Starting phenix.real_space_refine
on Wed Feb  4 13:00:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9his_52200/02_2026/9his_52200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9his_52200/02_2026/9his_52200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9his_52200/02_2026/9his_52200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9his_52200/02_2026/9his_52200.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9his_52200/02_2026/9his_52200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9his_52200/02_2026/9his_52200.map"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    6696      2.51       5
     N    1713      2.21       5
     O    2077      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10517
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 3522
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3522
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 18, 'TRANS': 429}
          Chain breaks: 2
    Chain: "I"
      Number of atoms: 1337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1337
          Classifications: {'peptide': 169}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 161}
    Chain: "J"
      Number of atoms: 1547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1547
          Classifications: {'peptide': 188}
          Link IDs: {'PTRANS': 5, 'TRANS': 182}
    Chain: "G"
      Number of atoms: 4065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 4065
          Classifications: {'peptide': 520}
          Link IDs: {'PTRANS': 16, 'TRANS': 503}
    Chain: "G"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 46
          Unusual residues: {'TDA': 1, 'Z41': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'TDA:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 2.00, per 1000 atoms: 0.19
  Number of scatterers: 10517
  At special positions: 0
  Unit cell: (133.2, 116.92, 148, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    2077      8.00
     N    1713      7.00
     C    6696      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 470.2 milliseconds
  

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  CYS G  18 "
  Number of C-beta restraints generated:  2454

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 21 sheets defined
      18.1% alpha, 38.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'H' and resid 69 through 75
      removed outlier: 3.851A  pdb=" N   ASP H  73 " --> pdb=" O   VAL H  70 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 111 through 115
      removed outlier: 4.208A  pdb=" N   VAL H 115 " --> pdb=" O   THR H 112 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 273 through 277
      removed outlier: 3.638A  pdb=" N   GLY H 277 " --> pdb=" O   ASP H 274 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 487 through 489
      No H-bonds generated for 'chain 'H' and resid 487 through 489'
    Processing helix  chain 'I' and resid 31 through 50
      removed outlier: 3.626A  pdb=" N   ALA I  48 " --> pdb=" O   ALA I  44 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 51 through 56
    Processing helix  chain 'I' and resid 136 through 138
      No H-bonds generated for 'chain 'I' and resid 136 through 138'
    Processing helix  chain 'I' and resid 139 through 146
    Processing helix  chain 'I' and resid 147 through 149
      No H-bonds generated for 'chain 'I' and resid 147 through 149'
    Processing helix  chain 'J' and resid 29 through 32
    Processing helix  chain 'J' and resid 33 through 44
      removed outlier: 3.736A  pdb=" N   ALA J  37 " --> pdb=" O   ASP J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 52 through 56
    Processing helix  chain 'J' and resid 73 through 75
      No H-bonds generated for 'chain 'J' and resid 73 through 75'
    Processing helix  chain 'J' and resid 120 through 124
    Processing helix  chain 'J' and resid 126 through 131
      removed outlier: 4.285A  pdb=" N   TYR J 130 " --> pdb=" O   ALA J 126 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR J 131 " --> pdb=" O   ASN J 127 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 126 through 131'
    Processing helix  chain 'J' and resid 153 through 160
    Processing helix  chain 'J' and resid 166 through 171
      removed outlier: 3.986A  pdb=" N   LEU J 170 " --> pdb=" O   PRO J 166 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU J 171 " --> pdb=" O   ALA J 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 166 through 171'
    Processing helix  chain 'J' and resid 172 through 176
    Processing helix  chain 'J' and resid 187 through 191
    Processing helix  chain 'G' and resid 31 through 36
    Processing helix  chain 'G' and resid 119 through 123
      removed outlier: 3.637A  pdb=" N   LYS G 123 " --> pdb=" O   PRO G 120 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 184 through 187
    Processing helix  chain 'G' and resid 208 through 213
    Processing helix  chain 'G' and resid 226 through 246
    Processing helix  chain 'G' and resid 252 through 260
      removed outlier: 3.672A  pdb=" N   GLU G 258 " --> pdb=" O   GLN G 254 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA G 259 " --> pdb=" O   LEU G 255 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 332 through 341
      removed outlier: 3.621A  pdb=" N   LYS G 341 " --> pdb=" O   ASP G 337 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 361 through 369
    Processing helix  chain 'G' and resid 406 through 408
      No H-bonds generated for 'chain 'G' and resid 406 through 408'
    Processing helix  chain 'G' and resid 409 through 414
    Processing helix  chain 'G' and resid 440 through 459
    Processing helix  chain 'G' and resid 460 through 462
      No H-bonds generated for 'chain 'G' and resid 460 through 462'
    Processing helix  chain 'G' and resid 463 through 470
    Processing helix  chain 'G' and resid 515 through 520
    Processing helix  chain 'G' and resid 521 through 525
      removed outlier: 3.913A  pdb=" N   LYS G 525 " --> pdb=" O   PRO G 522 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 41 through 42
    Processing sheet with id=AA2, first strand: chain 'H' and resid 53 through 56
      removed outlier: 4.049A  pdb=" N   ASN H  64 " --> pdb=" O   ASN H 142 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   VAL H 125 " --> pdb=" O   LYS H  94 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   LYS H  94 " --> pdb=" O   VAL H 125 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER H 101 " --> pdb=" O   MET H  93 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 153 through 154
      removed outlier: 3.739A  pdb=" N   ALA H 161 " --> pdb=" O   ILE H 480 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 153 through 154
      removed outlier: 4.065A  pdb=" N   LYS H 479 " --> pdb=" O   GLY H 473 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 172 through 177
    Processing sheet with id=AA6, first strand: chain 'H' and resid 222 through 229
      removed outlier: 6.052A  pdb=" N   SER H 226 " --> pdb=" O   LEU H 237 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   LEU H 237 " --> pdb=" O   SER H 226 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 265 through 272
      removed outlier: 8.061A  pdb=" N   THR H 266 " --> pdb=" O   GLU H 291 " (cutoff:3.500A)
      removed outlier: 8.454A  pdb=" N   GLU H 291 " --> pdb=" O   THR H 266 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   LEU H 268 " --> pdb=" O   ILE H 289 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ILE H 289 " --> pdb=" O   LEU H 268 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR H 270 " --> pdb=" O   ALA H 287 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   THR H 315 " --> pdb=" O   PHE H 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 324 through 332
      removed outlier: 5.786A  pdb=" N   ASN H 325 " --> pdb=" O   ASN H 345 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ASN H 345 " --> pdb=" O   ASN H 325 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 382 through 389
      removed outlier: 5.706A  pdb=" N   ASP H 383 " --> pdb=" O   LYS H 398 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   LYS H 398 " --> pdb=" O   ASP H 383 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 57 through 60
      removed outlier: 3.828A  pdb=" N   TYR I  70 " --> pdb=" O   TYR I 158 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   PHE I 181 " --> pdb=" O   THR I 100 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   THR I 100 " --> pdb=" O   PHE I 181 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ILE I 183 " --> pdb=" O   LYS I  98 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LYS I  98 " --> pdb=" O   ILE I 183 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   LEU I 185 " --> pdb=" O   TYR I  96 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   TYR I  96 " --> pdb=" O   LEU I 185 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP I 108 " --> pdb=" O   GLY I  99 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 57 through 60
      removed outlier: 3.828A  pdb=" N   TYR I  70 " --> pdb=" O   TYR I 158 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   PHE I 181 " --> pdb=" O   THR I 100 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   THR I 100 " --> pdb=" O   PHE I 181 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ILE I 183 " --> pdb=" O   LYS I  98 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LYS I  98 " --> pdb=" O   ILE I 183 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   LEU I 185 " --> pdb=" O   TYR I  96 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   TYR I  96 " --> pdb=" O   LEU I 185 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 48 through 51
      removed outlier: 7.930A  pdb=" N   GLU J  68 " --> pdb=" O   ILE J  80 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   ILE J  80 " --> pdb=" O   GLU J  68 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   HIS J 181 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ALA J 180 " --> pdb=" O   THR J 208 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   THR J 208 " --> pdb=" O   ALA J 180 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE J 104 " --> pdb=" O   ASP J 205 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ASP J 107 " --> pdb=" O   THR J 113 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   THR J 113 " --> pdb=" O   ASP J 107 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 48 through 51
      removed outlier: 7.930A  pdb=" N   GLU J  68 " --> pdb=" O   ILE J  80 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   ILE J  80 " --> pdb=" O   GLU J  68 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   HIS J 181 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ALA J 180 " --> pdb=" O   THR J 208 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   THR J 208 " --> pdb=" O   ALA J 180 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL J 135 " --> pdb=" O   ILE J 150 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 373 through 378
      removed outlier: 5.880A  pdb=" N   LEU G 374 " --> pdb=" O   THR G 533 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   THR G 533 " --> pdb=" O   LEU G 374 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   THR G  47 " --> pdb=" O   THR G 359 " (cutoff:3.500A)
      removed outlier: 9.835A  pdb=" N   ILE G 354 " --> pdb=" O   PRO G 481 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   THR G 356 " --> pdb=" O   LEU G 479 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   THR G 399 " --> pdb=" O   VAL G 482 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'G' and resid 373 through 378
      removed outlier: 5.880A  pdb=" N   LEU G 374 " --> pdb=" O   THR G 533 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   THR G 533 " --> pdb=" O   LEU G 374 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   THR G  47 " --> pdb=" O   THR G 359 " (cutoff:3.500A)
      removed outlier: 9.835A  pdb=" N   ILE G 354 " --> pdb=" O   PRO G 481 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   THR G 356 " --> pdb=" O   LEU G 479 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ARG G 500 " --> pdb=" O   THR G 485 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 189 through 200
      removed outlier: 6.403A  pdb=" N   ILE G 194 " --> pdb=" O   GLU G 164 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   GLU G 164 " --> pdb=" O   ILE G 194 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY G 196 " --> pdb=" O   VAL G 162 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ARG G 159 " --> pdb=" O   ASP G 268 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   SER G 267 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ALA G  78 " --> pdb=" O   SER G 267 " (cutoff:3.500A)
      removed outlier: 10.604A  pdb=" N   TYR G 269 " --> pdb=" O   TYR G  76 " (cutoff:3.500A)
      removed outlier: 12.383A  pdb=" N   TYR G  76 " --> pdb=" O   TYR G 269 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE G  80 " --> pdb=" O   TYR G  64 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   TYR G  64 " --> pdb=" O   PHE G  80 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 220 through 222
      removed outlier: 3.591A  pdb=" N   ALA G 140 " --> pdb=" O   VAL G 285 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLN G 279 " --> pdb=" O   TRP G 146 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ASP G 148 " --> pdb=" O   ILE G 277 " (cutoff:3.500A)
      removed outlier: 8.915A  pdb=" N   ILE G 277 " --> pdb=" O   ASP G 148 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TYR G 150 " --> pdb=" O   LEU G 275 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU G 275 " --> pdb=" O   TYR G 150 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   TYR G  64 " --> pdb=" O   PHE G  80 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE G  80 " --> pdb=" O   TYR G  64 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 97 through 100
      removed outlier: 3.612A  pdb=" N   SER G 108 " --> pdb=" O   VAL G  99 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 126 through 130
      removed outlier: 3.692A  pdb=" N   GLY G 136 " --> pdb=" O   ILE G 128 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ASP G 130 " --> pdb=" O   ILE G 134 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   ILE G 134 " --> pdb=" O   ASP G 130 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 345 through 347
    Processing sheet with id=AC3, first strand: chain 'G' and resid 380 through 382

    404 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.14 -     1.29: 1815
        1.29 -     1.43: 2819
        1.43 -     1.58: 6050
        1.58 -     1.72: 0
        1.72 -     1.87: 53
  Bond restraints: 10737
  Sorted by residual:
  bond pdb=" C   CYS G  18 "
       pdb=" O   CYS G  18 "
    ideal  model  delta    sigma   weight residual
    1.231  1.143  0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" N   ASP G  19 "
       pdb=" CA  ASP G  19 "
    ideal  model  delta    sigma   weight residual
    1.454  1.505 -0.051 1.17e-02 7.31e+03 1.88e+01
  bond pdb=" C16 Z41 G 602 "
       pdb=" O2  Z41 G 602 "
    ideal  model  delta    sigma   weight residual
    1.332  1.400 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C19 Z41 G 602 "
       pdb=" O3  Z41 G 602 "
    ideal  model  delta    sigma   weight residual
    1.333  1.398 -0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" C21 TDA G 601 "
       pdb=" O22 TDA G 601 "
    ideal  model  delta    sigma   weight residual
    1.247  1.193  0.054 2.00e-02 2.50e+03 7.39e+00
  ... (remaining 10732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.54: 14521
        4.54 -     9.09: 39
        9.09 -    13.63: 3
       13.63 -    18.17: 1
       18.17 -    22.71: 1
  Bond angle restraints: 14565
  Sorted by residual:
  angle pdb=" C   CYS G  18 "
        pdb=" CA  CYS G  18 "
        pdb=" CB  CYS G  18 "
      ideal   model   delta    sigma   weight residual
     110.10  132.81  -22.71 1.90e+00 2.77e-01 1.43e+02
  angle pdb=" CA  CYS G  18 "
        pdb=" C   CYS G  18 "
        pdb=" N   ASP G  19 "
      ideal   model   delta    sigma   weight residual
     116.20  127.56  -11.36 2.00e+00 2.50e-01 3.23e+01
  angle pdb=" N   CYS G  18 "
        pdb=" CA  CYS G  18 "
        pdb=" C   CYS G  18 "
      ideal   model   delta    sigma   weight residual
     111.00   96.42   14.58 2.80e+00 1.28e-01 2.71e+01
  angle pdb=" CA  CYS G  18 "
        pdb=" C   CYS G  18 "
        pdb=" O   CYS G  18 "
      ideal   model   delta    sigma   weight residual
     120.80  111.98    8.82 1.70e+00 3.46e-01 2.69e+01
  angle pdb=" C   CYS G  18 "
        pdb=" N   ASP G  19 "
        pdb=" CA  ASP G  19 "
      ideal   model   delta    sigma   weight residual
     122.64  115.51    7.13 1.70e+00 3.46e-01 1.76e+01
  ... (remaining 14560 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 5979
       17.77 -    35.54: 314
       35.54 -    53.31: 57
       53.31 -    71.08: 18
       71.08 -    88.85: 6
  Dihedral angle restraints: 6374
    sinusoidal: 2526
      harmonic: 3848
  Sorted by residual:
  dihedral pdb=" CA  VAL I  95 "
           pdb=" C   VAL I  95 "
           pdb=" N   TYR I  96 "
           pdb=" CA  TYR I  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.58   29.42     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  GLN G 434 "
           pdb=" C   GLN G 434 "
           pdb=" N   TYR G 435 "
           pdb=" CA  TYR G 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.20   25.80     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  LYS G 129 "
           pdb=" C   LYS G 129 "
           pdb=" N   ASP G 130 "
           pdb=" CA  ASP G 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.63   25.37     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 6371 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.876: 1613
       0.876 -    1.752: 0
       1.752 -    2.629: 0
       2.629 -    3.505: 0
       3.505 -    4.381: 1
  Chirality restraints: 1614
  Sorted by residual:
  chirality pdb=" CA  CYS G  18 "
            pdb=" N   CYS G  18 "
            pdb=" C   CYS G  18 "
            pdb=" CB  CYS G  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.87    4.38 2.00e-01 2.50e+01 4.80e+02
  chirality pdb=" CB  ILE G  56 "
            pdb=" CA  ILE G  56 "
            pdb=" CG1 ILE G  56 "
            pdb=" CG2 ILE G  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  ILE H  62 "
            pdb=" N   ILE H  62 "
            pdb=" C   ILE H  62 "
            pdb=" CB  ILE H  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.84e-01
  ... (remaining 1611 not shown)

  Planarity restraints: 1875
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE H 195 "   -0.036 5.00e-02 4.00e+02   5.52e-02 4.88e+00
        pdb=" N   PRO H 196 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO H 196 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO H 196 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS H 378 "    0.033 5.00e-02 4.00e+02   5.03e-02 4.06e+00
        pdb=" N   PRO H 379 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO H 379 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO H 379 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR J 155 "   -0.014 2.00e-02 2.50e+03   1.37e-02 3.73e+00
        pdb=" CG  TYR J 155 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR J 155 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR J 155 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR J 155 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR J 155 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR J 155 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR J 155 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1872 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 716
        2.74 -     3.28: 10410
        3.28 -     3.82: 15757
        3.82 -     4.36: 19760
        4.36 -     4.90: 34372
  Nonbonded interactions: 81015
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H 168 "
            pdb=" OE1 GLN H 475 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" NZ  LYS I  83 "
            pdb=" O   PHE I 188 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" NZ  LYS I  83 "
            pdb=" OD1 ASP I 187 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OG1 THR H  92 "
            pdb=" O   SER H 101 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OD1 ASN G 490 "
            pdb=" OG1 THR G 493 "
     model   vdw
     2.294 3.040
  ... (remaining 81010 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.970
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088  10739  Z= 0.217
  Angle     :  0.808  22.715  14565  Z= 0.423
  Chirality :  0.120   4.381   1614
  Planarity :  0.005   0.055   1875
  Dihedral  : 12.266  88.852   3920
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.40 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.23), residues: 1313
  helix: -1.05 (0.39), residues: 169
  sheet:  0.54 (0.27), residues: 335
  loop : -1.38 (0.22), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  38 
 TYR   0.032   0.002   TYR J 155 
 PHE   0.020   0.002   PHE J  55 
 TRP   0.033   0.003   TRP H 129 
 HIS   0.003   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (10737)
  covalent geometry    : angle       0.80808 (14565)
  hydrogen bonds       : bond        0.18250 (  339)
  hydrogen bonds       : angle       7.85081 ( 1032)
  Misc. bond           : bond        0.07126 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  203 ARG cc_start: 0.8712 (mmt90) cc_final: 0.8130 (mmt180)
REVERT: H  274 ASP cc_start: 0.8963 (t0) cc_final: 0.8550 (t0)
REVERT: I   39 PHE cc_start: 0.8682 (t80) cc_final: 0.8397 (t80)
REVERT: I   53 ARG cc_start: 0.7907 (mmt180) cc_final: 0.7232 (mmt-90)
REVERT: I  170 THR cc_start: 0.8888 (p) cc_final: 0.8680 (t)
REVERT: J   32 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7850 (mp0)
REVERT: J   56 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8038 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1115
  time to fit residues: 25.0961
Evaluate side-chains
  88 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  97 ASN
G 213 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.083520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.062655 restraints weight = 29035.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 3.37
r_work: 0.2904 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10739  Z= 0.138
  Angle     :  0.614   6.158  14565  Z= 0.335
  Chirality :  0.048   0.279   1614
  Planarity :  0.004   0.049   1875
  Dihedral  :  7.843  57.249   1471
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.92 %
    Favored  : 93.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.23), residues: 1313
  helix: -0.60 (0.39), residues: 172
  sheet:  0.53 (0.27), residues: 349
  loop : -1.36 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG I  58 
 TYR   0.020   0.001   TYR I 163 
 PHE   0.015   0.001   PHE H 230 
 TRP   0.015   0.002   TRP H 307 
 HIS   0.003   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10737)
  covalent geometry    : angle       0.61375 (14565)
  hydrogen bonds       : bond        0.04363 (  339)
  hydrogen bonds       : angle       5.26720 ( 1032)
  Misc. bond           : bond        0.00134 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  145 MET cc_start: 0.8169 (ttp) cc_final: 0.7956 (ttp)
REVERT: H  203 ARG cc_start: 0.8876 (mmt90) cc_final: 0.8038 (mmt180)
REVERT: J   56 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8123 (mm-30)
REVERT: J  196 GLN cc_start: 0.9000 (mt0) cc_final: 0.8683 (mm110)
REVERT: G   20 ASP cc_start: 0.8116 (m-30) cc_final: 0.7685 (p0)
REVERT: G   29 MET cc_start: 0.9075 (ptm) cc_final: 0.8811 (ptt)
  outliers start: 7
  outliers final: 7
  residues processed: 96
  average time/residue: 0.0974
  time to fit residues: 12.9558
Evaluate side-chains
  87 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  224 VAL
Chi-restraints excluded: chain I residue   63 THR
Chi-restraints excluded: chain I residue  108 ASP
Chi-restraints excluded: chain I residue  139 ILE
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue   72 LEU
Chi-restraints excluded: chain G residue  488 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 106 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 123 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
H 137 ASN
** H 186 GLN ** 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 = 0.3347 r_free = 0.3347 target = 0.079071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.058232 restraints weight = 29778.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 3.36
r_work: 0.2818 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  10739  Z= 0.281
  Angle     :  0.665  10.062  14565  Z= 0.358
  Chirality :  0.050   0.343   1614
  Planarity :  0.005   0.050   1875
  Dihedral  :  7.484  60.858   1471
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  7.83 %
    Favored  : 91.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.23), residues: 1313
  helix: -0.64 (0.39), residues: 172
  sheet: -0.01 (0.26), residues: 374
  loop : -1.43 (0.22), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 484 
 TYR   0.019   0.002   TYR I 163 
 PHE   0.017   0.002   PHE J 209 
 TRP   0.016   0.002   TRP H 307 
 HIS   0.005   0.001   HIS G 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00666 (10737)
  covalent geometry    : angle       0.66539 (14565)
  hydrogen bonds       : bond        0.04940 (  339)
  hydrogen bonds       : angle       5.31068 ( 1032)
  Misc. bond           : bond        0.00123 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   93 MET cc_start: 0.6878 (mpp) cc_final: 0.6601 (mpp)
REVERT: H  203 ARG cc_start: 0.8980 (mmt90) cc_final: 0.8042 (mmt180)
REVERT: H  229 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7860 (tmm-80)
REVERT: H  370 MET cc_start: 0.9508 (mmp) cc_final: 0.9129 (mmp)
REVERT: H  427 MET cc_start: 0.8718 (mmt) cc_final: 0.8497 (mmt)
REVERT: I  112 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8404 (mmtt)
REVERT: J   74 ASP cc_start: 0.9001 (m-30) cc_final: 0.8416 (t0)
REVERT: J   78 MET cc_start: 0.9006 (tmm) cc_final: 0.8676 (ttt)
  outliers start: 13
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1109
  time to fit residues: 13.2301
Evaluate side-chains
  83 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  135 VAL
Chi-restraints excluded: chain H residue  224 VAL
Chi-restraints excluded: chain H residue  229 ARG
Chi-restraints excluded: chain I residue   63 THR
Chi-restraints excluded: chain I residue  108 ASP
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue   72 LEU
Chi-restraints excluded: chain G residue  110 THR
Chi-restraints excluded: chain G residue  197 THR
Chi-restraints excluded: chain G residue  488 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0570
   chunk 14 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.1102

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

Flipped N/Q/H residues before XYZ refinement:
H 136 GLN
** H 186 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.081126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.060177 restraints weight = 29390.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 3.39
r_work: 0.2866 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10739  Z= 0.127
  Angle     :  0.552   7.661  14565  Z= 0.299
  Chirality :  0.045   0.160   1614
  Planarity :  0.004   0.047   1875
  Dihedral  :  7.026  65.196   1471
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.80 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.57 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.23), residues: 1313
  helix: -0.06 (0.41), residues: 166
  sheet:  0.13 (0.26), residues: 372
  loop : -1.19 (0.22), residues: 775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H 166 
 TYR   0.019   0.001   TYR I 163 
 PHE   0.019   0.001   PHE I 107 
 TRP   0.012   0.001   TRP H 129 
 HIS   0.003   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10737)
  covalent geometry    : angle       0.55213 (14565)
  hydrogen bonds       : bond        0.03768 (  339)
  hydrogen bonds       : angle       4.86691 ( 1032)
  Misc. bond           : bond        0.00100 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   93 MET cc_start: 0.6825 (mpp) cc_final: 0.6493 (mpp)
REVERT: H  145 MET cc_start: 0.8155 (ttp) cc_final: 0.7949 (ttp)
REVERT: H  229 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7551 (tmm-80)
REVERT: I   77 MET cc_start: 0.7894 (ttp) cc_final: 0.7489 (ttp)
REVERT: J   74 ASP cc_start: 0.9008 (m-30) cc_final: 0.8329 (t0)
REVERT: J   78 MET cc_start: 0.8970 (tmm) cc_final: 0.8541 (ttt)
REVERT: G   29 MET cc_start: 0.9063 (ptm) cc_final: 0.8832 (ptt)
  outliers start: 12
  outliers final: 9
  residues processed: 90
  average time/residue: 0.1098
  time to fit residues: 13.7339
Evaluate side-chains
  81 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  111 LEU
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  229 ARG
Chi-restraints excluded: chain H residue  358 VAL
Chi-restraints excluded: chain I residue   81 VAL
Chi-restraints excluded: chain I residue  108 ASP
Chi-restraints excluded: chain I residue  139 ILE
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue  104 ILE
Chi-restraints excluded: chain G residue  197 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 129 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 34 optimal weight:    0.1980
   chunk 26 optimal weight:    8.9990
   chunk 68 optimal weight:    8.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.080128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.059331 restraints weight = 28977.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 3.35
r_work: 0.2869 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10739  Z= 0.133
  Angle     :  0.543   8.814  14565  Z= 0.291
  Chirality :  0.045   0.192   1614
  Planarity :  0.004   0.047   1875
  Dihedral  :  6.699  63.218   1471
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.56 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.10 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.23), residues: 1313
  helix:  0.10 (0.41), residues: 166
  sheet:  0.13 (0.26), residues: 375
  loop : -1.10 (0.23), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 166 
 TYR   0.015   0.001   TYR I 163 
 PHE   0.020   0.001   PHE I 107 
 TRP   0.011   0.001   TRP H 307 
 HIS   0.004   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10737)
  covalent geometry    : angle       0.54341 (14565)
  hydrogen bonds       : bond        0.03664 (  339)
  hydrogen bonds       : angle       4.75959 ( 1032)
  Misc. bond           : bond        0.00077 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   93 MET cc_start: 0.6872 (mpp) cc_final: 0.6555 (mpp)
REVERT: H  145 MET cc_start: 0.8145 (ttp) cc_final: 0.7943 (ttp)
REVERT: H  229 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7733 (tmm-80)
REVERT: H  424 ARG cc_start: 0.3226 (OUTLIER) cc_final: 0.2337 (tpt170)
REVERT: I   58 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8311 (ptt90)
REVERT: I   77 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7493 (ttp)
REVERT: J   74 ASP cc_start: 0.9023 (m-30) cc_final: 0.8321 (t0)
REVERT: J   78 MET cc_start: 0.8949 (tmm) cc_final: 0.8562 (ttt)
REVERT: G   29 MET cc_start: 0.9056 (ptm) cc_final: 0.8825 (ptt)
  outliers start: 21
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1184
  time to fit residues: 14.6060
Evaluate side-chains
  88 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  135 VAL
Chi-restraints excluded: chain H residue  148 MET
Chi-restraints excluded: chain H residue  229 ARG
Chi-restraints excluded: chain H residue  358 VAL
Chi-restraints excluded: chain H residue  424 ARG
Chi-restraints excluded: chain I residue   58 ARG
Chi-restraints excluded: chain I residue   63 THR
Chi-restraints excluded: chain I residue   77 MET
Chi-restraints excluded: chain I residue   81 VAL
Chi-restraints excluded: chain I residue  108 ASP
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  139 ILE
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue  104 ILE
Chi-restraints excluded: chain G residue  197 THR
Chi-restraints excluded: chain G residue  488 SER
Chi-restraints excluded: chain G residue  530 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 106 optimal weight:   10.0000
   chunk 124 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 54 optimal weight:    5.9990
   chunk 113 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.080747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.060022 restraints weight = 29006.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 3.33
r_work: 0.2882 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10739  Z= 0.113
  Angle     :  0.517   7.249  14565  Z= 0.277
  Chirality :  0.044   0.157   1614
  Planarity :  0.003   0.045   1875
  Dihedral  :  6.242  57.406   1471
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.80 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.36 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.23), residues: 1313
  helix:  0.32 (0.42), residues: 164
  sheet:  0.18 (0.26), residues: 371
  loop : -1.03 (0.23), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H 166 
 TYR   0.014   0.001   TYR I 163 
 PHE   0.025   0.001   PHE I 107 
 TRP   0.010   0.001   TRP H 129 
 HIS   0.004   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (10737)
  covalent geometry    : angle       0.51714 (14565)
  hydrogen bonds       : bond        0.03410 (  339)
  hydrogen bonds       : angle       4.62069 ( 1032)
  Misc. bond           : bond        0.00050 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  229 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7760 (tmm-80)
REVERT: H  471 MET cc_start: 0.8782 (mtp) cc_final: 0.8525 (mtp)
REVERT: I   58 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8281 (ptt90)
REVERT: I   77 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7465 (ttp)
REVERT: J   74 ASP cc_start: 0.9036 (m-30) cc_final: 0.8273 (t0)
REVERT: J   78 MET cc_start: 0.8932 (tmm) cc_final: 0.8552 (ttt)
REVERT: G   29 MET cc_start: 0.9026 (ptm) cc_final: 0.8811 (ptt)
  outliers start: 20
  outliers final: 13
  residues processed: 88
  average time/residue: 0.1125
  time to fit residues: 13.7444
Evaluate side-chains
  82 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue  135 VAL
Chi-restraints excluded: chain H residue  229 ARG
Chi-restraints excluded: chain H residue  358 VAL
Chi-restraints excluded: chain I residue   58 ARG
Chi-restraints excluded: chain I residue   77 MET
Chi-restraints excluded: chain I residue   81 VAL
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  139 ILE
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue  104 ILE
Chi-restraints excluded: chain G residue  197 THR
Chi-restraints excluded: chain G residue  488 SER
Chi-restraints excluded: chain G residue  492 THR
Chi-restraints excluded: chain G residue  530 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 116 optimal weight:    0.1980
   chunk 114 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0570
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 475 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.082099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.061206 restraints weight = 29236.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 3.43
r_work: 0.2864 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10739  Z= 0.095
  Angle     :  0.502   6.802  14565  Z= 0.269
  Chirality :  0.044   0.163   1614
  Planarity :  0.003   0.045   1875
  Dihedral  :  5.929  57.279   1471
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.18 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.23 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.23), residues: 1313
  helix:  0.52 (0.42), residues: 164
  sheet:  0.04 (0.26), residues: 368
  loop : -0.94 (0.23), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG H 166 
 TYR   0.012   0.001   TYR I 163 
 PHE   0.025   0.001   PHE I 107 
 TRP   0.014   0.001   TRP I 155 
 HIS   0.004   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 (10737)
  covalent geometry    : angle       0.50150 (14565)
  hydrogen bonds       : bond        0.03232 (  339)
  hydrogen bonds       : angle       4.51649 ( 1032)
  Misc. bond           : bond        0.00042 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  424 ARG cc_start: 0.3365 (OUTLIER) cc_final: 0.2460 (tpt170)
REVERT: H  471 MET cc_start: 0.8792 (mtp) cc_final: 0.8525 (mtp)
REVERT: I   58 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8332 (ptt90)
REVERT: I   77 MET cc_start: 0.7909 (ttp) cc_final: 0.7445 (ttp)
REVERT: J   78 MET cc_start: 0.8917 (tmm) cc_final: 0.8534 (ttt)
  outliers start: 17
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0986
  time to fit residues: 11.7925
Evaluate side-chains
  81 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue  148 MET
Chi-restraints excluded: chain H residue  358 VAL
Chi-restraints excluded: chain H residue  424 ARG
Chi-restraints excluded: chain I residue   58 ARG
Chi-restraints excluded: chain I residue   63 THR
Chi-restraints excluded: chain I residue   81 VAL
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  139 ILE
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue  104 ILE
Chi-restraints excluded: chain G residue  197 THR
Chi-restraints excluded: chain G residue  492 THR
Chi-restraints excluded: chain G residue  530 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 126 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
H 172 GLN
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  36 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 = 0.3376 r_free = 0.3376 target = 0.080697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.059985 restraints weight = 29361.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 3.37
r_work: 0.2844 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10739  Z= 0.182
  Angle     :  0.551   6.780  14565  Z= 0.295
  Chirality :  0.046   0.160   1614
  Planarity :  0.004   0.046   1875
  Dihedral  :  6.169  59.030   1471
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.79 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.40 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.23), residues: 1313
  helix:  0.44 (0.42), residues: 165
  sheet: -0.01 (0.26), residues: 372
  loop : -0.98 (0.23), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H 166 
 TYR   0.013   0.001   TYR G 435 
 PHE   0.027   0.001   PHE I 107 
 TRP   0.010   0.001   TRP H 129 
 HIS   0.003   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (10737)
  covalent geometry    : angle       0.55070 (14565)
  hydrogen bonds       : bond        0.03719 (  339)
  hydrogen bonds       : angle       4.67497 ( 1032)
  Misc. bond           : bond        0.00067 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  229 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7572 (tmm-80)
REVERT: H  424 ARG cc_start: 0.3452 (OUTLIER) cc_final: 0.2580 (tpt170)
REVERT: H  471 MET cc_start: 0.8826 (mtp) cc_final: 0.8561 (mtp)
REVERT: I   58 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8253 (ptt90)
REVERT: I  112 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8546 (mmtt)
REVERT: J   78 MET cc_start: 0.8957 (tmm) cc_final: 0.8676 (ttt)
REVERT: G   29 MET cc_start: 0.9042 (ptm) cc_final: 0.8819 (ptt)
  outliers start: 23
  outliers final: 18
  residues processed: 88
  average time/residue: 0.1035
  time to fit residues: 12.5466
Evaluate side-chains
  88 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue  135 VAL
Chi-restraints excluded: chain H residue  148 MET
Chi-restraints excluded: chain H residue  229 ARG
Chi-restraints excluded: chain H residue  358 VAL
Chi-restraints excluded: chain H residue  424 ARG
Chi-restraints excluded: chain I residue   58 ARG
Chi-restraints excluded: chain I residue   63 THR
Chi-restraints excluded: chain I residue   81 VAL
Chi-restraints excluded: chain I residue  108 ASP
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  139 ILE
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue   72 LEU
Chi-restraints excluded: chain J residue  104 ILE
Chi-restraints excluded: chain G residue   41 LEU
Chi-restraints excluded: chain G residue  197 THR
Chi-restraints excluded: chain G residue  492 THR
Chi-restraints excluded: chain G residue  528 LEU
Chi-restraints excluded: chain G residue  530 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 113 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9980
   chunk 123 optimal weight:    0.3980
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.061605 restraints weight = 29328.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 3.38
r_work: 0.2844 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10739  Z= 0.099
  Angle     :  0.509   6.818  14565  Z= 0.274
  Chirality :  0.044   0.163   1614
  Planarity :  0.003   0.055   1875
  Dihedral  :  5.920  59.692   1471
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.95 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.45 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.23), residues: 1313
  helix:  0.63 (0.41), residues: 164
  sheet: -0.02 (0.26), residues: 376
  loop : -0.87 (0.23), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG H 166 
 TYR   0.013   0.001   TYR I 163 
 PHE   0.029   0.001   PHE I 107 
 TRP   0.011   0.001   TRP H 129 
 HIS   0.004   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (10737)
  covalent geometry    : angle       0.50937 (14565)
  hydrogen bonds       : bond        0.03295 (  339)
  hydrogen bonds       : angle       4.51605 ( 1032)
  Misc. bond           : bond        0.00041 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  229 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7724 (tmm-80)
REVERT: H  424 ARG cc_start: 0.3545 (OUTLIER) cc_final: 0.2724 (tpt170)
REVERT: H  471 MET cc_start: 0.8807 (mtp) cc_final: 0.8556 (mtp)
REVERT: I   58 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8272 (ptt90)
REVERT: I  112 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8562 (mmtt)
REVERT: J   78 MET cc_start: 0.8922 (tmm) cc_final: 0.8578 (ttt)
  outliers start: 16
  outliers final: 12
  residues processed: 85
  average time/residue: 0.1083
  time to fit residues: 12.7692
Evaluate side-chains
  82 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue  148 MET
Chi-restraints excluded: chain H residue  229 ARG
Chi-restraints excluded: chain H residue  358 VAL
Chi-restraints excluded: chain H residue  424 ARG
Chi-restraints excluded: chain I residue   58 ARG
Chi-restraints excluded: chain I residue   81 VAL
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  139 ILE
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue  104 ILE
Chi-restraints excluded: chain G residue   41 LEU
Chi-restraints excluded: chain G residue  197 THR
Chi-restraints excluded: chain G residue  492 THR
Chi-restraints excluded: chain G residue  530 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0030
   chunk 121 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.081237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.060571 restraints weight = 28662.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 3.33
r_work: 0.2899 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10739  Z= 0.104
  Angle     :  0.510   7.685  14565  Z= 0.272
  Chirality :  0.044   0.159   1614
  Planarity :  0.003   0.059   1875
  Dihedral  :  5.732  59.287   1471
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.18 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.45 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.23), residues: 1313
  helix:  0.76 (0.42), residues: 164
  sheet: -0.03 (0.26), residues: 376
  loop : -0.84 (0.23), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG H 166 
 TYR   0.013   0.001   TYR I 163 
 PHE   0.030   0.001   PHE I 107 
 TRP   0.011   0.001   TRP I 155 
 HIS   0.004   0.001   HIS I  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (10737)
  covalent geometry    : angle       0.51002 (14565)
  hydrogen bonds       : bond        0.03255 (  339)
  hydrogen bonds       : angle       4.46131 ( 1032)
  Misc. bond           : bond        0.00037 (    2)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  229 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7731 (tmm-80)
REVERT: H  471 MET cc_start: 0.8789 (mtp) cc_final: 0.8546 (mtp)
REVERT: I   58 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8253 (ptt90)
REVERT: J   78 MET cc_start: 0.8909 (tmm) cc_final: 0.8559 (ttt)
  outliers start: 15
  outliers final: 12
  residues processed: 82
  average time/residue: 0.1178
  time to fit residues: 13.4076
Evaluate side-chains
  81 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue  148 MET
Chi-restraints excluded: chain H residue  229 ARG
Chi-restraints excluded: chain H residue  358 VAL
Chi-restraints excluded: chain I residue   58 ARG
Chi-restraints excluded: chain I residue   63 THR
Chi-restraints excluded: chain I residue   81 VAL
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  171 THR
Chi-restraints excluded: chain J residue  104 ILE
Chi-restraints excluded: chain G residue   41 LEU
Chi-restraints excluded: chain G residue  197 THR
Chi-restraints excluded: chain G residue  492 THR
Chi-restraints excluded: chain G residue  530 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 120 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
H 172 GLN
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  36 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 = 0.3379 r_free = 0.3379 target = 0.080373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.059615 restraints weight = 29719.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.37
r_work: 0.2850 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  10739  Z= 0.246
  Angle     :  0.598   7.465  14565  Z= 0.320
  Chirality :  0.046   0.158   1614
  Planarity :  0.004   0.060   1875
  Dihedral  :  6.192  57.124   1471
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.40 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.84 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.23), residues: 1313
  helix:  0.47 (0.41), residues: 165
  sheet: -0.13 (0.26), residues: 377
  loop : -1.07 (0.22), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H 166 
 TYR   0.014   0.002   TYR G 435 
 PHE   0.028   0.002   PHE I 107 
 TRP   0.012   0.001   TRP H 129 
 HIS   0.004   0.001   HIS G 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 (10737)
  covalent geometry    : angle       0.59792 (14565)
  hydrogen bonds       : bond        0.04049 (  339)
  hydrogen bonds       : angle       4.84571 ( 1032)
  Misc. bond           : bond        0.00070 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2232.24 seconds
wall clock time: 38 minutes 57.92 seconds (2337.92 seconds total)