Starting phenix.real_space_refine
on Mon Jun 16 11:01:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wa5_37391/06_2025/8wa5_37391.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wa5_37391/06_2025/8wa5_37391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wa5_37391/06_2025/8wa5_37391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wa5_37391/06_2025/8wa5_37391.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wa5_37391/06_2025/8wa5_37391.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wa5_37391/06_2025/8wa5_37391.cif"
  }
  resolution = 2.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=  -0.002 sd=   0.089
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9918 atoms to isotropic.
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: 9
    Type Number    sf(0)   Gaussians
     K       3      8.98       5
     Al      1      5.89       5
     P       1      5.49       5
     Mg      1      5.21       5
     S      66      5.16       5
     C    6368      2.51       5
     N    1648      2.21       5
     O    1837      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9929
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 987, 7662
          Classifications: {'peptide': 987}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 47, 'TRANS': 939}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2100
          Classifications: {'peptide': 262}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 240}
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 37
          Unusual residues: {'  K': 3, ' MG': 1, 'ALF': 1, 'CLR': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 124
          Unusual residues: {'NAG': 5, 'PCW': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 6.32, per 1000 atoms: 0.64
  Number of scatterers: 9929
  At special positions: 0
  Unit cell: (82.17, 87.98, 174.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     K       3     19.00
     S      66     16.00
     P       1     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1837      8.00
     N    1648      7.00
     C    6368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 201 " - pdb=" SG  CYS B 262 " distance=2.03

  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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG B 302 " - " ASN B  99 "
      " NAG B 303 " - " ASN B 161 "
      " NAG B 304 " - " ASN B 221 "
      " NAG B 305 " - " ASN B 193 "
      " NAG B 306 " - " ASN B 146 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.62
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2338

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 9 sheets defined
      52.2% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 55
    Processing helix  chain 'A' and resid 56 through 65
    Processing helix  chain 'A' and resid 73 through 85
    Processing helix  chain 'A' and resid 96 through 105
    Processing helix  chain 'A' and resid 107 through 130
      removed outlier: 3.531A  pdb=" N   GLU A 130 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 160
      removed outlier: 4.230A  pdb=" N   LEU A 139 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 174
      removed outlier: 3.917A  pdb=" N   SER A 169 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 274 through 285
    Processing helix  chain 'A' and resid 291 through 324
      removed outlier: 4.251A  pdb=" N   TYR A 324 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 341
    Processing helix  chain 'A' and resid 344 through 362
    Processing helix  chain 'A' and resid 371 through 376
      removed outlier: 3.903A  pdb=" N   THR A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LEU A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 371 through 376'
    Processing helix  chain 'A' and resid 424 through 437
    Processing helix  chain 'A' and resid 450 through 454
    Processing helix  chain 'A' and resid 459 through 473
    Processing helix  chain 'A' and resid 475 through 482
    Processing helix  chain 'A' and resid 519 through 526
    Processing helix  chain 'A' and resid 540 through 556
    Processing helix  chain 'A' and resid 581 through 585
      removed outlier: 3.759A  pdb=" N   MET A 585 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 618
    Processing helix  chain 'A' and resid 629 through 640
    Processing helix  chain 'A' and resid 649 through 658
    Processing helix  chain 'A' and resid 660 through 664
    Processing helix  chain 'A' and resid 665 through 669
    Processing helix  chain 'A' and resid 676 through 682
    Processing helix  chain 'A' and resid 683 through 694
    Processing helix  chain 'A' and resid 703 through 717
      removed outlier: 3.626A  pdb=" N   LEU A 717 " --> pdb=" O   SER A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 737
    Processing helix  chain 'A' and resid 748 through 755
    Processing helix  chain 'A' and resid 765 through 791
      removed outlier: 4.117A  pdb=" N   LYS A 791 " --> pdb=" O   TYR A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 806
      Proline residue:  A 798  - end of helix
    Processing helix  chain 'A' and resid 812 through 822
    Processing helix  chain 'A' and resid 824 through 830
    Processing helix  chain 'A' and resid 831 through 834
    Processing helix  chain 'A' and resid 839 through 843
    Processing helix  chain 'A' and resid 855 through 885
      removed outlier: 3.921A  pdb=" N   ILE A 866 " --> pdb=" O   SER A 862 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE A 869 " --> pdb=" O   GLN A 865 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU A 885 " --> pdb=" O   ALA A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 888 through 893
    Processing helix  chain 'A' and resid 895 through 900
    Processing helix  chain 'A' and resid 916 through 946
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 961 through 981
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 994 through 1000
    Processing helix  chain 'A' and resid 1001 through 1022
    Processing helix  chain 'A' and resid 1025 through 1031
    Processing helix  chain 'B' and resid 33 through 66
    Processing helix  chain 'B' and resid 103 through 119
      removed outlier: 4.685A  pdb=" N   GLY B 108 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   LEU B 109 " --> pdb=" O   THR B 105 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLY B 119 " --> pdb=" O   ARG B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 126
      removed outlier: 6.020A  pdb=" N   ALA B 123 " --> pdb=" O   TYR B 120 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLU B 126 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 164
      removed outlier: 6.665A  pdb=" N   ASN B 161 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY B 164 " --> pdb=" O   ASN B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 223
      removed outlier: 4.132A  pdb=" N   THR B 223 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 189
      removed outlier: 4.853A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   CYS A 258 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS A 221 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   GLU A 260 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   GLY A 219 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   THR A 262 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ALA A 217 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   GLN A 264 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ASP A 211 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   CYS A 220 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189
      removed outlier: 4.853A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   CYS A 258 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS A 221 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   GLU A 260 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   GLY A 219 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   THR A 262 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ALA A 217 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   GLN A 264 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ASP A 211 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367
      removed outlier: 6.350A  pdb=" N   GLY A 740 " --> pdb=" O   MET A 757 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   LEU A 759 " --> pdb=" O   GLY A 740 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ALA A 742 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL A 721 " --> pdb=" O   ILE A 739 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   VAL A 741 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL A 723 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   MET A 743 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   GLY A 725 " --> pdb=" O   MET A 743 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   ILE A 382 " --> pdb=" O   ILE A 623 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   VAL A 625 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   SER A 384 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   VAL A 622 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 8.497A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   MET A 624 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.223A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS A 399 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 9.216A  pdb=" N   LEU A 592 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
      removed outlier: 8.678A  pdb=" N   TYR A 568 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   PHE A 594 " --> pdb=" O   GLN A 566 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   GLN A 566 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   THR A 503 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LYS A 485 " --> pdb=" O   THR A 503 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.223A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS A 399 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   CYS A 527 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   PHE A 594 " --> pdb=" O   CYS A 527 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   SER A 529 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   GLY A 596 " --> pdb=" O   SER A 529 " (cutoff:3.500A)
      removed outlier: 9.149A  pdb=" N   LEU A 531 " --> pdb=" O   GLY A 596 " (cutoff:3.500A)
      removed outlier: 12.328A  pdb=" N   VAL A 598 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908
    Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85
    Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 99

    542 hydrogen bonds defined for protein.
    1515 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: 3.59

  Time building geometry restraints manager: 3.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3173
        1.34 -     1.46: 1696
        1.46 -     1.58: 5176
        1.58 -     1.70: 2
        1.70 -     1.82: 99
  Bond restraints: 10146
  Sorted by residual:
  bond pdb=" C11 PCW B 301 "
       pdb=" O3  PCW B 301 "
    ideal  model  delta    sigma   weight residual
    1.326  1.450 -0.124 2.00e-02 2.50e+03 3.86e+01
  bond pdb=" C31 PCW B 301 "
       pdb=" O2  PCW B 301 "
    ideal  model  delta    sigma   weight residual
    1.333  1.454 -0.121 2.00e-02 2.50e+03 3.65e+01
  bond pdb=" F3  ALF A1104 "
       pdb="AL   ALF A1104 "
    ideal  model  delta    sigma   weight residual
    1.685  1.800 -0.115 2.00e-02 2.50e+03 3.31e+01
  bond pdb=" F1  ALF A1104 "
       pdb="AL   ALF A1104 "
    ideal  model  delta    sigma   weight residual
    1.684  1.799 -0.115 2.00e-02 2.50e+03 3.28e+01
  bond pdb=" F2  ALF A1104 "
       pdb="AL   ALF A1104 "
    ideal  model  delta    sigma   weight residual
    1.685  1.798 -0.113 2.00e-02 2.50e+03 3.20e+01
  ... (remaining 10141 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.16: 13779
       14.16 -    28.32: 5
       28.32 -    42.48: 0
       42.48 -    56.64: 0
       56.64 -    70.80: 2
  Bond angle restraints: 13786
  Sorted by residual:
  angle pdb=" F1  ALF A1104 "
        pdb="AL   ALF A1104 "
        pdb=" F2  ALF A1104 "
      ideal   model   delta    sigma   weight residual
     108.68  179.48  -70.80 3.00e+00 1.11e-01 5.57e+02
  angle pdb=" F3  ALF A1104 "
        pdb="AL   ALF A1104 "
        pdb=" F4  ALF A1104 "
      ideal   model   delta    sigma   weight residual
     109.63  179.70  -70.07 3.00e+00 1.11e-01 5.46e+02
  angle pdb=" F2  ALF A1104 "
        pdb="AL   ALF A1104 "
        pdb=" F3  ALF A1104 "
      ideal   model   delta    sigma   weight residual
     109.59   89.70   19.89 3.00e+00 1.11e-01 4.40e+01
  angle pdb=" F2  ALF A1104 "
        pdb="AL   ALF A1104 "
        pdb=" F4  ALF A1104 "
      ideal   model   delta    sigma   weight residual
     110.21   90.39   19.82 3.00e+00 1.11e-01 4.36e+01
  angle pdb=" F1  ALF A1104 "
        pdb="AL   ALF A1104 "
        pdb=" F4  ALF A1104 "
      ideal   model   delta    sigma   weight residual
     109.02   89.51   19.51 3.00e+00 1.11e-01 4.23e+01
  ... (remaining 13781 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.65: 6002
       34.65 -    69.29: 192
       69.29 -   103.94: 16
      103.94 -   138.59: 0
      138.59 -   173.24: 1
  Dihedral angle restraints: 6211
    sinusoidal: 2583
      harmonic: 3628
  Sorted by residual:
  dihedral pdb=" N   PCW B 301 "
           pdb=" C4  PCW B 301 "
           pdb=" C5  PCW B 301 "
           pdb=" O4P PCW B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -66.66  106.58 -173.24     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CA  LEU A 376 "
           pdb=" C   LEU A 376 "
           pdb=" N   GLY A 377 "
           pdb=" CA  GLY A 377 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.75   20.25     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  PHE A 764 "
           pdb=" C   PHE A 764 "
           pdb=" N   ALA A 765 "
           pdb=" CA  ALA A 765 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.37   17.63     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 6208 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1421
       0.074 -    0.148: 143
       0.148 -    0.222: 4
       0.222 -    0.296: 2
       0.296 -    0.370: 1
  Chirality restraints: 1571
  Sorted by residual:
  chirality pdb=" C1  NAG B 304 "
            pdb=" ND2 ASN B 221 "
            pdb=" C2  NAG B 304 "
            pdb=" O5  NAG B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.03   -0.37 2.00e-01 2.50e+01 3.42e+00
  chirality pdb=" C1  NAG B 306 "
            pdb=" ND2 ASN B 146 "
            pdb=" C2  NAG B 306 "
            pdb=" O5  NAG B 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ASN B 221 "
            pdb=" N   ASN B 221 "
            pdb=" C   ASN B 221 "
            pdb=" CB  ASN B 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1568 not shown)

  Planarity restraints: 1766
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 302 "   -0.270 2.00e-02 2.50e+03   2.26e-01 6.40e+02
        pdb=" C7  NAG B 302 "    0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG B 302 "   -0.180 2.00e-02 2.50e+03
        pdb=" N2  NAG B 302 "    0.382 2.00e-02 2.50e+03
        pdb=" O7  NAG B 302 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 303 "   -0.175 2.00e-02 2.50e+03   1.45e-01 2.61e+02
        pdb=" C7  NAG B 303 "    0.049 2.00e-02 2.50e+03
        pdb=" C8  NAG B 303 "   -0.129 2.00e-02 2.50e+03
        pdb=" N2  NAG B 303 "    0.233 2.00e-02 2.50e+03
        pdb=" O7  NAG B 303 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 304 "    0.056 2.00e-02 2.50e+03   4.56e-02 2.60e+01
        pdb=" C7  NAG B 304 "   -0.015 2.00e-02 2.50e+03
        pdb=" C8  NAG B 304 "    0.042 2.00e-02 2.50e+03
        pdb=" N2  NAG B 304 "   -0.072 2.00e-02 2.50e+03
        pdb=" O7  NAG B 304 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1763 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.57: 54
        2.57 -     3.21: 9018
        3.21 -     3.85: 20178
        3.85 -     4.50: 27802
        4.50 -     5.14: 43895
  Nonbonded interactions: 100947
  Sorted by model distance:
  nonbonded pdb=" F2  ALF A1104 "
            pdb="MG    MG A1105 "
     model   vdw
     1.926 2.120
  nonbonded pdb=" OD1 ASP A 726 "
            pdb="MG    MG A1105 "
     model   vdw
     2.003 2.170
  nonbonded pdb=" O   THR A 387 "
            pdb="MG    MG A1105 "
     model   vdw
     2.004 2.170
  nonbonded pdb=" OD2 ASP A 385 "
            pdb="MG    MG A1105 "
     model   vdw
     2.153 2.170
  nonbonded pdb=" O   PRO B 145 "
            pdb=" OG1 THR B 148 "
     model   vdw
     2.200 3.040
  ... (remaining 100942 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.130
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.760
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.124  10155  Z= 0.234
  Angle     :  1.102  70.797  13807  Z= 0.428
  Chirality :  0.044   0.370   1571
  Planarity :  0.008   0.226   1761
  Dihedral  : 16.205 173.237   3864
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 15.99 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.23), residues: 1245
  helix:  1.94 (0.21), residues: 572
  sheet: -0.13 (0.38), residues: 177
  loop : -0.19 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 629 
 PHE   0.025   0.001   PHE A 300 
 TYR   0.016   0.001   TYR A 802 
 ARG   0.010   0.000   ARG A 428 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00577 (    5)
  link_NAG-ASN         : angle       2.39806 (   15)
  hydrogen bonds       : bond        0.13561 (  521)
  hydrogen bonds       : angle       5.87659 ( 1515)
  SS BOND              : bond        0.00087 (    3)
  SS BOND              : angle       0.56766 (    6)
  covalent geometry    : bond        0.00416 (10146)
  covalent geometry    : angle       1.10023 (13786)
  Misc. bond           : bond        0.11946 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 ARG cc_start: 0.6777 (mtm-85) cc_final: 0.6537 (mtm-85)
REVERT: A  677 MET cc_start: 0.6969 (mmp) cc_final: 0.6715 (mmt)
  outliers start: 9
  outliers final: 6
  residues processed: 126
  average time/residue: 1.4434
  time to fit residues: 193.5479
Evaluate side-chains
  121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain B residue   35 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 93 optimal weight:    0.5980
   chunk 52 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.144317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.109467 restraints weight = 11037.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.78
r_work: 0.3128 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.0873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10155  Z= 0.162
  Angle     :  0.817  30.895  13807  Z= 0.354
  Chirality :  0.046   0.379   1571
  Planarity :  0.005   0.050   1761
  Dihedral  :  8.213 166.788   1575
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 12.32 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.23), residues: 1245
  helix:  1.77 (0.21), residues: 588
  sheet:  0.05 (0.42), residues: 141
  loop : -0.10 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 915 
 HIS   0.005   0.001   HIS A 629 
 PHE   0.029   0.002   PHE A 300 
 TYR   0.023   0.002   TYR A 802 
 ARG   0.007   0.000   ARG A 428 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00337 (    5)
  link_NAG-ASN         : angle       2.97287 (   15)
  hydrogen bonds       : bond        0.04728 (  521)
  hydrogen bonds       : angle       4.71584 ( 1515)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       0.87554 (    6)
  covalent geometry    : bond        0.00379 (10146)
  covalent geometry    : angle       0.81167 (13786)
  Misc. bond           : bond        0.00324 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 113
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6473 (mt0)
REVERT: A  103 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7989 (ttp-170)
REVERT: A  171 LYS cc_start: 0.7108 (ttmt) cc_final: 0.6862 (ttmm)
REVERT: A  216 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8031 (pt0)
REVERT: A  414 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8224 (p0)
REVERT: A  428 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.7028 (mtm-85)
REVERT: A  560 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.7337 (mtm-85)
REVERT: A  650 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8175 (p)
REVERT: A  677 MET cc_start: 0.7812 (mmp) cc_final: 0.7564 (mmt)
REVERT: A  772 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8409 (tt0)
REVERT: A  933 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8888 (tp)
REVERT: B  115 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6873 (ptt90)
  outliers start: 44
  outliers final: 10
  residues processed: 141
  average time/residue: 1.4527
  time to fit residues: 218.3711
Evaluate side-chains
  125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  115 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 865 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.109540 restraints weight = 11171.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.83
r_work: 0.3131 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10155  Z= 0.133
  Angle     :  0.779  30.069  13807  Z= 0.332
  Chirality :  0.044   0.303   1571
  Planarity :  0.004   0.046   1761
  Dihedral  :  7.940 167.570   1571
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 13.26 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.24), residues: 1245
  helix:  1.91 (0.21), residues: 588
  sheet:  0.15 (0.42), residues: 136
  loop : -0.12 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 106 
 HIS   0.004   0.001   HIS A 629 
 PHE   0.028   0.002   PHE A 300 
 TYR   0.017   0.001   TYR A 802 
 ARG   0.004   0.000   ARG A 428 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00301 (    5)
  link_NAG-ASN         : angle       2.77466 (   15)
  hydrogen bonds       : bond        0.04228 (  521)
  hydrogen bonds       : angle       4.49235 ( 1515)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.72208 (    6)
  covalent geometry    : bond        0.00309 (10146)
  covalent geometry    : angle       0.77390 (13786)
  Misc. bond           : bond        0.00187 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 114
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 LYS cc_start: 0.7120 (ttmt) cc_final: 0.6871 (ttmm)
REVERT: A  202 MET cc_start: 0.7479 (mmp) cc_final: 0.7267 (mtm)
REVERT: A  414 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8283 (p0)
REVERT: A  428 ARG cc_start: 0.7145 (mtm-85) cc_final: 0.6931 (mtm-85)
REVERT: A  560 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7406 (mtm-85)
REVERT: A  677 MET cc_start: 0.7878 (mmp) cc_final: 0.7619 (mmt)
REVERT: A  682 MET cc_start: 0.8036 (mtm) cc_final: 0.7731 (ttm)
REVERT: A  844 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7900 (mtt-85)
REVERT: A  865 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8091 (mt0)
REVERT: A  933 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8877 (tp)
REVERT: B   84 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8444 (pt)
REVERT: B  115 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6836 (ptt90)
  outliers start: 41
  outliers final: 11
  residues processed: 141
  average time/residue: 1.4315
  time to fit residues: 214.9559
Evaluate side-chains
  123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  865 GLN
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 TRP
Chi-restraints excluded: chain B residue  115 ARG
Chi-restraints excluded: chain B residue  183 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 865 GLN
A 884 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.144479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.109855 restraints weight = 11090.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.84
r_work: 0.3131 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10155  Z= 0.126
  Angle     :  0.776  30.189  13807  Z= 0.329
  Chirality :  0.044   0.297   1571
  Planarity :  0.004   0.046   1761
  Dihedral  :  7.765 168.816   1570
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 13.55 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.23), residues: 1245
  helix:  1.94 (0.21), residues: 588
  sheet:  0.22 (0.42), residues: 135
  loop : -0.13 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 106 
 HIS   0.004   0.001   HIS A 629 
 PHE   0.028   0.001   PHE A 300 
 TYR   0.018   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 428 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00195 (    5)
  link_NAG-ASN         : angle       3.00217 (   15)
  hydrogen bonds       : bond        0.04072 (  521)
  hydrogen bonds       : angle       4.39610 ( 1515)
  SS BOND              : bond        0.00208 (    3)
  SS BOND              : angle       0.66285 (    6)
  covalent geometry    : bond        0.00292 (10146)
  covalent geometry    : angle       0.76983 (13786)
  Misc. bond           : bond        0.00092 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 LYS cc_start: 0.7138 (ttmt) cc_final: 0.6876 (ttmm)
REVERT: A  414 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8304 (p0)
REVERT: A  560 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7430 (mtm-85)
REVERT: A  650 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8163 (m)
REVERT: A  677 MET cc_start: 0.7881 (mmp) cc_final: 0.7640 (mmt)
REVERT: A  682 MET cc_start: 0.8098 (mtm) cc_final: 0.7800 (ttm)
REVERT: A  772 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8394 (tt0)
REVERT: A  844 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7895 (mtt-85)
REVERT: A  933 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8875 (tp)
REVERT: A 1031 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8428 (mt)
REVERT: B   84 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8408 (pt)
REVERT: B  115 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6815 (ptt90)
  outliers start: 36
  outliers final: 14
  residues processed: 128
  average time/residue: 1.3996
  time to fit residues: 191.0562
Evaluate side-chains
  125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 TRP
Chi-restraints excluded: chain B residue  115 ARG
Chi-restraints excluded: chain B residue  183 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 79 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 108 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107883 restraints weight = 11064.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.83
r_work: 0.3105 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10155  Z= 0.155
  Angle     :  0.795  30.405  13807  Z= 0.343
  Chirality :  0.045   0.278   1571
  Planarity :  0.005   0.047   1761
  Dihedral  :  7.859 171.621   1570
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 13.73 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.23), residues: 1245
  helix:  1.87 (0.21), residues: 586
  sheet:  0.08 (0.41), residues: 139
  loop : -0.17 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 401 
 HIS   0.005   0.001   HIS A 629 
 PHE   0.029   0.002   PHE A 300 
 TYR   0.021   0.002   TYR A 802 
 ARG   0.010   0.000   ARG A 428 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00250 (    5)
  link_NAG-ASN         : angle       3.28026 (   15)
  hydrogen bonds       : bond        0.04481 (  521)
  hydrogen bonds       : angle       4.45411 ( 1515)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       0.83361 (    6)
  covalent geometry    : bond        0.00365 (10146)
  covalent geometry    : angle       0.78817 (13786)
  Misc. bond           : bond        0.00104 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6742 (ttmt)
REVERT: A  216 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8444 (pt0)
REVERT: A  560 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7483 (mtm-85)
REVERT: A  650 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8186 (m)
REVERT: A  677 MET cc_start: 0.7858 (mmp) cc_final: 0.7621 (mmt)
REVERT: A  772 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8422 (tt0)
REVERT: A  844 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7888 (mtp-110)
REVERT: A  933 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8874 (tp)
REVERT: A 1031 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8513 (mt)
REVERT: B   84 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8555 (pt)
REVERT: B  115 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6840 (ptt90)
  outliers start: 39
  outliers final: 16
  residues processed: 130
  average time/residue: 1.4169
  time to fit residues: 196.4575
Evaluate side-chains
  129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LYS
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 TRP
Chi-restraints excluded: chain B residue  115 ARG
Chi-restraints excluded: chain B residue  183 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 119 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 19 optimal weight:    0.2980
   chunk 76 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 227 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.143354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.108866 restraints weight = 11117.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.82
r_work: 0.3118 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10155  Z= 0.131
  Angle     :  0.772  30.336  13807  Z= 0.329
  Chirality :  0.044   0.283   1571
  Planarity :  0.004   0.045   1761
  Dihedral  :  7.695 170.694   1570
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 14.39 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.23), residues: 1245
  helix:  1.96 (0.21), residues: 586
  sheet:  0.28 (0.42), residues: 137
  loop : -0.13 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 629 
 PHE   0.029   0.001   PHE A 300 
 TYR   0.017   0.001   TYR A 802 
 ARG   0.010   0.000   ARG A 428 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00235 (    5)
  link_NAG-ASN         : angle       2.87532 (   15)
  hydrogen bonds       : bond        0.04094 (  521)
  hydrogen bonds       : angle       4.34063 ( 1515)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       0.66791 (    6)
  covalent geometry    : bond        0.00305 (10146)
  covalent geometry    : angle       0.76679 (13786)
  Misc. bond           : bond        0.00091 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6848 (mt0)
REVERT: A  171 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6681 (ttmt)
REVERT: A  216 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8445 (pt0)
REVERT: A  650 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8181 (m)
REVERT: A  677 MET cc_start: 0.7844 (mmp) cc_final: 0.7589 (mmt)
REVERT: A  682 MET cc_start: 0.8361 (mtp) cc_final: 0.8057 (mtp)
REVERT: A  772 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (tt0)
REVERT: A  844 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7862 (mtt-85)
REVERT: A  933 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8872 (tp)
REVERT: A 1031 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8463 (mt)
REVERT: B   78 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8345 (mmtm)
REVERT: B  115 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6796 (ptt90)
REVERT: B  289 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7588 (mm-40)
  outliers start: 36
  outliers final: 16
  residues processed: 132
  average time/residue: 1.3963
  time to fit residues: 196.6308
Evaluate side-chains
  131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue  171 LYS
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 TRP
Chi-restraints excluded: chain B residue  115 ARG
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain B residue  289 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 121 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 115 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.142898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.108312 restraints weight = 11227.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.84
r_work: 0.3107 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10155  Z= 0.138
  Angle     :  0.788  30.367  13807  Z= 0.336
  Chirality :  0.044   0.253   1571
  Planarity :  0.004   0.046   1761
  Dihedral  :  7.620 172.526   1570
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 14.21 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.23), residues: 1245
  helix:  1.95 (0.21), residues: 586
  sheet:  0.29 (0.42), residues: 137
  loop : -0.12 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 401 
 HIS   0.004   0.001   HIS A 629 
 PHE   0.029   0.002   PHE A 300 
 TYR   0.019   0.001   TYR A 802 
 ARG   0.013   0.000   ARG A 850 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    5)
  link_NAG-ASN         : angle       3.28811 (   15)
  hydrogen bonds       : bond        0.04194 (  521)
  hydrogen bonds       : angle       4.35179 ( 1515)
  SS BOND              : bond        0.00236 (    3)
  SS BOND              : angle       0.72039 (    6)
  covalent geometry    : bond        0.00324 (10146)
  covalent geometry    : angle       0.78133 (13786)
  Misc. bond           : bond        0.00089 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 101
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6811 (mt0)
REVERT: A  171 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6670 (ttmt)
REVERT: A  650 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8147 (m)
REVERT: A  677 MET cc_start: 0.7835 (mmp) cc_final: 0.7583 (mmt)
REVERT: A  772 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8403 (tt0)
REVERT: A  844 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7875 (mtt-85)
REVERT: A  933 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8859 (tp)
REVERT: A 1031 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8493 (mt)
REVERT: B   78 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8318 (mmtm)
REVERT: B  115 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6825 (ptt90)
REVERT: B  289 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7530 (mm-40)
  outliers start: 37
  outliers final: 17
  residues processed: 124
  average time/residue: 1.5018
  time to fit residues: 198.0659
Evaluate side-chains
  128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue  171 LYS
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  587 PHE
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 TRP
Chi-restraints excluded: chain B residue  115 ARG
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain B residue  289 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 44 optimal weight:    9.9990
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 107 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.143138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.108799 restraints weight = 11194.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.83
r_work: 0.3114 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10155  Z= 0.131
  Angle     :  0.785  30.324  13807  Z= 0.333
  Chirality :  0.044   0.242   1571
  Planarity :  0.004   0.052   1761
  Dihedral  :  7.457 173.422   1570
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.68 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.24), residues: 1245
  helix:  1.99 (0.21), residues: 586
  sheet:  0.28 (0.42), residues: 138
  loop : -0.12 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 629 
 PHE   0.029   0.001   PHE A 300 
 TYR   0.017   0.001   TYR A 802 
 ARG   0.012   0.000   ARG A 850 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00307 (    5)
  link_NAG-ASN         : angle       3.03073 (   15)
  hydrogen bonds       : bond        0.04027 (  521)
  hydrogen bonds       : angle       4.30721 ( 1515)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       0.64553 (    6)
  covalent geometry    : bond        0.00305 (10146)
  covalent geometry    : angle       0.77876 (13786)
  Misc. bond           : bond        0.00083 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 102
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6629 (ttmt)
REVERT: A  650 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8152 (m)
REVERT: A  677 MET cc_start: 0.7824 (mmp) cc_final: 0.7568 (mmt)
REVERT: A  772 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8403 (tt0)
REVERT: A  844 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7862 (mtt-85)
REVERT: A  933 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8868 (tp)
REVERT: A 1031 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8462 (mt)
REVERT: B   78 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8329 (mmtm)
REVERT: B  115 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6811 (ptt90)
  outliers start: 34
  outliers final: 17
  residues processed: 123
  average time/residue: 1.4581
  time to fit residues: 190.7895
Evaluate side-chains
  124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LYS
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  587 PHE
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 TRP
Chi-restraints excluded: chain B residue  115 ARG
Chi-restraints excluded: chain B residue  183 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 89 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   chunk 120 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.143382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.108779 restraints weight = 11134.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.84
r_work: 0.3115 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10155  Z= 0.125
  Angle     :  0.779  30.272  13807  Z= 0.330
  Chirality :  0.044   0.229   1571
  Planarity :  0.004   0.055   1761
  Dihedral  :  7.413 173.938   1570
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.71 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.24), residues: 1245
  helix:  2.01 (0.22), residues: 586
  sheet:  0.20 (0.42), residues: 140
  loop : -0.15 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 629 
 PHE   0.029   0.001   PHE A 300 
 TYR   0.017   0.001   TYR A 802 
 ARG   0.013   0.000   ARG A 850 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00290 (    5)
  link_NAG-ASN         : angle       2.74874 (   15)
  hydrogen bonds       : bond        0.03978 (  521)
  hydrogen bonds       : angle       4.28444 ( 1515)
  SS BOND              : bond        0.00195 (    3)
  SS BOND              : angle       0.60660 (    6)
  covalent geometry    : bond        0.00289 (10146)
  covalent geometry    : angle       0.77414 (13786)
  Misc. bond           : bond        0.00074 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6614 (ttmt)
REVERT: A  650 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8143 (m)
REVERT: A  677 MET cc_start: 0.7822 (mmp) cc_final: 0.7556 (mmt)
REVERT: A  682 MET cc_start: 0.8338 (mtm) cc_final: 0.8003 (mtp)
REVERT: A  772 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8405 (tt0)
REVERT: A  844 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7870 (mtt-85)
REVERT: A  933 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8866 (tp)
REVERT: A 1031 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8471 (mt)
REVERT: B   78 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8316 (mmtm)
REVERT: B  115 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7180 (ptt90)
  outliers start: 26
  outliers final: 14
  residues processed: 118
  average time/residue: 1.5317
  time to fit residues: 192.0089
Evaluate side-chains
  119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LYS
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 TRP
Chi-restraints excluded: chain B residue  115 ARG
Chi-restraints excluded: chain B residue  183 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 117 optimal weight:    0.8980
   chunk 115 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 38 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:
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.142602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107926 restraints weight = 11060.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.82
r_work: 0.3103 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10155  Z= 0.143
  Angle     :  0.793  30.470  13807  Z= 0.340
  Chirality :  0.045   0.228   1571
  Planarity :  0.005   0.060   1761
  Dihedral  :  7.503 174.382   1570
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.90 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.23), residues: 1245
  helix:  1.95 (0.21), residues: 586
  sheet:  0.26 (0.42), residues: 137
  loop : -0.14 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 401 
 HIS   0.004   0.001   HIS A 629 
 PHE   0.029   0.002   PHE A 300 
 TYR   0.019   0.001   TYR A 802 
 ARG   0.014   0.000   ARG A 850 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00306 (    5)
  link_NAG-ASN         : angle       2.82440 (   15)
  hydrogen bonds       : bond        0.04216 (  521)
  hydrogen bonds       : angle       4.35531 ( 1515)
  SS BOND              : bond        0.00222 (    3)
  SS BOND              : angle       0.69277 (    6)
  covalent geometry    : bond        0.00338 (10146)
  covalent geometry    : angle       0.78810 (13786)
  Misc. bond           : bond        0.00094 (    1)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6807 (ttmm)
REVERT: A  650 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8170 (m)
REVERT: A  677 MET cc_start: 0.7840 (mmp) cc_final: 0.7575 (mmt)
REVERT: A  682 MET cc_start: 0.8358 (mtm) cc_final: 0.7979 (mtp)
REVERT: A  772 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (tt0)
REVERT: A  844 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7884 (mtt-85)
REVERT: A  933 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8861 (tp)
REVERT: A 1031 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8465 (mt)
REVERT: B   78 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8318 (mmtm)
REVERT: B  115 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6858 (ptt90)
  outliers start: 25
  outliers final: 17
  residues processed: 117
  average time/residue: 1.5000
  time to fit residues: 186.3649
Evaluate side-chains
  125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LYS
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  756 ASP
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 TRP
Chi-restraints excluded: chain B residue  115 ARG
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain B residue  289 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 121 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 110 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 177 GLN
A 188 GLN
A 446 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.143015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.108357 restraints weight = 11013.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.80
r_work: 0.3113 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10155  Z= 0.133
  Angle     :  0.791  30.372  13807  Z= 0.337
  Chirality :  0.044   0.229   1571
  Planarity :  0.004   0.061   1761
  Dihedral  :  7.494 174.865   1570
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.80 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.23), residues: 1245
  helix:  1.98 (0.21), residues: 586
  sheet:  0.22 (0.42), residues: 138
  loop : -0.12 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 629 
 PHE   0.029   0.001   PHE A 300 
 TYR   0.017   0.001   TYR A 802 
 ARG   0.014   0.000   ARG A 850 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00369 (    5)
  link_NAG-ASN         : angle       3.60756 (   15)
  hydrogen bonds       : bond        0.04060 (  521)
  hydrogen bonds       : angle       4.32378 ( 1515)
  SS BOND              : bond        0.00210 (    3)
  SS BOND              : angle       0.63487 (    6)
  covalent geometry    : bond        0.00309 (10146)
  covalent geometry    : angle       0.78248 (13786)
  Misc. bond           : bond        0.00088 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8497.61 seconds
wall clock time: 145 minutes 4.75 seconds (8704.75 seconds total)