Starting phenix.real_space_refine
on Wed Mar  4 00:41:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bsw_30169/03_2026/7bsw_30169_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bsw_30169/03_2026/7bsw_30169.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bsw_30169/03_2026/7bsw_30169_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bsw_30169/03_2026/7bsw_30169_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bsw_30169/03_2026/7bsw_30169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bsw_30169/03_2026/7bsw_30169.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       1      5.49       5
     S      45      5.16       5
     C    6078      2.51       5
     N    1504      2.21       5
     O    1696      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 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9329
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 815, 6596
          Classifications: {'peptide': 815}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 792}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 2613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2613
          Classifications: {'peptide': 324}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {'ALF': 1, 'PEE': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "C"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 66
          Unusual residues: {'MAN': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 2.33, per 1000 atoms: 0.25
  Number of scatterers: 9329
  At special positions: 0
  Unit cell: (97.2, 105.3, 141.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      45     16.00
     P       1     15.00
     Al      1     13.00
     F       4      9.00
     O    1696      8.00
     N    1504      7.00
     C    6078      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  91 " - pdb=" SG  CYS C 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 102 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 157 " - pdb=" SG  CYS C 171 " 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
      
  Atom "HETATM 9314  O5  NAG C 404 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM 9314  O5  NAG C 404 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-4
      " NAG C 402 " - " MAN C 403 "
    BETA1-4
      " NAG C 401 " - " NAG C 402 "
    NAG-ASN
      " NAG C 401 " - " ASN C 180 "
      " NAG C 404 " - " ASN C 294 "
      " NAG C 405 " - " ASN C 107 "
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 514.5 milliseconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 11 sheets defined
      44.2% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 64
      removed outlier: 4.197A  pdb=" N   PHE A  61 " --> pdb=" O   PRO A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 82
      removed outlier: 3.915A  pdb=" N   LEU A  73 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 93
    Processing helix  chain 'A' and resid 93 through 119
      removed outlier: 3.686A  pdb=" N   ILE A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ARG A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 141
      No H-bonds generated for 'chain 'A' and resid 139 through 141'
    Processing helix  chain 'A' and resid 286 through 314
      removed outlier: 3.752A  pdb=" N   PHE A 297 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 334
    Processing helix  chain 'A' and resid 335 through 351
      removed outlier: 3.503A  pdb=" N   LYS A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE A 341 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 355
    Processing helix  chain 'A' and resid 360 through 371
      removed outlier: 4.097A  pdb=" N   MET A 365 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 377
      removed outlier: 3.763A  pdb=" N   SER A 375 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASP A 377 " --> pdb=" O   PHE A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 400
    Processing helix  chain 'A' and resid 657 through 666
    Processing helix  chain 'A' and resid 679 through 688
      removed outlier: 4.005A  pdb=" N   SER A 683 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   CYS A 685 " --> pdb=" O   ALA A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 720
    Processing helix  chain 'A' and resid 754 through 762
      removed outlier: 3.821A  pdb=" N   LEU A 758 " --> pdb=" O   SER A 754 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 782
    Processing helix  chain 'A' and resid 791 through 802
      removed outlier: 3.657A  pdb=" N   LYS A 795 " --> pdb=" O   ALA A 791 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA A 796 " --> pdb=" O   PRO A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
    Processing helix  chain 'A' and resid 853 through 862
      removed outlier: 4.583A  pdb=" N   LYS A 857 " --> pdb=" O   LYS A 853 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A 859 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 886
      removed outlier: 4.246A  pdb=" N   ASN A 881 " --> pdb=" O   PHE A 877 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE A 884 " --> pdb=" O   LYS A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 891
    Processing helix  chain 'A' and resid 892 through 894
      No H-bonds generated for 'chain 'A' and resid 892 through 894'
    Processing helix  chain 'A' and resid 906 through 911
    Processing helix  chain 'A' and resid 918 through 926
    Processing helix  chain 'A' and resid 931 through 936
    Processing helix  chain 'A' and resid 938 through 945
      removed outlier: 3.600A  pdb=" N   TYR A 942 " --> pdb=" O   PRO A 939 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE A 945 " --> pdb=" O   TYR A 942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 951
    Processing helix  chain 'A' and resid 952 through 976
      removed outlier: 3.715A  pdb=" N   ALA A 964 " --> pdb=" O   THR A 960 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   PHE A 965 " --> pdb=" O   PHE A 961 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   THR A 968 " --> pdb=" O   ALA A 964 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   PHE A 971 " --> pdb=" O   GLY A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 979
      No H-bonds generated for 'chain 'A' and resid 977 through 979'
    Processing helix  chain 'A' and resid 992 through 1015
      removed outlier: 3.762A  pdb=" N   GLY A 996 " --> pdb=" O   ASN A 992 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   LEU A1011 " --> pdb=" O   VAL A1007 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1041
      removed outlier: 3.717A  pdb=" N   HIS A1023 " --> pdb=" O   THR A1019 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE A1024 " --> pdb=" O   TRP A1020 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A1041 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1062
      removed outlier: 3.676A  pdb=" N   GLN A1059 " --> pdb=" O   PHE A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1064 through 1077
      removed outlier: 3.648A  pdb=" N   LEU A1068 " --> pdb=" O   VAL A1064 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE A1075 " --> pdb=" O   ILE A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1088
    Processing helix  chain 'C' and resid 46 through 51
    Processing helix  chain 'C' and resid 52 through 71
      removed outlier: 4.060A  pdb=" N   GLY C  58 " --> pdb=" O   PHE C  54 " (cutoff:3.500A)
      Proline residue:  C  63  - end of helix
    Processing helix  chain 'C' and resid 91 through 95
    Processing helix  chain 'C' and resid 131 through 136
      removed outlier: 3.596A  pdb=" N   LYS C 136 " --> pdb=" O   ARG C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 144
    Processing helix  chain 'C' and resid 148 through 152
    Processing helix  chain 'C' and resid 172 through 177
      removed outlier: 3.547A  pdb=" N   SER C 177 " --> pdb=" O   ALA C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 212
    Processing helix  chain 'C' and resid 239 through 243
      removed outlier: 3.681A  pdb=" N   LEU C 243 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 262
    Processing helix  chain 'C' and resid 323 through 350
      removed outlier: 3.618A  pdb=" N   LEU C 339 " --> pdb=" O   ILE C 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150
      removed outlier: 4.123A  pdb=" N   VAL A 149 " --> pdb=" O   ILE A 257 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TYR A 258 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER A 163 " --> pdb=" O   TYR A 258 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 160
      removed outlier: 3.515A  pdb=" N   LEU A 245 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.814A  pdb=" N   TYR A 172 " --> pdb=" O   LYS A 252 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR A 250 " --> pdb=" O   THR A 174 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 223 through 224
      removed outlier: 3.855A  pdb=" N   GLY A 223 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391
    Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.987A  pdb=" N   VAL A 406 " --> pdb=" O   TRP A 671 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LEU A 673 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   THR A 408 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 8.965A  pdb=" N   LEU A 786 " --> pdb=" O   TYR A 747 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU A 749 " --> pdb=" O   LEU A 786 " (cutoff:3.500A)
      removed outlier: 8.349A  pdb=" N   CYS A 788 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE A 751 " --> pdb=" O   CYS A 788 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A 748 " --> pdb=" O   GLU A 696 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 812 through 815
      removed outlier: 5.650A  pdb=" N   SER A 813 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 81
      removed outlier: 3.517A  pdb=" N   ARG C 309 " --> pdb=" O   GLY C 123 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   TYR C 122 " --> pdb=" O   LEU C 272 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   LEU C 272 " --> pdb=" O   TYR C 122 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 110
      removed outlier: 3.588A  pdb=" N   PHE C 108 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   ARG C 290 " --> pdb=" O   ILE C 188 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE C 188 " --> pdb=" O   ARG C 290 " (cutoff:3.500A)

    331 hydrogen bonds defined for protein.
    936 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.40

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1518
        1.32 -     1.45: 2643
        1.45 -     1.57: 5325
        1.57 -     1.69: 2
        1.69 -     1.81: 71
  Bond restraints: 9559
  Sorted by residual:
  bond pdb=" F1  ALF A1101 "
       pdb="AL   ALF A1101 "
    ideal  model  delta    sigma   weight residual
    1.684  1.799 -0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" F3  ALF A1101 "
       pdb="AL   ALF A1101 "
    ideal  model  delta    sigma   weight residual
    1.685  1.799 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" F4  ALF A1101 "
       pdb="AL   ALF A1101 "
    ideal  model  delta    sigma   weight residual
    1.686  1.800 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" F2  ALF A1101 "
       pdb="AL   ALF A1101 "
    ideal  model  delta    sigma   weight residual
    1.685  1.797 -0.112 2.00e-02 2.50e+03 3.13e+01
  bond pdb=" N   THR C 100 "
       pdb=" CA  THR C 100 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 9.60e-03 1.09e+04 1.13e+01
  ... (remaining 9554 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.11: 12955
       14.11 -    28.22: 4
       28.22 -    42.32: 0
       42.32 -    56.43: 0
       56.43 -    70.54: 2
  Bond angle restraints: 12961
  Sorted by residual:
  angle pdb=" F1  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F2  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     108.68  179.22  -70.54 3.00e+00 1.11e-01 5.53e+02
  angle pdb=" F3  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F4  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     109.63  179.69  -70.06 3.00e+00 1.11e-01 5.45e+02
  angle pdb=" N   LYS A1088 "
        pdb=" CA  LYS A1088 "
        pdb=" C   LYS A1088 "
      ideal   model   delta    sigma   weight residual
     112.93  103.39    9.54 1.12e+00 7.97e-01 7.26e+01
  angle pdb=" F2  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F4  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     110.21   90.20   20.01 3.00e+00 1.11e-01 4.45e+01
  angle pdb=" F2  ALF A1101 "
        pdb="AL   ALF A1101 "
        pdb=" F3  ALF A1101 "
      ideal   model   delta    sigma   weight residual
     109.59   89.68   19.91 3.00e+00 1.11e-01 4.41e+01
  ... (remaining 12956 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.09: 5428
       26.09 -    52.18: 245
       52.18 -    78.27: 23
       78.27 -   104.35: 17
      104.35 -   130.44: 13
  Dihedral angle restraints: 5726
    sinusoidal: 2383
      harmonic: 3343
  Sorted by residual:
  dihedral pdb=" C3  PEE A1102 "
           pdb=" C1  PEE A1102 "
           pdb=" C2  PEE A1102 "
           pdb=" O3P PEE A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73  -67.71  130.44     1      3.00e+01 1.11e-03 1.76e+01
  dihedral pdb=" O2  PEE A1102 "
           pdb=" C1  PEE A1102 "
           pdb=" C2  PEE A1102 "
           pdb=" O3P PEE A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.04  170.89  129.15     1      3.00e+01 1.11e-03 1.74e+01
  dihedral pdb=" N   PEE A1102 "
           pdb=" C4  PEE A1102 "
           pdb=" C5  PEE A1102 "
           pdb=" O4P PEE A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.97 -178.16  121.19     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 5723 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.091: 1462
       1.091 -    2.182: 0
       2.182 -    3.272: 1
       3.272 -    4.363: 0
       4.363 -    5.454: 2
  Chirality restraints: 1465
  Sorted by residual:
  chirality pdb=" C1  NAG C 402 "
            pdb=" O4  NAG C 401 "
            pdb=" C2  NAG C 402 "
            pdb=" O5  NAG C 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    3.05   -5.45 2.00e-02 2.50e+03 7.44e+04
  chirality pdb=" C1  MAN C 403 "
            pdb=" O4  NAG C 402 "
            pdb=" C2  MAN C 403 "
            pdb=" O5  MAN C 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40   -2.42    4.82 2.00e-02 2.50e+03 5.81e+04
  chirality pdb=" C1  NAG C 404 "
            pdb=" ND2 ASN C 294 "
            pdb=" C2  NAG C 404 "
            pdb=" O5  NAG C 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.17   -2.23 2.00e-01 2.50e+01 1.25e+02
  ... (remaining 1462 not shown)

  Planarity restraints: 1614
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 294 "    0.271 2.00e-02 2.50e+03   4.91e-01 3.01e+03
        pdb=" CG  ASN C 294 "   -0.164 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 294 "    0.086 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 294 "   -0.831 2.00e-02 2.50e+03
        pdb=" C1  NAG C 404 "    0.639 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 402 "    0.275 2.00e-02 2.50e+03   2.27e-01 6.46e+02
        pdb=" C7  NAG C 402 "   -0.075 2.00e-02 2.50e+03
        pdb=" C8  NAG C 402 "    0.187 2.00e-02 2.50e+03
        pdb=" N2  NAG C 402 "   -0.377 2.00e-02 2.50e+03
        pdb=" O7  NAG C 402 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 401 "    0.130 2.00e-02 2.50e+03   1.10e-01 1.50e+02
        pdb=" C7  NAG C 401 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8  NAG C 401 "   -0.032 2.00e-02 2.50e+03
        pdb=" N2  NAG C 401 "   -0.175 2.00e-02 2.50e+03
        pdb=" O7  NAG C 401 "    0.104 2.00e-02 2.50e+03
  ... (remaining 1611 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.36: 56
        2.36 -     2.99: 5632
        2.99 -     3.63: 12950
        3.63 -     4.26: 20676
        4.26 -     4.90: 34904
  Nonbonded interactions: 74218
  Sorted by model distance:
  nonbonded pdb=" CD2 TYR A 876 "
            pdb=" CD1 ILE A 920 "
     model   vdw
     1.719 3.760
  nonbonded pdb=" OE2 GLU A 181 "
            pdb=" OD2 ASP A 676 "
     model   vdw
     1.869 3.040
  nonbonded pdb=" CG  ASN C 294 "
            pdb=" O5  NAG C 404 "
     model   vdw
     1.919 2.616
  nonbonded pdb=" OH  TYR A 876 "
            pdb=" O   VAL A1007 "
     model   vdw
     1.932 3.040
  nonbonded pdb=" OD1 ASN C 294 "
            pdb=" O5  NAG C 404 "
     model   vdw
     1.962 3.040
  ... (remaining 74213 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.570
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.368   9567  Z= 0.395
  Angle     :  1.593  70.538  12982  Z= 0.691
  Chirality :  0.206   5.454   1465
  Planarity :  0.008   0.227   1611
  Dihedral  : 16.587 130.443   3561
  Min Nonbonded Distance : 1.719

Molprobity Statistics.
  All-atom Clashscore : 37.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  3.74 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.22 (0.19), residues: 1129
  helix: -2.91 (0.19), residues: 474
  sheet: -3.89 (0.33), residues: 151
  loop : -3.83 (0.22), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 723 
 TYR   0.015   0.001   TYR C 350 
 PHE   0.012   0.001   PHE A 884 
 TRP   0.013   0.001   TRP A 323 
 HIS   0.005   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 9559)
  covalent geometry    : angle       1.22492 (12961)
  SS BOND              : bond        0.00430 (    3)
  SS BOND              : angle       1.04266 (    6)
  hydrogen bonds       : bond        0.19046 (  331)
  hydrogen bonds       : angle       7.82432 (  936)
  link_ALPHA1-4        : bond        0.36767 (    1)
  link_ALPHA1-4        : angle      31.57294 (    3)
  link_BETA1-4         : bond        0.23917 (    1)
  link_BETA1-4         : angle      30.00505 (    3)
  link_NAG-ASN         : bond        0.13033 (    3)
  link_NAG-ASN         : angle      29.40998 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 226
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 TYR cc_start: 0.7135 (m-80) cc_final: 0.6934 (m-80)
REVERT: A  352 ASN cc_start: 0.7848 (t0) cc_final: 0.7583 (t0)
REVERT: A  381 TYR cc_start: 0.7636 (t80) cc_final: 0.7290 (t80)
REVERT: A  399 GLU cc_start: 0.8819 (tt0) cc_final: 0.8576 (mt-10)
REVERT: A  826 GLU cc_start: 0.8349 (tp30) cc_final: 0.7985 (tp30)
REVERT: A  914 CYS cc_start: 0.8052 (m) cc_final: 0.7755 (m)
REVERT: A 1050 GLN cc_start: 0.8516 (pp30) cc_final: 0.8128 (pp30)
REVERT: C  106 ILE cc_start: 0.8564 (mm) cc_final: 0.8300 (mm)
REVERT: C  122 TYR cc_start: 0.8612 (p90) cc_final: 0.8400 (p90)
REVERT: C  310 MET cc_start: 0.8525 (ttp) cc_final: 0.7880 (tmm)
  outliers start: 7
  outliers final: 2
  residues processed: 231
  average time/residue: 0.1027
  time to fit residues: 32.1048
Evaluate side-chains
  144 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue  275 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
A 243 ASN
A 314 GLN
A 352 ASN
A 392 ASN
A 402 GLN
A 716 HIS
A 744 HIS
A 828 HIS
A 862 HIS
A1089 ASN
C  36 GLN
C 129 GLN
C 347 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.150254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.121763 restraints weight = 11450.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.119979 restraints weight = 16810.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.120991 restraints weight = 16629.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.120946 restraints weight = 11649.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.121547 restraints weight = 10805.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9567  Z= 0.145
  Angle     :  0.680  10.518  12982  Z= 0.339
  Chirality :  0.046   0.204   1465
  Planarity :  0.004   0.031   1611
  Dihedral  : 12.621 103.209   1381
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 10.72 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.67 (0.22), residues: 1129
  helix: -1.67 (0.22), residues: 477
  sheet: -3.58 (0.33), residues: 152
  loop : -2.73 (0.24), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 161 
 TYR   0.017   0.002   TYR A 108 
 PHE   0.020   0.002   PHE A1075 
 TRP   0.013   0.001   TRP A 323 
 HIS   0.009   0.002   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9559)
  covalent geometry    : angle       0.66664 (12961)
  SS BOND              : bond        0.00486 (    3)
  SS BOND              : angle       1.52715 (    6)
  hydrogen bonds       : bond        0.04616 (  331)
  hydrogen bonds       : angle       5.17762 (  936)
  link_ALPHA1-4        : bond        0.02794 (    1)
  link_ALPHA1-4        : angle       7.62446 (    3)
  link_BETA1-4         : bond        0.01567 (    1)
  link_BETA1-4         : angle       1.10977 (    3)
  link_NAG-ASN         : bond        0.00480 (    3)
  link_NAG-ASN         : angle       2.34633 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7323 (mmmt)
REVERT: A  747 TYR cc_start: 0.7005 (m-80) cc_final: 0.6402 (m-80)
REVERT: A  826 GLU cc_start: 0.8468 (tp30) cc_final: 0.8021 (tp30)
REVERT: A  851 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7484 (mmmm)
REVERT: A  877 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7956 (t80)
REVERT: A  910 MET cc_start: 0.8259 (mmm) cc_final: 0.7743 (mmm)
REVERT: A  975 TYR cc_start: 0.9118 (t80) cc_final: 0.8878 (t80)
REVERT: A 1014 ASP cc_start: 0.8629 (m-30) cc_final: 0.8267 (t0)
REVERT: A 1050 GLN cc_start: 0.8885 (pp30) cc_final: 0.8336 (pp30)
REVERT: C  310 MET cc_start: 0.8525 (ttp) cc_final: 0.8083 (tmm)
  outliers start: 25
  outliers final: 14
  residues processed: 194
  average time/residue: 0.0850
  time to fit residues: 23.9407
Evaluate side-chains
  172 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  341 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 89 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 352 ASN
A 397 ASN
A 828 HIS
A 864 HIS
C 347 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.168197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.157636 restraints weight = 10668.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.144611 restraints weight = 19612.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.142692 restraints weight = 16466.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.143208 restraints weight = 14836.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.142961 restraints weight = 12968.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9567  Z= 0.149
  Angle     :  0.636   7.650  12982  Z= 0.318
  Chirality :  0.045   0.176   1465
  Planarity :  0.004   0.036   1611
  Dihedral  :  9.675  81.484   1376
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.54 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.23), residues: 1129
  helix: -1.11 (0.23), residues: 478
  sheet: -3.04 (0.34), residues: 152
  loop : -2.36 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 262 
 TYR   0.014   0.001   TYR C 350 
 PHE   0.015   0.001   PHE A1039 
 TRP   0.014   0.001   TRP A 323 
 HIS   0.007   0.002   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9559)
  covalent geometry    : angle       0.63147 (12961)
  SS BOND              : bond        0.00715 (    3)
  SS BOND              : angle       0.97214 (    6)
  hydrogen bonds       : bond        0.04319 (  331)
  hydrogen bonds       : angle       4.82599 (  936)
  link_ALPHA1-4        : bond        0.01880 (    1)
  link_ALPHA1-4        : angle       3.62338 (    3)
  link_BETA1-4         : bond        0.00075 (    1)
  link_BETA1-4         : angle       1.36912 (    3)
  link_NAG-ASN         : bond        0.00124 (    3)
  link_NAG-ASN         : angle       1.76851 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7313 (mmmt)
REVERT: A  366 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8118 (tm-30)
REVERT: A  678 MET cc_start: 0.8099 (tpp) cc_final: 0.7168 (tpt)
REVERT: A  826 GLU cc_start: 0.8554 (tp30) cc_final: 0.8169 (tp30)
REVERT: A  840 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7919 (tp40)
REVERT: A  851 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7518 (mmmm)
REVERT: A  877 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8132 (t80)
REVERT: A 1014 ASP cc_start: 0.8585 (m-30) cc_final: 0.8381 (t0)
REVERT: A 1050 GLN cc_start: 0.8951 (pp30) cc_final: 0.8476 (pp30)
REVERT: C  310 MET cc_start: 0.8632 (ttp) cc_final: 0.8311 (tmm)
  outliers start: 31
  outliers final: 20
  residues processed: 177
  average time/residue: 0.0865
  time to fit residues: 22.2027
Evaluate side-chains
  169 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 101 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 109 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0670
   chunk 40 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    2.5924

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

Flipped N/Q/H residues before XYZ refinement:
A 352 ASN
A1089 ASN
C 347 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.163195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.153776 restraints weight = 10881.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.137331 restraints weight = 14919.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.137051 restraints weight = 12211.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.137048 restraints weight = 11124.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.137048 restraints weight = 11056.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9567  Z= 0.222
  Angle     :  0.696  10.004  12982  Z= 0.344
  Chirality :  0.047   0.186   1465
  Planarity :  0.004   0.031   1611
  Dihedral  :  9.032  82.599   1376
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 16.91 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.23), residues: 1129
  helix: -0.99 (0.23), residues: 478
  sheet: -2.92 (0.34), residues: 158
  loop : -2.16 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 262 
 TYR   0.014   0.002   TYR A 722 
 PHE   0.017   0.002   PHE A1039 
 TRP   0.015   0.001   TRP A 323 
 HIS   0.006   0.002   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 9559)
  covalent geometry    : angle       0.69155 (12961)
  SS BOND              : bond        0.00313 (    3)
  SS BOND              : angle       1.19918 (    6)
  hydrogen bonds       : bond        0.04713 (  331)
  hydrogen bonds       : angle       4.85764 (  936)
  link_ALPHA1-4        : bond        0.01597 (    1)
  link_ALPHA1-4        : angle       3.53644 (    3)
  link_BETA1-4         : bond        0.00241 (    1)
  link_BETA1-4         : angle       1.51224 (    3)
  link_NAG-ASN         : bond        0.00088 (    3)
  link_NAG-ASN         : angle       1.92664 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 155
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: A  369 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.9007 (mt)
REVERT: A  678 MET cc_start: 0.8124 (tpp) cc_final: 0.7885 (tpp)
REVERT: A  840 GLN cc_start: 0.8401 (tp-100) cc_final: 0.8080 (tp40)
REVERT: A  877 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8195 (t80)
REVERT: A  990 TYR cc_start: 0.9206 (m-10) cc_final: 0.9000 (m-80)
REVERT: A 1014 ASP cc_start: 0.8673 (m-30) cc_final: 0.8464 (t0)
REVERT: A 1050 GLN cc_start: 0.9031 (pp30) cc_final: 0.8493 (pp30)
REVERT: C  310 MET cc_start: 0.8723 (ttp) cc_final: 0.8336 (tmm)
  outliers start: 41
  outliers final: 27
  residues processed: 177
  average time/residue: 0.0862
  time to fit residues: 22.2303
Evaluate side-chains
  165 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  206 ARG
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9980
   chunk 106 optimal weight:    5.9990
   chunk 112 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A 352 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.163069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 107)---------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.136637 restraints weight = 10711.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.135530 restraints weight = 13019.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.134346 restraints weight = 10648.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.133649 restraints weight = 11614.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.134177 restraints weight = 9540.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9567  Z= 0.121
  Angle     :  0.616   9.553  12982  Z= 0.298
  Chirality :  0.043   0.186   1465
  Planarity :  0.003   0.030   1611
  Dihedral  :  8.162  81.730   1376
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.68 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.24), residues: 1129
  helix: -0.47 (0.24), residues: 470
  sheet: -2.43 (0.37), residues: 158
  loop : -1.91 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 262 
 TYR   0.015   0.001   TYR A 722 
 PHE   0.017   0.001   PHE A1039 
 TRP   0.013   0.001   TRP A 323 
 HIS   0.006   0.001   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9559)
  covalent geometry    : angle       0.61036 (12961)
  SS BOND              : bond        0.00415 (    3)
  SS BOND              : angle       0.75108 (    6)
  hydrogen bonds       : bond        0.03933 (  331)
  hydrogen bonds       : angle       4.54709 (  936)
  link_ALPHA1-4        : bond        0.02234 (    1)
  link_ALPHA1-4        : angle       3.95777 (    3)
  link_BETA1-4         : bond        0.00301 (    1)
  link_BETA1-4         : angle       0.98022 (    3)
  link_NAG-ASN         : bond        0.00221 (    3)
  link_NAG-ASN         : angle       2.14504 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.8307 (p0) cc_final: 0.8032 (p0)
REVERT: A  145 ASP cc_start: 0.8028 (p0) cc_final: 0.7738 (p0)
REVERT: A  399 GLU cc_start: 0.8745 (tt0) cc_final: 0.8315 (mt-10)
REVERT: A  678 MET cc_start: 0.8040 (tpp) cc_final: 0.7579 (tpt)
REVERT: A  786 LEU cc_start: 0.9108 (tt) cc_final: 0.8877 (tt)
REVERT: A  840 GLN cc_start: 0.8282 (tp-100) cc_final: 0.7888 (tp40)
REVERT: A  844 ASN cc_start: 0.8471 (m-40) cc_final: 0.8189 (m-40)
REVERT: A  851 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7430 (mmmm)
REVERT: A  877 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8254 (t80)
REVERT: A 1050 GLN cc_start: 0.9043 (pp30) cc_final: 0.8685 (pp30)
REVERT: C  310 MET cc_start: 0.8622 (ttp) cc_final: 0.8238 (tmm)
  outliers start: 31
  outliers final: 22
  residues processed: 172
  average time/residue: 0.0918
  time to fit residues: 22.8533
Evaluate side-chains
  156 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1088 LYS
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  345 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 108 optimal weight:    0.0970
   chunk 46 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 104 optimal weight:    0.5980
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 352 ASN
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.155887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.126032 restraints weight = 10995.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.125175 restraints weight = 17352.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.125497 restraints weight = 14577.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.126109 restraints weight = 12172.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.127215 restraints weight = 10121.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   9567  Z= 0.201
  Angle     :  0.670   8.470  12982  Z= 0.329
  Chirality :  0.046   0.170   1465
  Planarity :  0.004   0.031   1611
  Dihedral  :  7.852  82.269   1376
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 18.98 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.24), residues: 1129
  helix: -0.61 (0.23), residues: 477
  sheet: -2.14 (0.38), residues: 158
  loop : -1.87 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 262 
 TYR   0.017   0.002   TYR A 722 
 PHE   0.019   0.002   PHE A1039 
 TRP   0.015   0.001   TRP A 323 
 HIS   0.005   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 9559)
  covalent geometry    : angle       0.66423 (12961)
  SS BOND              : bond        0.00639 (    3)
  SS BOND              : angle       1.28091 (    6)
  hydrogen bonds       : bond        0.04524 (  331)
  hydrogen bonds       : angle       4.65414 (  936)
  link_ALPHA1-4        : bond        0.01981 (    1)
  link_ALPHA1-4        : angle       4.43657 (    3)
  link_BETA1-4         : bond        0.00574 (    1)
  link_BETA1-4         : angle       1.27191 (    3)
  link_NAG-ASN         : bond        0.00069 (    3)
  link_NAG-ASN         : angle       2.20640 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 143
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.8341 (p0) cc_final: 0.8030 (p0)
REVERT: A  111 TRP cc_start: 0.8144 (t60) cc_final: 0.7805 (t-100)
REVERT: A  145 ASP cc_start: 0.8055 (p0) cc_final: 0.7782 (p0)
REVERT: A  399 GLU cc_start: 0.8800 (tt0) cc_final: 0.8362 (mt-10)
REVERT: A  678 MET cc_start: 0.8050 (tpp) cc_final: 0.7581 (tpt)
REVERT: A  840 GLN cc_start: 0.8384 (tp-100) cc_final: 0.7999 (tp40)
REVERT: A  851 LYS cc_start: 0.7816 (mmtm) cc_final: 0.7267 (mmmm)
REVERT: A  877 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8050 (t80)
REVERT: A  910 MET cc_start: 0.8650 (mmm) cc_final: 0.8203 (tpt)
REVERT: A  950 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7786 (mtm)
REVERT: A  990 TYR cc_start: 0.9214 (m-10) cc_final: 0.9008 (m-80)
REVERT: A 1014 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7490 (t0)
REVERT: A 1050 GLN cc_start: 0.9091 (pp30) cc_final: 0.8706 (pp30)
  outliers start: 46
  outliers final: 33
  residues processed: 168
  average time/residue: 0.0905
  time to fit residues: 22.0427
Evaluate side-chains
  173 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  306 CYS
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue  950 MET
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1014 ASP
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.161245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.134782 restraints weight = 10869.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.134300 restraints weight = 13267.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.134330 restraints weight = 12204.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.132920 restraints weight = 12594.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.133750 restraints weight = 10513.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9567  Z= 0.147
  Angle     :  0.614   9.158  12982  Z= 0.302
  Chirality :  0.043   0.183   1465
  Planarity :  0.003   0.032   1611
  Dihedral  :  7.299  80.761   1376
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.16 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.25), residues: 1129
  helix: -0.30 (0.24), residues: 468
  sheet: -1.86 (0.40), residues: 158
  loop : -1.78 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 262 
 TYR   0.014   0.001   TYR C 350 
 PHE   0.021   0.001   PHE A1039 
 TRP   0.013   0.001   TRP A 323 
 HIS   0.005   0.001   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9559)
  covalent geometry    : angle       0.60652 (12961)
  SS BOND              : bond        0.00469 (    3)
  SS BOND              : angle       1.19049 (    6)
  hydrogen bonds       : bond        0.04103 (  331)
  hydrogen bonds       : angle       4.48587 (  936)
  link_ALPHA1-4        : bond        0.01982 (    1)
  link_ALPHA1-4        : angle       4.71407 (    3)
  link_BETA1-4         : bond        0.00242 (    1)
  link_BETA1-4         : angle       0.74414 (    3)
  link_NAG-ASN         : bond        0.00146 (    3)
  link_NAG-ASN         : angle       2.32405 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ASP cc_start: 0.8266 (p0) cc_final: 0.7837 (p0)
REVERT: A  678 MET cc_start: 0.8008 (tpp) cc_final: 0.7548 (tpt)
REVERT: A  747 TYR cc_start: 0.7257 (m-80) cc_final: 0.6840 (m-80)
REVERT: A  840 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8087 (tp40)
REVERT: A  844 ASN cc_start: 0.8497 (m-40) cc_final: 0.8194 (m-40)
REVERT: A  851 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7225 (mmmm)
REVERT: A  877 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8181 (t80)
REVERT: A  950 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7749 (mtm)
REVERT: A  990 TYR cc_start: 0.9181 (m-10) cc_final: 0.8957 (m-80)
REVERT: A 1014 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7535 (t0)
REVERT: A 1050 GLN cc_start: 0.8995 (pp30) cc_final: 0.8634 (pp30)
REVERT: C  310 MET cc_start: 0.8847 (tmm) cc_final: 0.8373 (tmm)
  outliers start: 39
  outliers final: 31
  residues processed: 169
  average time/residue: 0.0903
  time to fit residues: 22.0125
Evaluate side-chains
  172 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  822 SER
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue  950 MET
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1014 ASP
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.166516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.156425 restraints weight = 10608.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.153265 restraints weight = 16333.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.151592 restraints weight = 20985.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.149784 restraints weight = 19244.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.148599 restraints weight = 19481.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9567  Z= 0.118
  Angle     :  0.587   8.443  12982  Z= 0.288
  Chirality :  0.042   0.185   1465
  Planarity :  0.003   0.032   1611
  Dihedral  :  6.870  80.256   1376
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.14 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.25), residues: 1129
  helix: -0.12 (0.24), residues: 479
  sheet: -1.65 (0.41), residues: 160
  loop : -1.62 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 262 
 TYR   0.020   0.001   TYR A 722 
 PHE   0.020   0.001   PHE A1039 
 TRP   0.013   0.001   TRP C 260 
 HIS   0.005   0.001   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9559)
  covalent geometry    : angle       0.57967 (12961)
  SS BOND              : bond        0.00403 (    3)
  SS BOND              : angle       1.04836 (    6)
  hydrogen bonds       : bond        0.03756 (  331)
  hydrogen bonds       : angle       4.34746 (  936)
  link_ALPHA1-4        : bond        0.02049 (    1)
  link_ALPHA1-4        : angle       4.63844 (    3)
  link_BETA1-4         : bond        0.00347 (    1)
  link_BETA1-4         : angle       0.44427 (    3)
  link_NAG-ASN         : bond        0.00249 (    3)
  link_NAG-ASN         : angle       2.44300 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ASP cc_start: 0.8087 (p0) cc_final: 0.7710 (p0)
REVERT: A  399 GLU cc_start: 0.8712 (tt0) cc_final: 0.8047 (mt-10)
REVERT: A  840 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8043 (tp40)
REVERT: A  844 ASN cc_start: 0.8401 (m-40) cc_final: 0.8121 (m-40)
REVERT: A  851 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7410 (mmmm)
REVERT: A  877 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8097 (t80)
REVERT: A  882 LEU cc_start: 0.8717 (tp) cc_final: 0.8337 (tt)
REVERT: A  950 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7595 (mtm)
REVERT: A 1014 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7580 (t0)
REVERT: A 1050 GLN cc_start: 0.9064 (pp30) cc_final: 0.8733 (pp30)
REVERT: C  310 MET cc_start: 0.8948 (tmm) cc_final: 0.8491 (tmm)
  outliers start: 31
  outliers final: 25
  residues processed: 168
  average time/residue: 0.0914
  time to fit residues: 22.3415
Evaluate side-chains
  170 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  306 CYS
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue  950 MET
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1014 ASP
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  345 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 22 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 101 optimal weight:    0.2980
   chunk 15 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
C 131 HIS
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.166460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.155515 restraints weight = 10656.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.142950 restraints weight = 18826.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.140372 restraints weight = 16957.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.140177 restraints weight = 19323.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.140486 restraints weight = 14609.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   9567  Z= 0.122
  Angle     :  0.591   8.422  12982  Z= 0.291
  Chirality :  0.043   0.182   1465
  Planarity :  0.003   0.032   1611
  Dihedral  :  6.694  80.890   1376
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.04 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.26), residues: 1129
  helix:  0.02 (0.24), residues: 479
  sheet: -1.34 (0.42), residues: 159
  loop : -1.52 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 135 
 TYR   0.014   0.001   TYR C 122 
 PHE   0.024   0.001   PHE A 775 
 TRP   0.013   0.001   TRP A 323 
 HIS   0.005   0.001   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9559)
  covalent geometry    : angle       0.58312 (12961)
  SS BOND              : bond        0.00399 (    3)
  SS BOND              : angle       0.94443 (    6)
  hydrogen bonds       : bond        0.03742 (  331)
  hydrogen bonds       : angle       4.26656 (  936)
  link_ALPHA1-4        : bond        0.01929 (    1)
  link_ALPHA1-4        : angle       4.57772 (    3)
  link_BETA1-4         : bond        0.00266 (    1)
  link_BETA1-4         : angle       0.45085 (    3)
  link_NAG-ASN         : bond        0.00209 (    3)
  link_NAG-ASN         : angle       2.47010 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 TRP cc_start: 0.8145 (t60) cc_final: 0.7829 (t-100)
REVERT: A  145 ASP cc_start: 0.8256 (p0) cc_final: 0.7825 (p0)
REVERT: A  399 GLU cc_start: 0.8701 (tt0) cc_final: 0.8085 (mt-10)
REVERT: A  747 TYR cc_start: 0.7102 (m-80) cc_final: 0.6386 (m-80)
REVERT: A  840 GLN cc_start: 0.8434 (tp-100) cc_final: 0.8106 (tp40)
REVERT: A  844 ASN cc_start: 0.8474 (m-40) cc_final: 0.8195 (m-40)
REVERT: A  851 LYS cc_start: 0.7794 (mmtm) cc_final: 0.7248 (mmmm)
REVERT: A  877 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8087 (t80)
REVERT: A  882 LEU cc_start: 0.8729 (tp) cc_final: 0.8348 (tt)
REVERT: A  910 MET cc_start: 0.8772 (mmm) cc_final: 0.8345 (tpt)
REVERT: A  950 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7710 (mtm)
REVERT: A 1014 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7476 (t0)
REVERT: A 1050 GLN cc_start: 0.9114 (pp30) cc_final: 0.8790 (pp30)
REVERT: C  310 MET cc_start: 0.8986 (tmm) cc_final: 0.8502 (tmm)
  outliers start: 33
  outliers final: 28
  residues processed: 171
  average time/residue: 0.0916
  time to fit residues: 22.6328
Evaluate side-chains
  173 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  306 CYS
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue  950 MET
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1014 ASP
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  345 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 107 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0770
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.164452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.148337 restraints weight = 10767.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.144659 restraints weight = 14816.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.143104 restraints weight = 18036.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.142471 restraints weight = 18833.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.142657 restraints weight = 15087.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9567  Z= 0.120
  Angle     :  0.587   8.400  12982  Z= 0.289
  Chirality :  0.043   0.182   1465
  Planarity :  0.003   0.048   1611
  Dihedral  :  6.554  80.954   1376
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.63 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.26), residues: 1129
  helix:  0.06 (0.24), residues: 485
  sheet: -1.39 (0.42), residues: 169
  loop : -1.54 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 135 
 TYR   0.017   0.001   TYR C 122 
 PHE   0.021   0.001   PHE A1039 
 TRP   0.012   0.001   TRP A 323 
 HIS   0.005   0.001   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9559)
  covalent geometry    : angle       0.57903 (12961)
  SS BOND              : bond        0.00363 (    3)
  SS BOND              : angle       0.80496 (    6)
  hydrogen bonds       : bond        0.03741 (  331)
  hydrogen bonds       : angle       4.24569 (  936)
  link_ALPHA1-4        : bond        0.01764 (    1)
  link_ALPHA1-4        : angle       4.53585 (    3)
  link_BETA1-4         : bond        0.00459 (    1)
  link_BETA1-4         : angle       0.49363 (    3)
  link_NAG-ASN         : bond        0.00240 (    3)
  link_NAG-ASN         : angle       2.49842 (    9)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 144
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  111 TRP cc_start: 0.8193 (t60) cc_final: 0.7946 (t-100)
REVERT: A  145 ASP cc_start: 0.8031 (p0) cc_final: 0.7694 (p0)
REVERT: A  399 GLU cc_start: 0.8684 (tt0) cc_final: 0.8027 (mt-10)
REVERT: A  747 TYR cc_start: 0.7231 (m-80) cc_final: 0.6509 (m-80)
REVERT: A  840 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8070 (tp40)
REVERT: A  844 ASN cc_start: 0.8431 (m-40) cc_final: 0.8162 (m-40)
REVERT: A  851 LYS cc_start: 0.7770 (mmtm) cc_final: 0.7212 (mmmm)
REVERT: A  877 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8097 (t80)
REVERT: A  882 LEU cc_start: 0.8685 (tp) cc_final: 0.8322 (tt)
REVERT: A  950 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7685 (mtm)
REVERT: A 1014 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7511 (t0)
REVERT: A 1050 GLN cc_start: 0.9085 (pp30) cc_final: 0.8756 (pp30)
REVERT: C  310 MET cc_start: 0.8977 (tmm) cc_final: 0.8498 (tmm)
  outliers start: 32
  outliers final: 29
  residues processed: 163
  average time/residue: 0.0919
  time to fit residues: 21.6165
Evaluate side-chains
  171 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  306 CYS
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  822 SER
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue  950 MET
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1014 ASP
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  336 SER
Chi-restraints excluded: chain C residue  345 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0170
   chunk 95 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   overall best weight:    1.8022

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

Flipped N/Q/H residues before XYZ refinement:
A 716 HIS
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.161656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.137120 restraints weight = 10720.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.136256 restraints weight = 15521.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.136309 restraints weight = 14402.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.135641 restraints weight = 12354.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.135886 restraints weight = 10880.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   9567  Z= 0.165
  Angle     :  0.625   8.390  12982  Z= 0.309
  Chirality :  0.044   0.179   1465
  Planarity :  0.004   0.053   1611
  Dihedral  :  6.616  80.911   1376
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 21.93 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.25), residues: 1129
  helix: -0.07 (0.24), residues: 485
  sheet: -1.43 (0.42), residues: 169
  loop : -1.62 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 135 
 TYR   0.016   0.001   TYR C 122 
 PHE   0.028   0.001   PHE A 775 
 TRP   0.014   0.001   TRP A 323 
 HIS   0.005   0.001   HIS C 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9559)
  covalent geometry    : angle       0.61779 (12961)
  SS BOND              : bond        0.00446 (    3)
  SS BOND              : angle       0.92639 (    6)
  hydrogen bonds       : bond        0.04073 (  331)
  hydrogen bonds       : angle       4.34651 (  936)
  link_ALPHA1-4        : bond        0.01872 (    1)
  link_ALPHA1-4        : angle       4.48632 (    3)
  link_BETA1-4         : bond        0.00283 (    1)
  link_BETA1-4         : angle       0.62535 (    3)
  link_NAG-ASN         : bond        0.00143 (    3)
  link_NAG-ASN         : angle       2.42030 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1440.22 seconds
wall clock time: 25 minutes 45.27 seconds (1545.27 seconds total)