues: 1333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 119 
 TYR   0.025   0.002   TYR A 137 
 PHE   0.024   0.002   PHE B 294 
 TRP   0.040   0.003   TRP A 207 
 HIS   0.004   0.001   HIS J  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00506 /  0.23 (16273)
  covalent geometry    : angle       0.75668 /  0.39 (21969)
  hydrogen bonds       : bond        0.03551 /  2.40 (  363)
  hydrogen bonds       : angle       7.04871 /  4.81 (  951)

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

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

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4406 Ramachandran restraints generated.
    2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8036 (tmm) cc_final: 0.7603 (tmm)
REVERT: A  203 LEU cc_start: 0.8789 (tp) cc_final: 0.8384 (tp)
REVERT: A  277 GLU cc_start: 0.7970 (tp30) cc_final: 0.7558 (tp30)
REVERT: A  279 VAL cc_start: 0.8690 (t) cc_final: 0.8422 (t)
REVERT: A  317 ILE cc_start: 0.9428 (mp) cc_final: 0.8647 (tt)
REVERT: B   13 PHE cc_start: 0.7452 (t80) cc_final: 0.6772 (t80)
REVERT: B   48 MET cc_start: 0.7888 (mtm) cc_final: 0.7417 (mtm)
REVERT: B  142 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8893 (mmmm)
REVERT: B  177 TRP cc_start: 0.7903 (m-90) cc_final: 0.7320 (m-90)
REVERT: B  362 LEU cc_start: 0.7624 (tp) cc_final: 0.6835 (tp)
REVERT: B  550 PHE cc_start: 0.8794 (p90) cc_final: 0.8212 (p90)
REVERT: D   11 ASP cc_start: 0.8163 (p0) cc_final: 0.7912 (p0)
REVERT: D   19 TYR cc_start: 0.8520 (m-80) cc_final: 0.8316 (m-80)
REVERT: D   45 GLU cc_start: 0.9131 (mp0) cc_final: 0.8626 (mp0)
REVERT: D   47 MET cc_start: 0.7122 (tpp) cc_final: 0.6760 (ttt)
REVERT: D   55 LYS cc_start: 0.8546 (mptt) cc_final: 0.8245 (mmtt)
REVERT: D  118 ASN cc_start: 0.8907 (t0) cc_final: 0.8239 (p0)
REVERT: D  193 PHE cc_start: 0.8411 (p90) cc_final: 0.7723 (p90)
REVERT: D  195 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6561 (mm-30)
REVERT: J   68 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7299 (mm-30)
REVERT: K   61 MET cc_start: 0.9016 (ppp) cc_final: 0.7735 (ppp)
REVERT: K  163 ASN cc_start: 0.8564 (t0) cc_final: 0.8306 (t0)
REVERT: Q 1421 ARG cc_start: 0.8872 (mtm-85) cc_final: 0.8195 (mtm-85)
REVERT: Q 1427 LYS cc_start: 0.6375 (mmtt) cc_final: 0.5987 (mttt)
REVERT: U   75 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8949 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1205
  time to fit residues: 44.4734
Evaluate side-chains
  196 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 218
   random chunks:
   chunk 161 optimal weight:    7.9990
   chunk 143 optimal weight:   20.0000
   chunk 89 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 88 optimal weight:    9.9990
   chunk 135 optimal weight:    0.3980
   chunk 54 optimal weight:   50.0000
   chunk 214 optimal weight:    5.9990
   chunk 61 optimal weight:   40.0000
   chunk 91 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0270
   overall best weight:    3.8844

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 191 GLN
K 125 ASN
** U  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.075902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.068632 restraints weight = 99645.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.069910 restraints weight = 64584.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.070799 restraints weight = 45659.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.071452 restraints weight = 34596.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.071935 restraints weight = 27530.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16273  Z= 0.183
  Angle     :  0.725  12.190  21969  Z= 0.373
  Chirality :  0.049   0.214   2239
  Planarity :  0.005   0.080   3015
  Dihedral  :  5.997  51.346   2397
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.89 (0.17), residues: 2203
  helix: -0.78 (0.33), residues: 217
  sheet: -1.58 (0.20), residues: 650
  loop : -2.38 (0.16), residues: 1336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 347 
 TYR   0.034   0.002   TYR A 137 
 PHE   0.022   0.002   PHE B 294 
 TRP   0.094   0.003   TRP A 207 
 HIS   0.004   0.001   HIS A 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.18 (16273)
  covalent geometry    : angle       0.72483 /  0.37 (21969)
  hydrogen bonds       : bond        0.03403 /  2.34 (  363)
  hydrogen bonds       : angle       6.86548 /  4.68 (  951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2990.50 seconds
wall clock time: 52 minutes 36.33 seconds (3156.33 seconds total)