Starting phenix.real_space_refine
on Wed Sep 17 13:34:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j3x_61127/09_2025/9j3x_61127_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j3x_61127/09_2025/9j3x_61127.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j3x_61127/09_2025/9j3x_61127.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j3x_61127/09_2025/9j3x_61127.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j3x_61127/09_2025/9j3x_61127_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j3x_61127/09_2025/9j3x_61127_neut.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      46      5.16       5
     C    5934      2.51       5
     N    1372      2.21       5
     O    1536      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8894
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4264
          Classifications: {'peptide': 578}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 555}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 281
          Unresolved non-hydrogen angles: 361
          Unresolved non-hydrogen dihedrals: 227
          Unresolved non-hydrogen chiralities: 42
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3, 'PHE:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 110
    Chain: "A"
      Number of atoms: 183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 183
          Unusual residues: {'CLR': 1, 'NAG': 1, 'POV': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.34, per 1000 atoms: 0.38
  Number of scatterers: 8894
  At special positions: 0
  Unit cell: (125.19, 97.37, 72.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     P       6     15.00
     O    1536      8.00
     N    1372      7.00
     C    5934      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 905 " - " ASN A 309 "
      " NAG B 905 " - " ASN B 309 "
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 318.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      85.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 41
    Processing helix  chain 'A' and resid 42 through 63
      removed outlier: 3.536A  pdb=" N   PHE A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL A  53 " --> pdb=" O   CYS A  49 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ASN A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 80
    Processing helix  chain 'A' and resid 80 through 92
      removed outlier: 3.623A  pdb=" N   ALA A  84 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 125
      removed outlier: 3.842A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 141
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.585A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 165
    Processing helix  chain 'A' and resid 166 through 197
      removed outlier: 4.436A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      Proline residue:  A 182  - end of helix
      removed outlier: 3.621A  pdb=" N   PHE A 187 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP A 195 " --> pdb=" O   GLN A 191 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   THR A 196 " --> pdb=" O   LYS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 216
      removed outlier: 3.669A  pdb=" N   ILE A 206 " --> pdb=" O   ASN A 202 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.506A  pdb=" N   PHE A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A 231 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 250
      removed outlier: 4.449A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 264
      removed outlier: 3.853A  pdb=" N   SER A 255 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   MET A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 302
      removed outlier: 4.350A  pdb=" N   LEU A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
      Proline residue:  A 291  - end of helix
    Processing helix  chain 'A' and resid 306 through 322
      removed outlier: 3.705A  pdb=" N   GLY A 321 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 322 " --> pdb=" O   PHE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 337
      removed outlier: 4.412A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 3.899A  pdb=" N   PHE A 352 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
      removed outlier: 4.191A  pdb=" N   TYR A 359 " --> pdb=" O   ALA A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 404
      removed outlier: 4.272A  pdb=" N   TYR A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 436
      removed outlier: 3.536A  pdb=" N   THR A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   PHE A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS A 436 " --> pdb=" O   TRP A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 473
      removed outlier: 3.841A  pdb=" N   GLY A 462 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 503
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 511 through 515
      removed outlier: 3.736A  pdb=" N   PHE A 514 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE A 515 " --> pdb=" O   SER A 512 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 511 through 515'
    Processing helix  chain 'A' and resid 517 through 546
      removed outlier: 3.594A  pdb=" N   MET A 521 " --> pdb=" O   GLY A 517 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN A 543 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 682
      removed outlier: 3.635A  pdb=" N   VAL A 659 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU A 660 " --> pdb=" O   THR A 656 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 665 " --> pdb=" O   LEU A 661 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 666 " --> pdb=" O   CYS A 662 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ILE A 667 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY A 668 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER A 675 " --> pdb=" O   ALA A 671 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   CYS A 676 " --> pdb=" O   ASN A 672 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 680 " --> pdb=" O   CYS A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 702
    Processing helix  chain 'A' and resid 702 through 711
    Processing helix  chain 'B' and resid 38 through 41
    Processing helix  chain 'B' and resid 42 through 63
      removed outlier: 3.536A  pdb=" N   PHE B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL B  53 " --> pdb=" O   CYS B  49 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ASN B  63 " --> pdb=" O   ALA B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 80
    Processing helix  chain 'B' and resid 80 through 92
      removed outlier: 3.624A  pdb=" N   ALA B  84 " --> pdb=" O   PHE B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 125
      removed outlier: 3.842A  pdb=" N   LEU B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 141
      Proline residue:  B 138  - end of helix
    Processing helix  chain 'B' and resid 149 through 159
      removed outlier: 3.586A  pdb=" N   ILE B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 165
    Processing helix  chain 'B' and resid 166 through 197
      removed outlier: 4.436A  pdb=" N   TYR B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
      Proline residue:  B 182  - end of helix
      removed outlier: 3.621A  pdb=" N   PHE B 187 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP B 195 " --> pdb=" O   GLN B 191 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   THR B 196 " --> pdb=" O   LYS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 216
      removed outlier: 3.670A  pdb=" N   ILE B 206 " --> pdb=" O   ASN B 202 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU B 209 " --> pdb=" O   LYS B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 233
      removed outlier: 3.507A  pdb=" N   PHE B 221 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE B 231 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 250
      removed outlier: 4.449A  pdb=" N   ASN B 243 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   PHE B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 264
      removed outlier: 3.854A  pdb=" N   SER B 255 " --> pdb=" O   SER B 251 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 302
      removed outlier: 4.351A  pdb=" N   LEU B 290 " --> pdb=" O   LYS B 286 " (cutoff:3.500A)
      Proline residue:  B 291  - end of helix
    Processing helix  chain 'B' and resid 306 through 322
      removed outlier: 3.705A  pdb=" N   GLY B 321 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   VAL B 322 " --> pdb=" O   PHE B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 337
      removed outlier: 4.413A  pdb=" N   ALA B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 367
      removed outlier: 3.899A  pdb=" N   PHE B 352 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix
      removed outlier: 4.192A  pdb=" N   TYR B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 404
      removed outlier: 4.272A  pdb=" N   TYR B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL B 389 " --> pdb=" O   ASP B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 436
      removed outlier: 3.536A  pdb=" N   THR B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE B 434 " --> pdb=" O   MET B 430 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS B 436 " --> pdb=" O   TRP B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 473
      removed outlier: 3.841A  pdb=" N   GLY B 462 " --> pdb=" O   TYR B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 503
      Proline residue:  B 492  - end of helix
    Processing helix  chain 'B' and resid 511 through 515
      removed outlier: 3.737A  pdb=" N   PHE B 514 " --> pdb=" O   ASP B 511 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE B 515 " --> pdb=" O   SER B 512 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 511 through 515'
    Processing helix  chain 'B' and resid 517 through 546
      removed outlier: 3.594A  pdb=" N   MET B 521 " --> pdb=" O   GLY B 517 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN B 543 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 682
      removed outlier: 3.635A  pdb=" N   VAL B 659 " --> pdb=" O   LEU B 655 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   LEU B 660 " --> pdb=" O   THR B 656 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU B 665 " --> pdb=" O   LEU B 661 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE B 666 " --> pdb=" O   CYS B 662 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE B 667 " --> pdb=" O   LEU B 663 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER B 675 " --> pdb=" O   ALA B 671 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   CYS B 676 " --> pdb=" O   ASN B 672 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU B 680 " --> pdb=" O   CYS B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 702
    Processing helix  chain 'B' and resid 702 through 711

    662 hydrogen bonds defined for protein.
    1974 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: 1.38

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1340
        1.30 -     1.43: 2346
        1.43 -     1.56: 5306
        1.56 -     1.68: 24
        1.68 -     1.81: 74
  Bond restraints: 9090
  Sorted by residual:
  bond pdb=" CA  GLN A 143 "
       pdb=" C   GLN A 143 "
    ideal  model  delta    sigma   weight residual
    1.525  1.434  0.091 1.29e-02 6.01e+03 4.94e+01
  bond pdb=" CA  GLN B 143 "
       pdb=" C   GLN B 143 "
    ideal  model  delta    sigma   weight residual
    1.525  1.435  0.090 1.29e-02 6.01e+03 4.86e+01
  bond pdb=" C   ASP B 146 "
       pdb=" O   ASP B 146 "
    ideal  model  delta    sigma   weight residual
    1.236  1.175  0.061 1.28e-02 6.10e+03 2.25e+01
  bond pdb=" C   ASP A 146 "
       pdb=" O   ASP A 146 "
    ideal  model  delta    sigma   weight residual
    1.236  1.175  0.061 1.28e-02 6.10e+03 2.25e+01
  bond pdb=" C   GLN B 143 "
       pdb=" O   GLN B 143 "
    ideal  model  delta    sigma   weight residual
    1.234  1.177  0.056 1.19e-02 7.06e+03 2.24e+01
  ... (remaining 9085 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 11999
        2.94 -     5.87: 282
        5.87 -     8.81: 69
        8.81 -    11.74: 2
       11.74 -    14.68: 4
  Bond angle restraints: 12356
  Sorted by residual:
  angle pdb=" O   ALA B  62 "
        pdb=" C   ALA B  62 "
        pdb=" N   ASN B  63 "
      ideal   model   delta    sigma   weight residual
     122.08  129.89   -7.81 1.07e+00 8.73e-01 5.32e+01
  angle pdb=" O   ALA A  62 "
        pdb=" C   ALA A  62 "
        pdb=" N   ASN A  63 "
      ideal   model   delta    sigma   weight residual
     122.08  129.76   -7.68 1.07e+00 8.73e-01 5.16e+01
  angle pdb=" CA  LYS B 269 "
        pdb=" CB  LYS B 269 "
        pdb=" CG  LYS B 269 "
      ideal   model   delta    sigma   weight residual
     114.10  128.42  -14.32 2.00e+00 2.50e-01 5.13e+01
  angle pdb=" CA  LYS A 269 "
        pdb=" CB  LYS A 269 "
        pdb=" CG  LYS A 269 "
      ideal   model   delta    sigma   weight residual
     114.10  128.38  -14.28 2.00e+00 2.50e-01 5.10e+01
  angle pdb=" N   ASN A 198 "
        pdb=" CA  ASN A 198 "
        pdb=" C   ASN A 198 "
      ideal   model   delta    sigma   weight residual
     113.61  105.40    8.21 1.50e+00 4.44e-01 2.99e+01
  ... (remaining 12351 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.75: 4879
       22.75 -    45.50: 455
       45.50 -    68.26: 94
       68.26 -    91.01: 20
       91.01 -   113.76: 32
  Dihedral angle restraints: 5480
    sinusoidal: 2126
      harmonic: 3354
  Sorted by residual:
  dihedral pdb=" N2  NAG B 905 "
           pdb=" C1  NAG B 905 "
           pdb=" C2  NAG B 905 "
           pdb=" O5  NAG B 905 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -64.43 -113.76     1      3.00e+01 1.11e-03 1.50e+01
  dihedral pdb=" N2  NAG A 905 "
           pdb=" C1  NAG A 905 "
           pdb=" C2  NAG A 905 "
           pdb=" O5  NAG A 905 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -64.47 -113.72     1      3.00e+01 1.11e-03 1.50e+01
  dihedral pdb=" C3  NAG B 905 "
           pdb=" C1  NAG B 905 "
           pdb=" C2  NAG B 905 "
           pdb=" O5  NAG B 905 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.55   57.70 -113.25     1      3.00e+01 1.11e-03 1.49e+01
  ... (remaining 5477 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1145
       0.062 -    0.124: 264
       0.124 -    0.185: 41
       0.185 -    0.247: 10
       0.247 -    0.309: 6
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" C1  NAG B 905 "
            pdb=" ND2 ASN B 309 "
            pdb=" C2  NAG B 905 "
            pdb=" O5  NAG B 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" C1  NAG A 905 "
            pdb=" ND2 ASN A 309 "
            pdb=" C2  NAG A 905 "
            pdb=" O5  NAG A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  ASP B 146 "
            pdb=" N   ASP B 146 "
            pdb=" C   ASP B 146 "
            pdb=" CB  ASP B 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 371 "   -0.057 5.00e-02 4.00e+02   8.58e-02 1.18e+01
        pdb=" N   PRO A 372 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 372 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 372 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 371 "    0.056 5.00e-02 4.00e+02   8.56e-02 1.17e+01
        pdb=" N   PRO B 372 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO B 372 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 372 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 367 "    0.052 5.00e-02 4.00e+02   7.89e-02 9.96e+00
        pdb=" N   PRO B 368 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO B 368 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 368 "    0.044 5.00e-02 4.00e+02
  ... (remaining 1493 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2025
        2.78 -     3.31: 8354
        3.31 -     3.84: 14802
        3.84 -     4.37: 16538
        4.37 -     4.90: 29258
  Nonbonded interactions: 70977
  Sorted by model distance:
  nonbonded pdb=" O   SER A 101 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   SER B 101 "
            pdb=" OG  SER B 105 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   SER B 383 "
            pdb=" OG  SER B 387 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   SER A 383 "
            pdb=" OG  SER A 387 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   ILE B 357 "
            pdb=" OG  SER B 361 "
     model   vdw
     2.276 3.040
  ... (remaining 70972 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.890
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
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      :  0.007   0.091   9092  Z= 0.367
  Angle     :  1.120  14.679  12362  Z= 0.618
  Chirality :  0.058   0.309   1466
  Planarity :  0.009   0.086   1494
  Dihedral  : 20.906 113.760   3316
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.44 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 22.91 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole: -1.58 (0.22), residues: 1148
  helix: -0.72 (0.15), residues: 898
  sheet:  None (None), residues: 0
  loop : -1.67 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 270 
 TYR   0.034   0.003   TYR A 165 
 PHE   0.035   0.003   PHE B 221 
 TRP   0.014   0.002   TRP B 363 
 HIS   0.003   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 ( 9090)
  covalent geometry    : angle       1.11604 (12356)
  hydrogen bonds       : bond        0.13508 (  662)
  hydrogen bonds       : angle       6.25080 ( 1974)
  link_NAG-ASN         : bond        0.01626 (    2)
  link_NAG-ASN         : angle       4.66392 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 250
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   97 ASN cc_start: 0.7141 (m-40) cc_final: 0.6870 (p0)
REVERT: A  205 LYS cc_start: 0.7190 (tptp) cc_final: 0.6825 (pttt)
REVERT: A  276 PHE cc_start: 0.7699 (t80) cc_final: 0.7480 (t80)
REVERT: A  409 GLN cc_start: 0.5305 (mp10) cc_final: 0.4488 (pt0)
REVERT: A  429 MET cc_start: 0.6106 (tpp) cc_final: 0.5833 (mmt)
REVERT: A  430 MET cc_start: 0.4527 (mmt) cc_final: 0.1596 (ptt)
REVERT: A  657 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8006 (mtt-85)
REVERT: A  670 PHE cc_start: 0.6494 (t80) cc_final: 0.6210 (t80)
REVERT: B  114 PHE cc_start: 0.7831 (t80) cc_final: 0.7618 (t80)
REVERT: B  674 SER cc_start: 0.8465 (m) cc_final: 0.8225 (p)
REVERT: B  705 PHE cc_start: 0.8034 (t80) cc_final: 0.7774 (t80)
  outliers start: 14
  outliers final: 3
  residues processed: 257
  average time/residue: 0.0999
  time to fit residues: 35.3946
Evaluate side-chains
  185 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 181
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain B residue   61 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.1980
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0370
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.204503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.166465 restraints weight = 11348.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.26
r_work: 0.3806 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9092  Z= 0.136
  Angle     :  0.662  11.312  12362  Z= 0.329
  Chirality :  0.043   0.231   1466
  Planarity :  0.005   0.062   1494
  Dihedral  : 15.533 102.671   1622
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.92 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.08 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  0.84 (0.25), residues: 1148
  helix:  1.14 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.54 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.040   0.001   TYR A 104 
 PHE   0.023   0.002   PHE B 221 
 TRP   0.012   0.001   TRP A 678 
 HIS   0.003   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9090)
  covalent geometry    : angle       0.65584 (12356)
  hydrogen bonds       : bond        0.04164 (  662)
  hydrogen bonds       : angle       4.27652 ( 1974)
  link_NAG-ASN         : bond        0.00830 (    2)
  link_NAG-ASN         : angle       4.10287 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.8836 (t0) cc_final: 0.8454 (m-40)
REVERT: A   97 ASN cc_start: 0.7476 (m-40) cc_final: 0.7063 (p0)
REVERT: A  103 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6684 (mt)
REVERT: A  155 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8017 (tm-30)
REVERT: A  159 GLN cc_start: 0.8360 (tt0) cc_final: 0.8032 (tt0)
REVERT: A  170 TYR cc_start: 0.8193 (m-80) cc_final: 0.7245 (m-80)
REVERT: A  205 LYS cc_start: 0.7196 (tptp) cc_final: 0.6843 (pttt)
REVERT: A  409 GLN cc_start: 0.5437 (mp10) cc_final: 0.4756 (pt0)
REVERT: A  430 MET cc_start: 0.5069 (mmt) cc_final: 0.1634 (ptt)
REVERT: A  657 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7702 (mtt-85)
REVERT: B  206 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7496 (mt)
REVERT: B  299 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7027 (mm-30)
REVERT: B  338 MET cc_start: 0.7734 (ptp) cc_final: 0.7485 (ptt)
REVERT: B  358 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7027 (mtm)
REVERT: B  413 MET cc_start: 0.5658 (mmm) cc_final: 0.5456 (mmm)
REVERT: B  417 ASN cc_start: 0.7396 (m-40) cc_final: 0.6339 (t0)
REVERT: B  460 TRP cc_start: 0.6975 (m100) cc_final: 0.6662 (m100)
  outliers start: 28
  outliers final: 9
  residues processed: 210
  average time/residue: 0.0867
  time to fit residues: 26.0278
Evaluate side-chains
  180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  658 HIS
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0070
   chunk 113 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 102 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.3402

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
A 412 HIS
B 412 HIS
B 658 HIS
** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.190265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.150730 restraints weight = 11298.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.27
r_work: 0.3622 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.4084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   9092  Z= 0.191
  Angle     :  0.698  11.478  12362  Z= 0.345
  Chirality :  0.045   0.165   1466
  Planarity :  0.005   0.058   1494
  Dihedral  : 14.245  94.245   1616
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.53 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 22.08 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  1.46 (0.25), residues: 1148
  helix:  1.63 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.54 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 130 
 TYR   0.039   0.002   TYR A 104 
 PHE   0.031   0.002   PHE B 221 
 TRP   0.014   0.001   TRP A 193 
 HIS   0.005   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 9090)
  covalent geometry    : angle       0.69136 (12356)
  hydrogen bonds       : bond        0.04587 (  662)
  hydrogen bonds       : angle       4.24778 ( 1974)
  link_NAG-ASN         : bond        0.00535 (    2)
  link_NAG-ASN         : angle       4.30928 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 182
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.8958 (t0) cc_final: 0.8576 (m-40)
REVERT: A   71 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7725 (tppt)
REVERT: A   97 ASN cc_start: 0.7764 (m-40) cc_final: 0.7226 (p0)
REVERT: A  170 TYR cc_start: 0.8303 (m-80) cc_final: 0.7993 (m-80)
REVERT: A  217 ASN cc_start: 0.8001 (t0) cc_final: 0.7725 (m110)
REVERT: A  269 LYS cc_start: 0.7741 (mmtp) cc_final: 0.7342 (mmtp)
REVERT: A  316 TYR cc_start: 0.8201 (t80) cc_final: 0.7902 (t80)
REVERT: A  334 THR cc_start: 0.8971 (m) cc_final: 0.8770 (m)
REVERT: A  405 LYS cc_start: 0.7415 (mmtt) cc_final: 0.7169 (mttt)
REVERT: A  409 GLN cc_start: 0.5607 (mp10) cc_final: 0.4750 (pt0)
REVERT: B  177 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8471 (tt)
REVERT: B  297 MET cc_start: 0.7647 (mmt) cc_final: 0.7373 (mmt)
REVERT: B  299 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7321 (mm-30)
REVERT: B  302 ASP cc_start: 0.5831 (OUTLIER) cc_final: 0.5444 (t70)
REVERT: B  338 MET cc_start: 0.7943 (ptp) cc_final: 0.7734 (ptt)
REVERT: B  417 ASN cc_start: 0.7166 (m-40) cc_final: 0.6288 (t0)
REVERT: B  460 TRP cc_start: 0.7140 (m100) cc_final: 0.6662 (m100)
  outliers start: 45
  outliers final: 15
  residues processed: 211
  average time/residue: 0.0896
  time to fit residues: 26.8363
Evaluate side-chains
  183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 107 optimal weight:    9.9990
   chunk 81 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 96 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 335 GLN
B 658 HIS
** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.191973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.152367 restraints weight = 11526.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 2.28
r_work: 0.3647 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.4600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9092  Z= 0.140
  Angle     :  0.633  12.107  12362  Z= 0.310
  Chirality :  0.042   0.189   1466
  Planarity :  0.005   0.057   1494
  Dihedral  : 13.073  94.079   1612
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.44 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.15 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  2.02 (0.26), residues: 1148
  helix:  2.04 (0.18), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.42 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 657 
 TYR   0.037   0.002   TYR A 104 
 PHE   0.025   0.002   PHE B 221 
 TRP   0.011   0.001   TRP B 679 
 HIS   0.006   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9090)
  covalent geometry    : angle       0.62836 (12356)
  hydrogen bonds       : bond        0.03980 (  662)
  hydrogen bonds       : angle       4.00251 ( 1974)
  link_NAG-ASN         : bond        0.00633 (    2)
  link_NAG-ASN         : angle       3.65150 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 181
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7486 (tppt)
REVERT: A   97 ASN cc_start: 0.7600 (m-40) cc_final: 0.7372 (p0)
REVERT: A  155 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: A  170 TYR cc_start: 0.8138 (m-80) cc_final: 0.7786 (m-80)
REVERT: A  203 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7490 (tptp)
REVERT: A  303 LYS cc_start: 0.6606 (mttt) cc_final: 0.5694 (mmtp)
REVERT: A  316 TYR cc_start: 0.8283 (t80) cc_final: 0.8073 (t80)
REVERT: A  334 THR cc_start: 0.8811 (m) cc_final: 0.8538 (m)
REVERT: A  409 GLN cc_start: 0.5827 (mp10) cc_final: 0.4933 (pt0)
REVERT: B  297 MET cc_start: 0.7591 (mmt) cc_final: 0.7347 (mmt)
REVERT: B  413 MET cc_start: 0.5354 (mmm) cc_final: 0.5060 (mmm)
REVERT: B  417 ASN cc_start: 0.7186 (m-40) cc_final: 0.6335 (t0)
REVERT: B  460 TRP cc_start: 0.7050 (m100) cc_final: 0.6631 (m100)
  outliers start: 27
  outliers final: 14
  residues processed: 198
  average time/residue: 0.0856
  time to fit residues: 24.2790
Evaluate side-chains
  171 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 92 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
B 380 GLN
B 658 HIS
** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.189885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.150491 restraints weight = 11425.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 2.26
r_work: 0.3621 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9092  Z= 0.142
  Angle     :  0.631  13.086  12362  Z= 0.310
  Chirality :  0.042   0.170   1466
  Planarity :  0.004   0.059   1494
  Dihedral  : 12.519  92.540   1612
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.61 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.15 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  2.19 (0.26), residues: 1148
  helix:  2.16 (0.18), residues: 900
  sheet:  None (None), residues: 0
  loop : -1.31 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 270 
 TYR   0.038   0.001   TYR A 104 
 PHE   0.025   0.002   PHE B 221 
 TRP   0.013   0.001   TRP B 679 
 HIS   0.002   0.000   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9090)
  covalent geometry    : angle       0.62622 (12356)
  hydrogen bonds       : bond        0.04021 (  662)
  hydrogen bonds       : angle       3.96121 ( 1974)
  link_NAG-ASN         : bond        0.00601 (    2)
  link_NAG-ASN         : angle       3.57907 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7505 (tppt)
REVERT: A   97 ASN cc_start: 0.7701 (m-40) cc_final: 0.7371 (p0)
REVERT: A  155 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7473 (tm-30)
REVERT: A  159 GLN cc_start: 0.8272 (tt0) cc_final: 0.7608 (mt0)
REVERT: A  170 TYR cc_start: 0.8278 (m-80) cc_final: 0.7897 (m-80)
REVERT: A  203 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7476 (tptp)
REVERT: A  233 LEU cc_start: 0.7625 (tp) cc_final: 0.7373 (tp)
REVERT: A  303 LYS cc_start: 0.6735 (mttt) cc_final: 0.5821 (mmtp)
REVERT: A  334 THR cc_start: 0.8804 (m) cc_final: 0.8564 (m)
REVERT: A  409 GLN cc_start: 0.6132 (mp10) cc_final: 0.5138 (pt0)
REVERT: A  666 ILE cc_start: 0.8020 (pt) cc_final: 0.7778 (mt)
REVERT: B  297 MET cc_start: 0.7655 (mmt) cc_final: 0.7362 (mmt)
REVERT: B  299 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7334 (mm-30)
REVERT: B  417 ASN cc_start: 0.7265 (m-40) cc_final: 0.6456 (t0)
REVERT: B  460 TRP cc_start: 0.7104 (m100) cc_final: 0.6659 (m100)
  outliers start: 24
  outliers final: 14
  residues processed: 188
  average time/residue: 0.0876
  time to fit residues: 23.7561
Evaluate side-chains
  175 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 110 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 104 optimal weight:   30.0000
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 658 HIS
** B 672 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 = 0.4176 r_free = 0.4176 target = 0.187267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.147909 restraints weight = 11455.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.28
r_work: 0.3612 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.5321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9092  Z= 0.143
  Angle     :  0.639  11.755  12362  Z= 0.311
  Chirality :  0.043   0.180   1466
  Planarity :  0.004   0.060   1494
  Dihedral  : 12.370  91.223   1612
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.53 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 24.82 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  2.31 (0.26), residues: 1148
  helix:  2.23 (0.18), residues: 902
  sheet:  None (None), residues: 0
  loop : -1.24 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 657 
 TYR   0.034   0.001   TYR A 104 
 PHE   0.029   0.002   PHE A 102 
 TRP   0.015   0.001   TRP B 679 
 HIS   0.002   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9090)
  covalent geometry    : angle       0.63430 (12356)
  hydrogen bonds       : bond        0.03994 (  662)
  hydrogen bonds       : angle       3.93234 ( 1974)
  link_NAG-ASN         : bond        0.00593 (    2)
  link_NAG-ASN         : angle       3.42312 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7514 (tppt)
REVERT: A  159 GLN cc_start: 0.8374 (tt0) cc_final: 0.7903 (tt0)
REVERT: A  170 TYR cc_start: 0.8335 (m-80) cc_final: 0.8013 (m-80)
REVERT: A  203 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7574 (tptp)
REVERT: A  233 LEU cc_start: 0.7643 (tp) cc_final: 0.7416 (tp)
REVERT: A  303 LYS cc_start: 0.6818 (mttt) cc_final: 0.6030 (mmtp)
REVERT: A  316 TYR cc_start: 0.8145 (t80) cc_final: 0.7926 (t80)
REVERT: A  334 THR cc_start: 0.8803 (m) cc_final: 0.8552 (m)
REVERT: A  395 ILE cc_start: 0.8137 (mm) cc_final: 0.7726 (mt)
REVERT: A  409 GLN cc_start: 0.6300 (mp10) cc_final: 0.5445 (pt0)
REVERT: A  663 LEU cc_start: 0.7551 (tt) cc_final: 0.7235 (mt)
REVERT: B   63 ASN cc_start: 0.8213 (t0) cc_final: 0.7909 (t0)
REVERT: B  297 MET cc_start: 0.7663 (mmt) cc_final: 0.7406 (mmt)
REVERT: B  299 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7349 (mm-30)
REVERT: B  417 ASN cc_start: 0.7302 (m-40) cc_final: 0.6491 (t0)
REVERT: B  460 TRP cc_start: 0.7156 (m100) cc_final: 0.6701 (m100)
  outliers start: 22
  outliers final: 16
  residues processed: 184
  average time/residue: 0.0866
  time to fit residues: 22.9038
Evaluate side-chains
  180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0980
   chunk 34 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 101 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
B 658 HIS
** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.188516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.149707 restraints weight = 11569.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.25
r_work: 0.3642 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.5529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9092  Z= 0.131
  Angle     :  0.629  11.990  12362  Z= 0.306
  Chirality :  0.042   0.180   1466
  Planarity :  0.004   0.060   1494
  Dihedral  : 12.155  88.349   1612
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.70 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.34 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  2.43 (0.26), residues: 1148
  helix:  2.34 (0.18), residues: 900
  sheet:  None (None), residues: 0
  loop : -1.25 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 657 
 TYR   0.034   0.001   TYR A 104 
 PHE   0.027   0.001   PHE A 102 
 TRP   0.016   0.001   TRP B 679 
 HIS   0.002   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9090)
  covalent geometry    : angle       0.62379 (12356)
  hydrogen bonds       : bond        0.03822 (  662)
  hydrogen bonds       : angle       3.85009 ( 1974)
  link_NAG-ASN         : bond        0.00589 (    2)
  link_NAG-ASN         : angle       3.57474 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.7797 (ttmt) cc_final: 0.7459 (tppt)
REVERT: A   97 ASN cc_start: 0.7375 (m-40) cc_final: 0.6928 (p0)
REVERT: A  170 TYR cc_start: 0.8319 (m-80) cc_final: 0.7962 (m-80)
REVERT: A  205 LYS cc_start: 0.7537 (tptp) cc_final: 0.7203 (ptpt)
REVERT: A  303 LYS cc_start: 0.6657 (mttt) cc_final: 0.5890 (mmtp)
REVERT: A  316 TYR cc_start: 0.8083 (t80) cc_final: 0.7813 (t80)
REVERT: A  334 THR cc_start: 0.8701 (m) cc_final: 0.8462 (m)
REVERT: A  395 ILE cc_start: 0.8171 (mm) cc_final: 0.7763 (mt)
REVERT: A  409 GLN cc_start: 0.6279 (mp10) cc_final: 0.5540 (tt0)
REVERT: B   63 ASN cc_start: 0.8088 (t0) cc_final: 0.7823 (t0)
REVERT: B  297 MET cc_start: 0.7669 (mmt) cc_final: 0.7337 (mmt)
REVERT: B  299 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7286 (mm-30)
REVERT: B  417 ASN cc_start: 0.7186 (m-40) cc_final: 0.6404 (t0)
REVERT: B  460 TRP cc_start: 0.7085 (m100) cc_final: 0.6664 (m100)
  outliers start: 25
  outliers final: 18
  residues processed: 193
  average time/residue: 0.0901
  time to fit residues: 24.8955
Evaluate side-chains
  184 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 107 optimal weight:   20.0000
   chunk 1 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 672 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 = 0.4178 r_free = 0.4178 target = 0.187591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.148510 restraints weight = 11554.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.27
r_work: 0.3640 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9092  Z= 0.129
  Angle     :  0.642  12.451  12362  Z= 0.311
  Chirality :  0.042   0.178   1466
  Planarity :  0.004   0.060   1494
  Dihedral  : 12.034  88.911   1612
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.70 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 24.46 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  2.49 (0.26), residues: 1148
  helix:  2.36 (0.18), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.21 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 657 
 TYR   0.024   0.001   TYR B 104 
 PHE   0.029   0.002   PHE A 102 
 TRP   0.017   0.001   TRP B 679 
 HIS   0.002   0.000   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9090)
  covalent geometry    : angle       0.63739 (12356)
  hydrogen bonds       : bond        0.03776 (  662)
  hydrogen bonds       : angle       3.81359 ( 1974)
  link_NAG-ASN         : bond        0.00576 (    2)
  link_NAG-ASN         : angle       3.58762 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   71 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7447 (tppt)
REVERT: A   97 ASN cc_start: 0.7536 (m-40) cc_final: 0.7124 (p0)
REVERT: A  159 GLN cc_start: 0.8381 (tt0) cc_final: 0.7927 (tt0)
REVERT: A  170 TYR cc_start: 0.8343 (m-80) cc_final: 0.7939 (m-80)
REVERT: A  205 LYS cc_start: 0.7544 (tptp) cc_final: 0.7178 (ptpt)
REVERT: A  297 MET cc_start: 0.7857 (mmp) cc_final: 0.7647 (mmp)
REVERT: A  303 LYS cc_start: 0.6525 (mttt) cc_final: 0.5813 (mmtp)
REVERT: A  316 TYR cc_start: 0.8102 (t80) cc_final: 0.7815 (t80)
REVERT: A  334 THR cc_start: 0.8702 (m) cc_final: 0.8467 (m)
REVERT: A  395 ILE cc_start: 0.8187 (mm) cc_final: 0.7797 (mt)
REVERT: A  409 GLN cc_start: 0.6288 (mp10) cc_final: 0.5583 (tt0)
REVERT: B   63 ASN cc_start: 0.8008 (t0) cc_final: 0.7762 (t0)
REVERT: B  270 ARG cc_start: 0.6904 (mmm160) cc_final: 0.6371 (mmm160)
REVERT: B  297 MET cc_start: 0.7587 (mmt) cc_final: 0.7321 (mmt)
REVERT: B  417 ASN cc_start: 0.7213 (m-40) cc_final: 0.6407 (t0)
REVERT: B  460 TRP cc_start: 0.7119 (m100) cc_final: 0.6716 (m100)
  outliers start: 23
  outliers final: 20
  residues processed: 186
  average time/residue: 0.0915
  time to fit residues: 24.2461
Evaluate side-chains
  186 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  658 HIS
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 672 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 = 0.4164 r_free = 0.4164 target = 0.186602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.147531 restraints weight = 11493.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 2.25
r_work: 0.3606 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.5904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9092  Z= 0.135
  Angle     :  0.653  15.114  12362  Z= 0.315
  Chirality :  0.042   0.180   1466
  Planarity :  0.004   0.060   1494
  Dihedral  : 12.047  88.515   1612
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.61 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 24.94 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  2.52 (0.26), residues: 1148
  helix:  2.39 (0.18), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.23 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 235 
 TYR   0.032   0.001   TYR A 104 
 PHE   0.030   0.002   PHE A 102 
 TRP   0.020   0.001   TRP B 679 
 HIS   0.001   0.000   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9090)
  covalent geometry    : angle       0.64850 (12356)
  hydrogen bonds       : bond        0.03826 (  662)
  hydrogen bonds       : angle       3.84028 ( 1974)
  link_NAG-ASN         : bond        0.00572 (    2)
  link_NAG-ASN         : angle       3.54650 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   71 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7452 (tppt)
REVERT: A  159 GLN cc_start: 0.8418 (tt0) cc_final: 0.7963 (tt0)
REVERT: A  170 TYR cc_start: 0.8348 (m-80) cc_final: 0.7980 (m-80)
REVERT: A  240 TYR cc_start: 0.8505 (m-10) cc_final: 0.8225 (m-10)
REVERT: A  303 LYS cc_start: 0.6526 (mttt) cc_final: 0.5882 (mmtp)
REVERT: A  316 TYR cc_start: 0.8122 (t80) cc_final: 0.7874 (t80)
REVERT: A  334 THR cc_start: 0.8727 (m) cc_final: 0.8476 (m)
REVERT: A  395 ILE cc_start: 0.8165 (mm) cc_final: 0.7804 (mt)
REVERT: A  409 GLN cc_start: 0.6419 (mp10) cc_final: 0.5715 (tt0)
REVERT: A  678 TRP cc_start: 0.8247 (t-100) cc_final: 0.7872 (t60)
REVERT: B   63 ASN cc_start: 0.8001 (t0) cc_final: 0.7770 (t0)
REVERT: B  406 LYS cc_start: 0.8408 (tptt) cc_final: 0.7785 (tppt)
REVERT: B  413 MET cc_start: 0.5338 (mmm) cc_final: 0.5117 (tpt)
REVERT: B  417 ASN cc_start: 0.7294 (m-40) cc_final: 0.6531 (t0)
REVERT: B  460 TRP cc_start: 0.7172 (m100) cc_final: 0.6728 (m100)
  outliers start: 23
  outliers final: 19
  residues processed: 185
  average time/residue: 0.0895
  time to fit residues: 23.5994
Evaluate side-chains
  184 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  658 HIS
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  658 HIS
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 79 optimal weight:    0.8980
   chunk 110 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 101 optimal weight:   20.0000
   chunk 26 optimal weight:    0.7980
   chunk 111 optimal weight:    0.0980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 672 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 = 0.4174 r_free = 0.4174 target = 0.187584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.148225 restraints weight = 11537.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 2.27
r_work: 0.3634 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.6013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9092  Z= 0.131
  Angle     :  0.654  15.582  12362  Z= 0.314
  Chirality :  0.042   0.180   1466
  Planarity :  0.004   0.060   1494
  Dihedral  : 12.031  89.843   1612
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.61 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 25.30 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  2.54 (0.26), residues: 1148
  helix:  2.42 (0.18), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.31 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 270 
 TYR   0.025   0.001   TYR B 104 
 PHE   0.030   0.001   PHE A 102 
 TRP   0.020   0.001   TRP B 679 
 HIS   0.002   0.000   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9090)
  covalent geometry    : angle       0.64940 (12356)
  hydrogen bonds       : bond        0.03802 (  662)
  hydrogen bonds       : angle       3.81347 ( 1974)
  link_NAG-ASN         : bond        0.00583 (    2)
  link_NAG-ASN         : angle       3.57948 (    6)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7409 (tppt)
REVERT: A  159 GLN cc_start: 0.8390 (tt0) cc_final: 0.7942 (tt0)
REVERT: A  170 TYR cc_start: 0.8342 (m-80) cc_final: 0.7941 (m-80)
REVERT: A  240 TYR cc_start: 0.8400 (m-10) cc_final: 0.8136 (m-10)
REVERT: A  303 LYS cc_start: 0.6480 (mttt) cc_final: 0.5982 (mmtp)
REVERT: A  334 THR cc_start: 0.8714 (m) cc_final: 0.8433 (m)
REVERT: A  395 ILE cc_start: 0.8190 (mm) cc_final: 0.7834 (mt)
REVERT: A  409 GLN cc_start: 0.6455 (mp10) cc_final: 0.5774 (tt0)
REVERT: A  459 LEU cc_start: 0.8297 (tp) cc_final: 0.7996 (mp)
REVERT: A  678 TRP cc_start: 0.8257 (t-100) cc_final: 0.7882 (t60)
REVERT: B   63 ASN cc_start: 0.7910 (t0) cc_final: 0.7697 (t0)
REVERT: B  297 MET cc_start: 0.7575 (mmt) cc_final: 0.7307 (mmt)
REVERT: B  406 LYS cc_start: 0.8416 (tptt) cc_final: 0.7787 (tppt)
REVERT: B  417 ASN cc_start: 0.7215 (m-40) cc_final: 0.6687 (t0)
REVERT: B  451 TYR cc_start: 0.5333 (m-80) cc_final: 0.5071 (m-10)
REVERT: B  460 TRP cc_start: 0.7165 (m100) cc_final: 0.6733 (m100)
REVERT: B  688 LEU cc_start: 0.3122 (OUTLIER) cc_final: 0.2913 (tp)
  outliers start: 22
  outliers final: 17
  residues processed: 181
  average time/residue: 0.0884
  time to fit residues: 23.0117
Evaluate side-chains
  181 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  658 HIS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  658 HIS
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  688 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 107 optimal weight:    7.9990
   chunk 64 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   chunk 71 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 417 ASN
** B 672 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 = 0.4126 r_free = 0.4126 target = 0.183581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.143689 restraints weight = 11383.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.35
r_work: 0.3551 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.6131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9092  Z= 0.139
  Angle     :  0.677  15.638  12362  Z= 0.325
  Chirality :  0.042   0.182   1466
  Planarity :  0.004   0.060   1494
  Dihedral  : 12.009  88.517   1612
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.79 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 25.78 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 aren not related in a simple way.
  whole:  2.54 (0.26), residues: 1148
  helix:  2.39 (0.18), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.24 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 270 
 TYR   0.041   0.001   TYR A 104 
 PHE   0.030   0.001   PHE A 102 
 TRP   0.020   0.001   TRP B 679 
 HIS   0.001   0.000   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9090)
  covalent geometry    : angle       0.67264 (12356)
  hydrogen bonds       : bond        0.03853 (  662)
  hydrogen bonds       : angle       3.83133 ( 1974)
  link_NAG-ASN         : bond        0.00570 (    2)
  link_NAG-ASN         : angle       3.57005 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2120.16 seconds
wall clock time: 37 minutes 12.15 seconds (2232.15 seconds total)