Starting phenix.real_space_refine
on Mon May  4 06:45:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zs2_74675/05_2026/9zs2_74675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zs2_74675/05_2026/9zs2_74675.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zs2_74675/05_2026/9zs2_74675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zs2_74675/05_2026/9zs2_74675.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zs2_74675/05_2026/9zs2_74675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zs2_74675/05_2026/9zs2_74675.cif"
  }
  resolution = 4.4
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      30      5.49       5
     S      63      5.16       5
     C   11596      2.51       5
     N    3353      2.21       5
     O    3500      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18542
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 694, 5343
          Classifications: {'peptide': 694}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 650}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1883
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "F"
      Number of atoms: 1883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1883
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "G"
      Number of atoms: 1883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1883
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "H"
      Number of atoms: 1883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1883
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "I"
      Number of atoms: 2491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 320, 2491
          Classifications: {'peptide': 320}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 291}
    Chain: "J"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2547
          Classifications: {'peptide': 322}
          Link IDs: {'PTRANS': 24, 'TRANS': 297}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 629
          Classifications: {'RNA': 30}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 10, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 11, 'rna3p': 18}
  Time building chain proxies: 4.02, per 1000 atoms: 0.22
  Number of scatterers: 18542
  At special positions: 0
  Unit cell: (109.98, 111.86, 224.66, 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)
     S      63     16.00
     P      30     15.00
     O    3500      8.00
     N    3353      7.00
     C   11596      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: 1.61
  Conformation dependent library (CDL) restraints added in 763.7 milliseconds
  

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4194

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 23 sheets defined
      39.2% alpha, 16.2% beta
      0 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 1.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 26
      Proline residue:  A  21  - end of helix
    Processing helix  chain 'A' and resid 33 through 41
    Processing helix  chain 'A' and resid 55 through 71
    Processing helix  chain 'A' and resid 88 through 92
      removed outlier: 3.802A  pdb=" N   LEU A  92 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 146
      removed outlier: 4.449A  pdb=" N   ALA A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 152
    Processing helix  chain 'A' and resid 153 through 170
    Processing helix  chain 'A' and resid 182 through 204
      removed outlier: 3.682A  pdb=" N   GLN A 204 " --> pdb=" O   HIS A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 211
    Processing helix  chain 'A' and resid 230 through 236
    Processing helix  chain 'A' and resid 241 through 272
      removed outlier: 6.820A  pdb=" N   ALA A 247 " --> pdb=" O   GLN A 243 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LYS A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 296 through 317
    Processing helix  chain 'A' and resid 336 through 357
    Processing helix  chain 'A' and resid 358 through 361
      removed outlier: 3.815A  pdb=" N   LEU A 361 " --> pdb=" O   ARG A 358 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 358 through 361'
    Processing helix  chain 'A' and resid 405 through 418
      removed outlier: 3.658A  pdb=" N   ILE A 418 " --> pdb=" O   LEU A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 427
    Processing helix  chain 'A' and resid 466 through 469
    Processing helix  chain 'A' and resid 470 through 477
    Processing helix  chain 'A' and resid 533 through 538
    Processing helix  chain 'A' and resid 565 through 570
    Processing helix  chain 'A' and resid 578 through 595
    Processing helix  chain 'A' and resid 595 through 604
    Processing helix  chain 'A' and resid 605 through 608
      removed outlier: 3.503A  pdb=" N   ALA A 608 " --> pdb=" O   PRO A 605 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 605 through 608'
    Processing helix  chain 'A' and resid 625 through 644
    Processing helix  chain 'A' and resid 664 through 681
      removed outlier: 4.123A  pdb=" N   LEU A 668 " --> pdb=" O   PRO A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 701
    Processing helix  chain 'E' and resid 49 through 66
      removed outlier: 3.598A  pdb=" N   LEU E  53 " --> pdb=" O   PRO E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 87
    Processing helix  chain 'E' and resid 89 through 104
    Processing helix  chain 'E' and resid 106 through 110
      removed outlier: 3.669A  pdb=" N   ASP E 109 " --> pdb=" O   SER E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 112 through 120
    Processing helix  chain 'E' and resid 132 through 139
    Processing helix  chain 'E' and resid 188 through 206
      removed outlier: 4.348A  pdb=" N   LEU E 192 " --> pdb=" O   SER E 188 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 230 through 237
    Processing helix  chain 'F' and resid 49 through 66
      removed outlier: 4.014A  pdb=" N   LEU F  53 " --> pdb=" O   PRO F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 87
      removed outlier: 3.618A  pdb=" N   TYR F  81 " --> pdb=" O   SER F  77 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 89 through 104
    Processing helix  chain 'F' and resid 106 through 110
      removed outlier: 3.894A  pdb=" N   ASP F 109 " --> pdb=" O   SER F 106 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 112 through 119
    Processing helix  chain 'F' and resid 132 through 139
    Processing helix  chain 'F' and resid 189 through 206
    Processing helix  chain 'F' and resid 210 through 214
    Processing helix  chain 'F' and resid 230 through 237
    Processing helix  chain 'G' and resid 49 through 66
      removed outlier: 3.907A  pdb=" N   LEU G  53 " --> pdb=" O   PRO G  49 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 67 through 72
    Processing helix  chain 'G' and resid 77 through 87
    Processing helix  chain 'G' and resid 89 through 104
    Processing helix  chain 'G' and resid 106 through 110
      removed outlier: 3.556A  pdb=" N   ASP G 109 " --> pdb=" O   SER G 106 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS G 110 " --> pdb=" O   GLY G 107 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 106 through 110'
    Processing helix  chain 'G' and resid 112 through 120
    Processing helix  chain 'G' and resid 132 through 139
    Processing helix  chain 'G' and resid 189 through 206
      removed outlier: 3.591A  pdb=" N   GLU G 203 " --> pdb=" O   LEU G 199 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU G 204 " --> pdb=" O   LYS G 200 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY G 206 " --> pdb=" O   LEU G 202 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 210 through 214
    Processing helix  chain 'G' and resid 230 through 237
    Processing helix  chain 'H' and resid 49 through 65
      removed outlier: 3.661A  pdb=" N   LEU H  53 " --> pdb=" O   PRO H  49 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 77 through 87
    Processing helix  chain 'H' and resid 89 through 104
      removed outlier: 3.629A  pdb=" N   GLY H 104 " --> pdb=" O   LEU H 100 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 106 through 110
      removed outlier: 3.892A  pdb=" N   ASP H 109 " --> pdb=" O   SER H 106 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 112 through 120
      removed outlier: 3.606A  pdb=" N   ALA H 116 " --> pdb=" O   SER H 112 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 132 through 139
    Processing helix  chain 'H' and resid 188 through 206
      removed outlier: 4.220A  pdb=" N   LEU H 192 " --> pdb=" O   SER H 188 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 230 through 237
      removed outlier: 3.885A  pdb=" N   GLN H 236 " --> pdb=" O   PRO H 232 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 29 through 54
      removed outlier: 7.558A  pdb=" N   GLU I  47 " --> pdb=" O   GLU I  43 " (cutoff:3.500A)
      removed outlier: 9.149A  pdb=" N   ALA I  48 " --> pdb=" O   SER I  44 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY I  49 " --> pdb=" O   LEU I  45 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 82 through 86
    Processing helix  chain 'I' and resid 91 through 101
      removed outlier: 4.160A  pdb=" N   LYS I  96 " --> pdb=" O   ALA I  92 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   GLN I  97 " --> pdb=" O   ARG I  93 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLN I 100 " --> pdb=" O   LYS I  96 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 107 through 109
      No H-bonds generated for 'chain 'I' and resid 107 through 109'
    Processing helix  chain 'I' and resid 112 through 120
      removed outlier: 4.576A  pdb=" N   GLY I 117 " --> pdb=" O   ALA I 114 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 179 through 194
    Processing helix  chain 'I' and resid 198 through 202
    Processing helix  chain 'I' and resid 239 through 243
    Processing helix  chain 'I' and resid 256 through 261
    Processing helix  chain 'J' and resid 151 through 169
      removed outlier: 3.904A  pdb=" N   LEU J 155 " --> pdb=" O   PRO J 151 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN J 169 " --> pdb=" O   SER J 165 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 184 through 194
    Processing helix  chain 'J' and resid 208 through 215
      removed outlier: 3.750A  pdb=" N   HIS J 211 " --> pdb=" O   ARG J 208 " (cutoff:3.500A)
      Proline residue:  J 213  - end of helix
    Processing helix  chain 'J' and resid 287 through 294
    Processing helix  chain 'J' and resid 296 through 308
    Processing helix  chain 'J' and resid 308 through 319
      removed outlier: 3.558A  pdb=" N   CYS J 312 " --> pdb=" O   THR J 308 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU J 319 " --> pdb=" O   GLU J 315 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 336 through 347
      removed outlier: 3.581A  pdb=" N   LEU J 347 " --> pdb=" O   LEU J 343 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 347 through 353
    Processing helix  chain 'J' and resid 366 through 371
      removed outlier: 3.810A  pdb=" N   SER J 369 " --> pdb=" O   GLY J 366 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LYS J 370 " --> pdb=" O   ALA J 367 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 279 through 283
      removed outlier: 5.760A  pdb=" N   GLN A 279 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   VAL A 290 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 397 through 399
    Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 461
      removed outlier: 6.349A  pdb=" N   ARG A 437 " --> pdb=" O   LEU A 479 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   LEU A 479 " --> pdb=" O   ARG A 437 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 611 through 616
      removed outlier: 6.813A  pdb=" N   PHE A 621 " --> pdb=" O   VAL A 613 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   ALA A 615 " --> pdb=" O   ASP A 619 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   ASP A 619 " --> pdb=" O   ALA A 615 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 690
    Processing sheet with id=AA6, first strand: chain 'E' and resid 124 through 126
      removed outlier: 3.589A  pdb=" N   ALA E  11 " --> pdb=" O   PHE E 177 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN E   5 " --> pdb=" O   GLN E 183 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   THR E  12 " --> pdb=" O   ALA E 222 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   ALA E 222 " --> pdb=" O   THR E  12 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL E  14 " --> pdb=" O   PHE E 220 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   PHE E 220 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 33 through 35
      removed outlier: 4.390A  pdb=" N   ILE E  33 " --> pdb=" O   PHE E 165 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   GLU E 167 " --> pdb=" O   ILE E  33 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   SER E  35 " --> pdb=" O   GLU E 167 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   HIS E 162 " --> pdb=" O   CYS E 152 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   CYS E 152 " --> pdb=" O   HIS E 162 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 124 through 126
      removed outlier: 3.723A  pdb=" N   GLU F 130 " --> pdb=" O   ASP F 176 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 124 through 126
      removed outlier: 4.555A  pdb=" N   THR F  12 " --> pdb=" O   ALA F 222 " (cutoff:3.500A)
      removed outlier: 5.445A  pdb=" N   ALA F 222 " --> pdb=" O   THR F  12 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL F  14 " --> pdb=" O   PHE F 220 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   PHE F 220 " --> pdb=" O   VAL F  14 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 146 through 151
    Processing sheet with id=AB2, first strand: chain 'G' and resid 124 through 126
      removed outlier: 3.575A  pdb=" N   ALA G  11 " --> pdb=" O   PHE G 177 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ASN G   5 " --> pdb=" O   GLN G 183 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   THR G  12 " --> pdb=" O   ALA G 222 " (cutoff:3.500A)
      removed outlier: 5.441A  pdb=" N   ALA G 222 " --> pdb=" O   THR G  12 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL G  14 " --> pdb=" O   PHE G 220 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   PHE G 220 " --> pdb=" O   VAL G  14 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 146 through 153
      removed outlier: 4.919A  pdb=" N   CYS G 152 " --> pdb=" O   HIS G 162 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   HIS G 162 " --> pdb=" O   CYS G 152 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 124 through 126
      removed outlier: 3.521A  pdb=" N   ASN H   5 " --> pdb=" O   GLN H 183 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   THR H   8 " --> pdb=" O   LEU H 225 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   LEU H 225 " --> pdb=" O   THR H   8 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ARG H  10 " --> pdb=" O   LEU H 223 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   LEU H 223 " --> pdb=" O   ARG H  10 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 153
      removed outlier: 4.217A  pdb=" N   CYS H 152 " --> pdb=" O   HIS H 162 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   HIS H 162 " --> pdb=" O   CYS H 152 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 213 through 214
      removed outlier: 8.870A  pdb=" N   GLY H 214 " --> pdb=" O   LEU J 217 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   VAL J 219 " --> pdb=" O   GLY H 214 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   GLN J 273 " --> pdb=" O   GLY J 220 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 64 through 66
      removed outlier: 4.236A  pdb=" N   ARG I  15 " --> pdb=" O   GLN I 211 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'I' and resid 74 through 76
    Processing sheet with id=AB9, first strand: chain 'I' and resid 130 through 136
    Processing sheet with id=AC1, first strand: chain 'I' and resid 277 through 278
    Processing sheet with id=AC2, first strand: chain 'I' and resid 247 through 250
    Processing sheet with id=AC3, first strand: chain 'I' and resid 293 through 294
      removed outlier: 4.110A  pdb=" N   LEU I 293 " --> pdb=" O   HIS I 308 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'J' and resid 260 through 263
    Processing sheet with id=AC5, first strand: chain 'J' and resid 378 through 380

    770 hydrogen bonds defined for protein.
    2142 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 2.82

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 5979
        1.34 -     1.46: 3167
        1.46 -     1.58: 9728
        1.58 -     1.70: 59
        1.70 -     1.82: 89
  Bond restraints: 19022
  Sorted by residual:
  bond pdb=" C   GLU J 315 "
       pdb=" O   GLU J 315 "
    ideal  model  delta    sigma   weight residual
    1.236  1.272 -0.036 1.19e-02 7.06e+03 9.00e+00
  bond pdb=" N   ASP A 217 "
       pdb=" CA  ASP A 217 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.29e-02 6.01e+03 6.69e+00
  bond pdb=" N   GLY A 216 "
       pdb=" CA  GLY A 216 "
    ideal  model  delta    sigma   weight residual
    1.452  1.477 -0.024 9.50e-03 1.11e+04 6.58e+00
  bond pdb=" N   GLU J 321 "
       pdb=" CA  GLU J 321 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.56e+00
  bond pdb=" N   LEU A 213 "
       pdb=" CA  LEU A 213 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 1.10e-02 8.26e+03 5.95e+00
  ... (remaining 19017 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 25525
        2.50 -     5.00: 379
        5.00 -     7.50: 39
        7.50 -    10.00: 1
       10.00 -    12.50: 4
  Bond angle restraints: 25948
  Sorted by residual:
  angle pdb=" N   LEU A 213 "
        pdb=" CA  LEU A 213 "
        pdb=" C   LEU A 213 "
      ideal   model   delta    sigma   weight residual
     112.57  106.10    6.47 1.13e+00 7.83e-01 3.28e+01
  angle pdb=" CB  MET I  70 "
        pdb=" CG  MET I  70 "
        pdb=" SD  MET I  70 "
      ideal   model   delta    sigma   weight residual
     112.70  100.20   12.50 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" CB  MET G 201 "
        pdb=" CG  MET G 201 "
        pdb=" SD  MET G 201 "
      ideal   model   delta    sigma   weight residual
     112.70  125.10  -12.40 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" N   ILE A 378 "
        pdb=" CA  ILE A 378 "
        pdb=" C   ILE A 378 "
      ideal   model   delta    sigma   weight residual
     112.96  109.05    3.91 1.00e+00 1.00e+00 1.53e+01
  angle pdb=" N   GLU A 262 "
        pdb=" CA  GLU A 262 "
        pdb=" CB  GLU A 262 "
      ideal   model   delta    sigma   weight residual
     110.28  115.66   -5.38 1.55e+00 4.16e-01 1.21e+01
  ... (remaining 25943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.32: 10504
       19.32 -    38.64: 747
       38.64 -    57.96: 103
       57.96 -    77.28: 34
       77.28 -    96.60: 7
  Dihedral angle restraints: 11395
    sinusoidal: 4859
      harmonic: 6536
  Sorted by residual:
  dihedral pdb=" CA  ARG J 201 "
           pdb=" C   ARG J 201 "
           pdb=" N   ARG J 202 "
           pdb=" CA  ARG J 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.30  -46.70     0      5.00e+00 4.00e-02 8.72e+01
  dihedral pdb=" CA  THR J 200 "
           pdb=" C   THR J 200 "
           pdb=" N   ARG J 201 "
           pdb=" CA  ARG J 201 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -147.22  -32.78     0      5.00e+00 4.00e-02 4.30e+01
  dihedral pdb=" CA  VAL A 395 "
           pdb=" C   VAL A 395 "
           pdb=" N   GLU A 396 "
           pdb=" CA  GLU A 396 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.37   28.63     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 11392 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 2333
       0.051 -    0.103: 461
       0.103 -    0.154: 76
       0.154 -    0.205: 6
       0.205 -    0.256: 1
  Chirality restraints: 2877
  Sorted by residual:
  chirality pdb=" CA  LEU J 316 "
            pdb=" N   LEU J 316 "
            pdb=" C   LEU J 316 "
            pdb=" CB  LEU J 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  ASP A  95 "
            pdb=" N   ASP A  95 "
            pdb=" C   ASP A  95 "
            pdb=" CB  ASP A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  ILE H   6 "
            pdb=" CA  ILE H   6 "
            pdb=" CG1 ILE H   6 "
            pdb=" CG2 ILE H   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.64e-01
  ... (remaining 2874 not shown)

  Planarity restraints: 3314
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 528 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.26e+00
        pdb=" C   ASN A 528 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ASN A 528 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLY A 529 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS J 314 "   -0.011 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" C   HIS J 314 "    0.036 2.00e-02 2.50e+03
        pdb=" O   HIS J 314 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLU J 315 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 488 "   -0.032 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO A 489 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 489 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 489 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 3311 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 6079
        2.85 -     3.36: 18438
        3.36 -     3.87: 31823
        3.87 -     4.39: 36734
        4.39 -     4.90: 58305
  Nonbonded interactions: 151379
  Sorted by model distance:
  nonbonded pdb=" O   SER A 258 "
            pdb=" OE1 GLU A 262 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   ASN A 528 "
            pdb=" OD1 ASN A 528 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   ASP A 639 "
            pdb=" CB  TYR A 643 "
     model   vdw
     2.398 2.752
  nonbonded pdb=" O   GLY A 216 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.422 3.040
  nonbonded pdb=" O   ALA J 317 "
            pdb=" C   TRP J 318 "
     model   vdw
     2.444 3.270
  ... (remaining 151374 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 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     17.490
  Find NCS groups from input model:        0.150
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
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   0.046  19022  Z= 0.181
  Angle     :  0.761  12.496  25948  Z= 0.418
  Chirality :  0.042   0.256   2877
  Planarity :  0.005   0.061   3314
  Dihedral  : 13.460  96.596   7201
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.19 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  0.32 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.18), residues: 2290
  helix:  0.41 (0.18), residues: 785
  sheet: -0.64 (0.26), residues: 371
  loop : -0.79 (0.19), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 142 
 TYR   0.016   0.002   TYR A 519 
 PHE   0.028   0.002   PHE I  34 
 TRP   0.029   0.002   TRP A 423 
 HIS   0.008   0.001   HIS J  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (19022)
  covalent geometry    : angle       0.76078 (25948)
  hydrogen bonds       : bond        0.12445 (  768)
  hydrogen bonds       : angle       7.54103 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 0.718 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.9016 (m-30)
REVERT: A  236 PHE cc_start: 0.9680 (t80) cc_final: 0.9387 (t80)
REVERT: E   47 TYR cc_start: 0.9549 (p90) cc_final: 0.9105 (p90)
REVERT: E  220 PHE cc_start: 0.8957 (m-80) cc_final: 0.8493 (m-80)
REVERT: G   61 LEU cc_start: 0.9342 (mt) cc_final: 0.9027 (pp)
REVERT: G  220 PHE cc_start: 0.8372 (m-10) cc_final: 0.7881 (m-10)
REVERT: I   66 ILE cc_start: 0.9690 (mm) cc_final: 0.9482 (tp)
REVERT: I   75 LEU cc_start: 0.9813 (mt) cc_final: 0.9588 (mp)
REVERT: I  135 MET cc_start: 0.8135 (tmm) cc_final: 0.7848 (tmm)
  outliers start: 6
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1438
  time to fit residues: 31.3501
Evaluate side-chains
  101 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 216 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 194 optimal weight:    7.9990
   chunk 227 optimal weight:   30.0000
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0870
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.0970
   chunk 103 optimal weight:    6.9990
   chunk 200 optimal weight:    8.9990
   overall best weight:    2.8362

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 GLN
A 279 GLN
A 651 HIS
A 671 GLN
** E   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  83 GLN
E 238 GLN
E 242 HIS
** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 151 ASN
** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 320 HIS
I 321 HIS
J 218 GLN
J 323 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.046655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.028377 restraints weight = 202103.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.029076 restraints weight = 156053.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.029538 restraints weight = 129909.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.029727 restraints weight = 115254.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.030056 restraints weight = 107393.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  19022  Z= 0.190
  Angle     :  0.652  12.053  25948  Z= 0.325
  Chirality :  0.040   0.190   2877
  Planarity :  0.004   0.056   3314
  Dihedral  : 11.012  94.412   2929
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.80 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.51 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.17), residues: 2290
  helix:  0.81 (0.18), residues: 805
  sheet: -0.46 (0.25), residues: 363
  loop : -0.91 (0.19), residues: 1122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J 345 
 TYR   0.015   0.002   TYR E  47 
 PHE   0.018   0.002   PHE A 614 
 TRP   0.026   0.002   TRP J 318 
 HIS   0.006   0.001   HIS I  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (19022)
  covalent geometry    : angle       0.65197 (25948)
  hydrogen bonds       : bond        0.03916 (  768)
  hydrogen bonds       : angle       5.93897 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 0.683 
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: symmetry clash
   revert: symmetry clash
REVERT: A  236 PHE cc_start: 0.9675 (t80) cc_final: 0.9297 (t80)
REVERT: A  288 LEU cc_start: 0.9759 (tt) cc_final: 0.9387 (mm)
REVERT: E    1 MET cc_start: 0.7849 (mmp) cc_final: 0.7195 (mmp)
REVERT: E  220 PHE cc_start: 0.8767 (m-80) cc_final: 0.8322 (m-10)
REVERT: G   61 LEU cc_start: 0.9337 (mt) cc_final: 0.9028 (mt)
REVERT: H   19 LEU cc_start: 0.9377 (tp) cc_final: 0.8819 (mt)
REVERT: I   66 ILE cc_start: 0.9678 (mm) cc_final: 0.9383 (tp)
REVERT: I  135 MET cc_start: 0.8156 (tmm) cc_final: 0.7948 (tmm)
REVERT: I  157 SER cc_start: 0.9352 (t) cc_final: 0.9085 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1355
  time to fit residues: 25.4696
Evaluate side-chains
  91 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 81 optimal weight:    0.0050
   chunk 228 optimal weight:   20.0000
   chunk 179 optimal weight:   20.0000
   chunk 159 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 46 optimal weight:   20.0000
   chunk 121 optimal weight:   20.0000
   chunk 185 optimal weight:    7.9990
   chunk 164 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    3.0000

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 GLN
A 457 GLN
A 588 GLN
A 609 ASN
A 630 GLN
E  45 GLN
** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  95 GLN
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 341 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.045838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.027833 restraints weight = 202216.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.028537 restraints weight = 153949.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.029004 restraints weight = 128073.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.029194 restraints weight = 112727.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.029524 restraints weight = 104761.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  19022  Z= 0.189
  Angle     :  0.637  10.973  25948  Z= 0.318
  Chirality :  0.040   0.158   2877
  Planarity :  0.004   0.077   3314
  Dihedral  : 11.069  93.145   2929
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.37 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.41 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.17), residues: 2290
  helix:  0.75 (0.18), residues: 811
  sheet: -0.39 (0.26), residues: 362
  loop : -0.91 (0.19), residues: 1117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 642 
 TYR   0.015   0.002   TYR A 430 
 PHE   0.017   0.002   PHE A 614 
 TRP   0.016   0.002   TRP I 116 
 HIS   0.006   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (19022)
  covalent geometry    : angle       0.63656 (25948)
  hydrogen bonds       : bond        0.03938 (  768)
  hydrogen bonds       : angle       5.79181 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.771 
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  236 PHE cc_start: 0.9688 (t80) cc_final: 0.9282 (t80)
REVERT: A  288 LEU cc_start: 0.9739 (tt) cc_final: 0.9375 (mm)
REVERT: A  389 MET cc_start: 0.7958 (ppp) cc_final: 0.7705 (ppp)
REVERT: E    1 MET cc_start: 0.7850 (mmp) cc_final: 0.7579 (mmp)
REVERT: E  207 LEU cc_start: 0.9268 (tp) cc_final: 0.8970 (tt)
REVERT: E  220 PHE cc_start: 0.8859 (m-80) cc_final: 0.8378 (m-10)
REVERT: G   61 LEU cc_start: 0.9308 (mt) cc_final: 0.9004 (pp)
REVERT: H   19 LEU cc_start: 0.9346 (tp) cc_final: 0.8779 (mt)
REVERT: I   66 ILE cc_start: 0.9659 (mm) cc_final: 0.9329 (tp)
REVERT: I  157 SER cc_start: 0.9385 (t) cc_final: 0.9174 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1514
  time to fit residues: 26.3017
Evaluate side-chains
  83 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 119 optimal weight:   20.0000
   chunk 195 optimal weight:    6.9990
   chunk 120 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 179 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 220 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 186 optimal weight:   20.0000
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 321 HIS
J 419 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.045091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.027510 restraints weight = 200513.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.028196 restraints weight = 155648.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.028655 restraints weight = 129085.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.028978 restraints weight = 113745.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.029110 restraints weight = 104214.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  19022  Z= 0.207
  Angle     :  0.659  10.240  25948  Z= 0.329
  Chirality :  0.040   0.164   2877
  Planarity :  0.005   0.060   3314
  Dihedral  : 11.185  91.569   2929
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.85 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.17), residues: 2290
  helix:  0.58 (0.18), residues: 815
  sheet: -0.35 (0.27), residues: 358
  loop : -0.97 (0.19), residues: 1117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 627 
 TYR   0.017   0.002   TYR A 340 
 PHE   0.016   0.002   PHE A 614 
 TRP   0.020   0.002   TRP I 116 
 HIS   0.008   0.001   HIS A   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (19022)
  covalent geometry    : angle       0.65852 (25948)
  hydrogen bonds       : bond        0.03831 (  768)
  hydrogen bonds       : angle       5.76619 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.584 
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: A  236 PHE cc_start: 0.9698 (t80) cc_final: 0.9289 (t80)
REVERT: A  389 MET cc_start: 0.8014 (ppp) cc_final: 0.7778 (ppp)
REVERT: E    1 MET cc_start: 0.7865 (mmp) cc_final: 0.7423 (mmp)
REVERT: E  207 LEU cc_start: 0.9198 (tp) cc_final: 0.8924 (tt)
REVERT: E  220 PHE cc_start: 0.8973 (m-80) cc_final: 0.8379 (m-10)
REVERT: G   61 LEU cc_start: 0.9311 (mt) cc_final: 0.9008 (mt)
REVERT: G  201 MET cc_start: 0.9694 (mpp) cc_final: 0.9082 (mmt)
REVERT: I   70 MET cc_start: 0.8866 (tpt) cc_final: 0.8597 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1365
  time to fit residues: 22.5955
Evaluate side-chains
  72 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 140 optimal weight:    7.9990
   chunk 166 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 231 optimal weight:   10.0000
   chunk 209 optimal weight:    0.0030
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 148 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 68 optimal weight:   20.0000
   chunk 128 optimal weight:    4.9990
   overall best weight:    1.7194

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 590 HIS
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 296 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 = 0.3381 r_free = 0.3381 target = 0.045977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.028241 restraints weight = 197654.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.028979 restraints weight = 151100.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.029435 restraints weight = 125027.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.029751 restraints weight = 110318.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.029899 restraints weight = 101340.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  19022  Z= 0.132
  Angle     :  0.582   9.984  25948  Z= 0.290
  Chirality :  0.039   0.161   2877
  Planarity :  0.004   0.059   3314
  Dihedral  : 11.109  92.877   2929
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.33 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.65 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.18), residues: 2290
  helix:  0.85 (0.18), residues: 805
  sheet: -0.35 (0.27), residues: 348
  loop : -0.86 (0.19), residues: 1137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG J 345 
 TYR   0.013   0.001   TYR A 340 
 PHE   0.016   0.001   PHE A 614 
 TRP   0.013   0.001   TRP A 157 
 HIS   0.007   0.001   HIS H  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (19022)
  covalent geometry    : angle       0.58232 (25948)
  hydrogen bonds       : bond        0.03409 (  768)
  hydrogen bonds       : angle       5.57339 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.683 
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: A  236 PHE cc_start: 0.9687 (t80) cc_final: 0.9286 (t80)
REVERT: A  389 MET cc_start: 0.8018 (ppp) cc_final: 0.7805 (ppp)
REVERT: A  434 LEU cc_start: 0.9520 (mt) cc_final: 0.9296 (mm)
REVERT: E    1 MET cc_start: 0.7598 (mmp) cc_final: 0.7209 (mmt)
REVERT: E  207 LEU cc_start: 0.9227 (tp) cc_final: 0.8975 (tt)
REVERT: E  220 PHE cc_start: 0.8994 (m-80) cc_final: 0.8418 (m-10)
REVERT: G   61 LEU cc_start: 0.9303 (mt) cc_final: 0.8988 (pp)
REVERT: I   66 ILE cc_start: 0.9643 (mm) cc_final: 0.9303 (tp)
REVERT: I   70 MET cc_start: 0.8769 (tpt) cc_final: 0.8435 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1383
  time to fit residues: 23.7924
Evaluate side-chains
  77 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 133 optimal weight:    0.5980
   chunk 205 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 47 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 123 optimal weight:    8.9990
   chunk 176 optimal weight:    0.0670
   chunk 38 optimal weight:    0.0270
   chunk 196 optimal weight:    3.9990
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 GLN
E 151 ASN
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 136 HIS
J 189 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.047254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.029202 restraints weight = 191685.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.029934 restraints weight = 145466.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.030421 restraints weight = 120424.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.030746 restraints weight = 106026.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.030885 restraints weight = 97426.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  19022  Z= 0.098
  Angle     :  0.564   9.662  25948  Z= 0.276
  Chirality :  0.039   0.182   2877
  Planarity :  0.004   0.058   3314
  Dihedral  : 10.922  93.260   2929
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.72 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.49 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.18), residues: 2290
  helix:  1.01 (0.19), residues: 807
  sheet: -0.33 (0.27), residues: 348
  loop : -0.68 (0.19), residues: 1135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 345 
 TYR   0.012   0.001   TYR A 643 
 PHE   0.014   0.001   PHE A 614 
 TRP   0.015   0.001   TRP A 311 
 HIS   0.006   0.001   HIS I 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 (19022)
  covalent geometry    : angle       0.56426 (25948)
  hydrogen bonds       : bond        0.03109 (  768)
  hydrogen bonds       : angle       5.30623 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.731 
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: A  236 PHE cc_start: 0.9678 (t80) cc_final: 0.9307 (t80)
REVERT: E    1 MET cc_start: 0.7177 (mmp) cc_final: 0.6903 (mmp)
REVERT: E  207 LEU cc_start: 0.9271 (tp) cc_final: 0.9030 (tt)
REVERT: G   61 LEU cc_start: 0.9292 (mt) cc_final: 0.8963 (pp)
REVERT: H  103 PHE cc_start: 0.9530 (m-80) cc_final: 0.9139 (m-80)
REVERT: I   70 MET cc_start: 0.8765 (tpt) cc_final: 0.8512 (tpt)
REVERT: J  327 ASP cc_start: 0.7651 (p0) cc_final: 0.7404 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1414
  time to fit residues: 24.7938
Evaluate side-chains
  82 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 128 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 163 optimal weight:    0.0370
   chunk 219 optimal weight:   10.0000
   chunk 193 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 220 optimal weight:    7.9990
   overall best weight:    1.9864

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 GLN
A 692 ASN
E 151 ASN
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 296 ASN ** 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 = 0.3387 r_free = 0.3387 target = 0.046124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.028387 restraints weight = 199324.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.029127 restraints weight = 151219.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.029601 restraints weight = 124983.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.029924 restraints weight = 109829.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.030147 restraints weight = 100764.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  19022  Z= 0.141
  Angle     :  0.572   9.101  25948  Z= 0.284
  Chirality :  0.038   0.158   2877
  Planarity :  0.004   0.059   3314
  Dihedral  : 10.896  90.198   2929
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.89 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.01 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.18), residues: 2290
  helix:  1.04 (0.19), residues: 807
  sheet: -0.44 (0.27), residues: 355
  loop : -0.69 (0.19), residues: 1128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 345 
 TYR   0.017   0.001   TYR A 184 
 PHE   0.034   0.002   PHE I  34 
 TRP   0.014   0.001   TRP I 116 
 HIS   0.006   0.001   HIS H  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (19022)
  covalent geometry    : angle       0.57211 (25948)
  hydrogen bonds       : bond        0.03267 (  768)
  hydrogen bonds       : angle       5.35995 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.688 
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: A  166 MET cc_start: 0.9718 (tpt) cc_final: 0.9494 (tmm)
REVERT: A  236 PHE cc_start: 0.9678 (t80) cc_final: 0.9290 (t80)
REVERT: A  389 MET cc_start: 0.8213 (ppp) cc_final: 0.7916 (ppp)
REVERT: E    1 MET cc_start: 0.7339 (mmp) cc_final: 0.7038 (mmp)
REVERT: E  207 LEU cc_start: 0.9271 (tp) cc_final: 0.9013 (tt)
REVERT: E  220 PHE cc_start: 0.8961 (m-80) cc_final: 0.8110 (m-10)
REVERT: G   61 LEU cc_start: 0.9255 (mt) cc_final: 0.8947 (mt)
REVERT: H  103 PHE cc_start: 0.9546 (m-80) cc_final: 0.9147 (m-80)
REVERT: I   66 ILE cc_start: 0.9697 (mm) cc_final: 0.9416 (tp)
REVERT: I   70 MET cc_start: 0.8797 (tpt) cc_final: 0.8512 (tpt)
REVERT: J  327 ASP cc_start: 0.7593 (p0) cc_final: 0.7334 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 105
  average time/residue: 0.1378
  time to fit residues: 23.1182
Evaluate side-chains
  81 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 198 optimal weight:    7.9990
   chunk 160 optimal weight:    3.9990
   chunk 143 optimal weight:   40.0000
   chunk 166 optimal weight:    0.8980
   chunk 123 optimal weight:    3.9990
   chunk 171 optimal weight:    1.9990
   chunk 153 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 176 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  18 ASN
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 111 GLN
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 321 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.045984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.028326 restraints weight = 197837.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.029040 restraints weight = 149274.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.029486 restraints weight = 123703.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.029678 restraints weight = 109353.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.030025 restraints weight = 101749.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  19022  Z= 0.133
  Angle     :  0.571   9.035  25948  Z= 0.282
  Chirality :  0.038   0.180   2877
  Planarity :  0.004   0.059   3314
  Dihedral  : 10.925  90.440   2929
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.93 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.18), residues: 2290
  helix:  1.03 (0.19), residues: 798
  sheet: -0.43 (0.27), residues: 355
  loop : -0.69 (0.19), residues: 1137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I 130 
 TYR   0.015   0.001   TYR A 184 
 PHE   0.014   0.001   PHE I  34 
 TRP   0.015   0.001   TRP I 116 
 HIS   0.008   0.001   HIS H  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (19022)
  covalent geometry    : angle       0.57113 (25948)
  hydrogen bonds       : bond        0.03206 (  768)
  hydrogen bonds       : angle       5.32516 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.778 
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  236 PHE cc_start: 0.9668 (t80) cc_final: 0.9281 (t80)
REVERT: A  389 MET cc_start: 0.8147 (ppp) cc_final: 0.7854 (ppp)
REVERT: E    1 MET cc_start: 0.7339 (mmp) cc_final: 0.6999 (mmp)
REVERT: E  207 LEU cc_start: 0.9273 (tp) cc_final: 0.9029 (tt)
REVERT: E  220 PHE cc_start: 0.9068 (m-80) cc_final: 0.8193 (m-10)
REVERT: G   61 LEU cc_start: 0.9290 (mt) cc_final: 0.8985 (pp)
REVERT: H  103 PHE cc_start: 0.9550 (m-80) cc_final: 0.9149 (m-80)
REVERT: H  215 TYR cc_start: 0.8698 (m-80) cc_final: 0.8401 (m-80)
REVERT: I   70 MET cc_start: 0.8791 (tpt) cc_final: 0.8545 (tpt)
REVERT: I  213 MET cc_start: 0.8695 (mmt) cc_final: 0.8181 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1337
  time to fit residues: 22.5247
Evaluate side-chains
  76 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 177 optimal weight:    4.9990
   chunk 205 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 225 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 133 optimal weight:    7.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 692 ASN
** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  95 GLN
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 321 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.045127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.027730 restraints weight = 199150.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.028414 restraints weight = 152291.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.028847 restraints weight = 126338.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.029147 restraints weight = 111870.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.029272 restraints weight = 103071.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  19022  Z= 0.169
  Angle     :  0.605   8.905  25948  Z= 0.302
  Chirality :  0.039   0.165   2877
  Planarity :  0.004   0.060   3314
  Dihedral  : 10.988  90.345   2929
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  5.72 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.64 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.18), residues: 2290
  helix:  0.96 (0.18), residues: 799
  sheet: -0.50 (0.27), residues: 355
  loop : -0.74 (0.19), residues: 1136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 178 
 TYR   0.016   0.001   TYR A 340 
 PHE   0.018   0.002   PHE I  34 
 TRP   0.017   0.002   TRP I 116 
 HIS   0.008   0.001   HIS A 426 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (19022)
  covalent geometry    : angle       0.60485 (25948)
  hydrogen bonds       : bond        0.03421 (  768)
  hydrogen bonds       : angle       5.43719 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.789 
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: A  117 MET cc_start: 0.8482 (tpt) cc_final: 0.8173 (tpt)
REVERT: A  236 PHE cc_start: 0.9665 (t80) cc_final: 0.9267 (t80)
REVERT: A  389 MET cc_start: 0.8185 (ppp) cc_final: 0.7874 (ppp)
REVERT: E    1 MET cc_start: 0.7525 (mmp) cc_final: 0.7118 (mmp)
REVERT: E  207 LEU cc_start: 0.9290 (tp) cc_final: 0.9044 (tt)
REVERT: E  220 PHE cc_start: 0.9003 (m-80) cc_final: 0.8160 (m-10)
REVERT: F   61 LEU cc_start: 0.9594 (mt) cc_final: 0.9359 (mt)
REVERT: F  201 MET cc_start: 0.9693 (mpp) cc_final: 0.9413 (mpp)
REVERT: G   61 LEU cc_start: 0.9280 (mt) cc_final: 0.8977 (pp)
REVERT: H  103 PHE cc_start: 0.9560 (m-80) cc_final: 0.9164 (m-80)
REVERT: H  201 MET cc_start: 0.6657 (ptp) cc_final: 0.5832 (ptp)
REVERT: H  215 TYR cc_start: 0.8735 (m-80) cc_final: 0.8475 (m-80)
REVERT: I   70 MET cc_start: 0.8847 (tpt) cc_final: 0.8622 (tpt)
REVERT: I  213 MET cc_start: 0.8747 (mmt) cc_final: 0.8321 (mmt)
REVERT: J  327 ASP cc_start: 0.7727 (p0) cc_final: 0.7473 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 98
  average time/residue: 0.1331
  time to fit residues: 20.6603
Evaluate side-chains
  76 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 167 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 208 optimal weight:    7.9990
   chunk 229 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 105 optimal weight:    5.9990
   chunk 135 optimal weight:    3.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 296 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 = 0.3360 r_free = 0.3360 target = 0.045154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.027676 restraints weight = 202464.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.028347 restraints weight = 153965.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.028785 restraints weight = 128465.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.029120 restraints weight = 113220.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.029249 restraints weight = 103847.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  19022  Z= 0.154
  Angle     :  0.591   8.966  25948  Z= 0.294
  Chirality :  0.039   0.177   2877
  Planarity :  0.004   0.060   3314
  Dihedral  : 11.024  91.640   2929
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  5.46 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.18), residues: 2290
  helix:  0.97 (0.18), residues: 794
  sheet: -0.54 (0.28), residues: 355
  loop : -0.74 (0.19), residues: 1141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I 130 
 TYR   0.017   0.001   TYR A 340 
 PHE   0.017   0.002   PHE I  34 
 TRP   0.015   0.001   TRP I 116 
 HIS   0.008   0.001   HIS H  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (19022)
  covalent geometry    : angle       0.59088 (25948)
  hydrogen bonds       : bond        0.03340 (  768)
  hydrogen bonds       : angle       5.41356 ( 2142)

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

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

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4580 Ramachandran restraints generated.
    2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.698 
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  117 MET cc_start: 0.8507 (tpt) cc_final: 0.8221 (tpt)
REVERT: A  236 PHE cc_start: 0.9655 (t80) cc_final: 0.9287 (t80)
REVERT: A  389 MET cc_start: 0.8187 (ppp) cc_final: 0.7892 (ppp)
REVERT: E    1 MET cc_start: 0.7454 (mmp) cc_final: 0.7040 (mmp)
REVERT: E  207 LEU cc_start: 0.9289 (tp) cc_final: 0.9051 (tt)
REVERT: E  220 PHE cc_start: 0.9021 (m-80) cc_final: 0.8159 (m-10)
REVERT: F   61 LEU cc_start: 0.9605 (mt) cc_final: 0.9327 (mt)
REVERT: G   61 LEU cc_start: 0.9293 (mt) cc_final: 0.9056 (pp)
REVERT: G  201 MET cc_start: 0.9454 (mpp) cc_final: 0.9124 (mpp)
REVERT: H  103 PHE cc_start: 0.9568 (m-80) cc_final: 0.9173 (m-80)
REVERT: H  215 TYR cc_start: 0.8725 (m-80) cc_final: 0.8415 (m-80)
REVERT: I   70 MET cc_start: 0.8765 (tpt) cc_final: 0.8556 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1386
  time to fit residues: 20.8931
Evaluate side-chains
  72 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 232
   random chunks:
   chunk 165 optimal weight:    6.9990
   chunk 191 optimal weight:    9.9990
   chunk 153 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0970
   chunk 129 optimal weight:    0.5980
   chunk 194 optimal weight:    0.9990
   chunk 102 optimal weight:    0.5980
   chunk 185 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9990
   chunk 126 optimal weight:    4.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 GLN
A 279 GLN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 239 HIS ** 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 = 0.3394 r_free = 0.3394 target = 0.046414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.028537 restraints weight = 197101.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.029290 restraints weight = 149647.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.029765 restraints weight = 123152.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.029955 restraints weight = 108520.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.030282 restraints weight = 100776.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  19022  Z= 0.100
  Angle     :  0.558   8.755  25948  Z= 0.273
  Chirality :  0.039   0.172   2877
  Planarity :  0.004   0.060   3314
  Dihedral  : 10.887  92.688   2929
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.59 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.18), residues: 2290
  helix:  1.07 (0.19), residues: 807
  sheet: -0.54 (0.28), residues: 359
  loop : -0.60 (0.20), residues: 1124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 130 
 TYR   0.012   0.001   TYR A 184 
 PHE   0.019   0.001   PHE I  34 
 TRP   0.015   0.001   TRP A 311 
 HIS   0.006   0.001   HIS H  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (19022)
  covalent geometry    : angle       0.55768 (25948)
  hydrogen bonds       : bond        0.03017 (  768)
  hydrogen bonds       : angle       5.18325 ( 2142)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3587.27 seconds
wall clock time: 62 minutes 50.80 seconds (3770.80 seconds total)