Starting phenix.real_space_refine
on Fri Feb 14 01:38:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bsw_30169/02_2025/7bsw_30169_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bsw_30169/02_2025/7bsw_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bsw_30169/02_2025/7bsw_30169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bsw_30169/02_2025/7bsw_30169.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bsw_30169/02_2025/7bsw_30169_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bsw_30169/02_2025/7bsw_30169_trim.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.58, per 1000 atoms: 0.60
  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: 2.99
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.04
  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: 2.88

  Time building geometry restraints manager: 3.37 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:             0.170
  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:          0.280
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     24.360
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.200
-------------------------------------------------------------------------------
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      :  0.005   0.115   9559  Z= 0.314
  Angle     :  1.225  70.538  12961  Z= 0.602
  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 : 37.17
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.013   0.001   TRP A 323 
 HIS   0.005   0.001   HIS C 348 
 PHE   0.012   0.001   PHE A 884 
 TYR   0.015   0.001   TYR C 350 
 ARG   0.005   0.000   ARG A 723 

*********************** 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  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  352 ASN cc_start: 0.7848 (t0) cc_final: 0.7585 (t0)
REVERT: A  381 TYR cc_start: 0.7636 (t80) cc_final: 0.7287 (t80)
REVERT: A  399 GLU cc_start: 0.8819 (tt0) cc_final: 0.8579 (mt-10)
REVERT: A  826 GLU cc_start: 0.8349 (tp30) cc_final: 0.7988 (tp30)
REVERT: A  914 CYS cc_start: 0.8052 (m) cc_final: 0.7751 (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: 0.8611 (p90) cc_final: 0.8410 (p90)
REVERT: C  310 MET cc_start: 0.8525 (ttp) cc_final: 0.7885 (tmm)
  outliers start: 7
  outliers final: 2
  residues processed: 231
  average time/residue: 0.2557
  time to fit residues: 79.4039
Evaluate side-chains
  145 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
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 95 optimal weight:    0.3980
   chunk 85 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 65 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 653 GLN
A 716 HIS
A 744 HIS
A 828 HIS
A 862 HIS
A 864 HIS
A1089 ASN
C  36 GLN
C 129 GLN
C 347 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.163821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.153344 restraints weight = 10701.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.139040 restraints weight = 18017.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.137798 restraints weight = 15851.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9559  Z= 0.338
  Angle     :  0.722   8.185  12961  Z= 0.365
  Chirality :  0.049   0.194   1465
  Planarity :  0.004   0.031   1611
  Dihedral  : 12.730 103.102   1381
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 12.78 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.91 (0.22), residues: 1129
  helix: -1.90 (0.21), residues: 477
  sheet: -3.80 (0.31), residues: 158
  loop : -2.77 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 323 
 HIS   0.009   0.002   HIS C 302 
 PHE   0.021   0.002   PHE A1075 
 TYR   0.016   0.002   TYR A 879 
 ARG   0.004   0.001   ARG C 215 

*********************** 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
  196 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 170
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7367 (mmmt)
REVERT: A  747 TYR cc_start: 0.7018 (m-80) cc_final: 0.6475 (m-80)
REVERT: A  826 GLU cc_start: 0.8557 (tp30) cc_final: 0.8164 (tp30)
REVERT: A  877 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8081 (t80)
REVERT: A  914 CYS cc_start: 0.8454 (m) cc_final: 0.8172 (m)
REVERT: A  975 TYR cc_start: 0.9184 (t80) cc_final: 0.8850 (t80)
REVERT: A 1014 ASP cc_start: 0.8630 (m-30) cc_final: 0.8377 (t0)
REVERT: A 1050 GLN cc_start: 0.8918 (pp30) cc_final: 0.8286 (pp30)
REVERT: C  310 MET cc_start: 0.8639 (ttp) cc_final: 0.8259 (tmm)
  outliers start: 26
  outliers final: 18
  residues processed: 184
  average time/residue: 0.2196
  time to fit residues: 58.0603
Evaluate side-chains
  178 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
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  127 ILE
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  264 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  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   50 VAL
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 56 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 6 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 95 optimal weight:    0.5980
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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
C 347 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.162497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 103)---------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.135114 restraints weight = 10760.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.132586 restraints weight = 12567.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.131169 restraints weight = 8399.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9559  Z= 0.212
  Angle     :  0.621   7.621  12961  Z= 0.312
  Chirality :  0.044   0.183   1465
  Planarity :  0.004   0.034   1611
  Dihedral  :  9.839  85.263   1376
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.44 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.23), residues: 1129
  helix: -1.21 (0.23), residues: 479
  sheet: -3.20 (0.33), residues: 158
  loop : -2.37 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 323 
 HIS   0.007   0.001   HIS C 302 
 PHE   0.015   0.001   PHE A1039 
 TYR   0.016   0.001   TYR A 108 
 ARG   0.003   0.000   ARG C 161 

*********************** 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
  195 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 162
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7161 (mmmt)
REVERT: A  366 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: A  698 LEU cc_start: 0.8313 (mt) cc_final: 0.7930 (tp)
REVERT: A  826 GLU cc_start: 0.8656 (tp30) cc_final: 0.8293 (tp30)
REVERT: A  877 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8137 (t80)
REVERT: A  910 MET cc_start: 0.8512 (mmm) cc_final: 0.8287 (mmm)
REVERT: A  933 ASP cc_start: 0.7985 (m-30) cc_final: 0.7783 (m-30)
REVERT: A 1014 ASP cc_start: 0.8639 (m-30) cc_final: 0.8420 (t0)
REVERT: A 1050 GLN cc_start: 0.8981 (pp30) cc_final: 0.8431 (pp30)
REVERT: C  310 MET cc_start: 0.8521 (ttp) cc_final: 0.8145 (tmm)
  outliers start: 33
  outliers final: 19
  residues processed: 180
  average time/residue: 0.1977
  time to fit residues: 51.5613
Evaluate side-chains
  167 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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  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  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  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 101 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 87 optimal weight:    7.9990
   chunk 109 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 844 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 = 0.3709 r_free = 0.3709 target = 0.154933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.129019 restraints weight = 10987.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.127379 restraints weight = 14621.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.128370 restraints weight = 13903.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   9559  Z= 0.423
  Angle     :  0.747  10.203  12961  Z= 0.373
  Chirality :  0.049   0.192   1465
  Planarity :  0.004   0.033   1611
  Dihedral  :  9.154  83.253   1376
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 16.13 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.23), residues: 1129
  helix: -1.22 (0.22), residues: 477
  sheet: -3.04 (0.34), residues: 158
  loop : -2.32 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 323 
 HIS   0.007   0.002   HIS A1023 
 PHE   0.028   0.002   PHE A1075 
 TYR   0.016   0.002   TYR C 350 
 ARG   0.003   0.000   ARG A 206 

*********************** 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
  203 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 155
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 TRP cc_start: 0.8166 (t60) cc_final: 0.7786 (t-100)
REVERT: A  174 THR cc_start: 0.9566 (OUTLIER) cc_final: 0.9366 (t)
REVERT: A  366 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8142 (tm-30)
REVERT: A  826 GLU cc_start: 0.8761 (tp30) cc_final: 0.8519 (tp30)
REVERT: A  877 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8126 (t80)
REVERT: A  950 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8020 (mtm)
REVERT: A 1014 ASP cc_start: 0.8710 (m-30) cc_final: 0.8390 (t0)
REVERT: A 1050 GLN cc_start: 0.9072 (pp30) cc_final: 0.8516 (pp30)
REVERT: C  310 MET cc_start: 0.8833 (ttp) cc_final: 0.8250 (tmm)
  outliers start: 48
  outliers final: 31
  residues processed: 183
  average time/residue: 0.1889
  time to fit residues: 49.9579
Evaluate side-chains
  177 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
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  174 THR
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  295 TYR
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  717 GLU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  860 LEU
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 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  183 LEU
Chi-restraints excluded: chain C residue  212 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 84 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 10 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 111 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A 844 ASN
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.164456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.153167 restraints weight = 10729.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.149969 restraints weight = 17172.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.148700 restraints weight = 20804.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9559  Z= 0.174
  Angle     :  0.605   9.700  12961  Z= 0.298
  Chirality :  0.043   0.185   1465
  Planarity :  0.003   0.034   1611
  Dihedral  :  8.216  82.111   1376
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.06 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.24), residues: 1129
  helix: -0.64 (0.24), residues: 469
  sheet: -2.67 (0.36), residues: 163
  loop : -2.06 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 323 
 HIS   0.006   0.001   HIS C 302 
 PHE   0.014   0.001   PHE A1039 
 TYR   0.016   0.001   TYR A 722 
 ARG   0.003   0.000   ARG A 113 

*********************** 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
  189 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 159
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 TYR cc_start: 0.6776 (m-10) cc_final: 0.6432 (m-10)
REVERT: A  145 ASP cc_start: 0.8013 (p0) cc_final: 0.7758 (p0)
REVERT: A  174 THR cc_start: 0.9576 (OUTLIER) cc_final: 0.9365 (t)
REVERT: A  399 GLU cc_start: 0.8750 (tt0) cc_final: 0.8270 (mt-10)
REVERT: A  747 TYR cc_start: 0.6993 (m-80) cc_final: 0.6781 (m-80)
REVERT: A  877 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8148 (t80)
REVERT: A  910 MET cc_start: 0.8802 (mmm) cc_final: 0.8515 (mmm)
REVERT: A 1014 ASP cc_start: 0.8521 (m-30) cc_final: 0.8275 (t0)
REVERT: A 1050 GLN cc_start: 0.9007 (pp30) cc_final: 0.8675 (pp30)
REVERT: C  310 MET cc_start: 0.8707 (ttp) cc_final: 0.8321 (tmm)
REVERT: C  322 ASN cc_start: 0.8086 (t0) cc_final: 0.6466 (p0)
  outliers start: 30
  outliers final: 22
  residues processed: 177
  average time/residue: 0.2099
  time to fit residues: 52.7937
Evaluate side-chains
  162 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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  141 ILE
Chi-restraints excluded: chain A residue  174 THR
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  717 GLU
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 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  212 VAL
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 87 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.153053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.125350 restraints weight = 11039.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.123737 restraints weight = 15032.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.124665 restraints weight = 15283.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9559  Z= 0.310
  Angle     :  0.649   8.566  12961  Z= 0.323
  Chirality :  0.045   0.182   1465
  Planarity :  0.004   0.031   1611
  Dihedral  :  7.968  82.341   1376
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.04 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.24), residues: 1129
  helix: -0.74 (0.23), residues: 471
  sheet: -2.56 (0.36), residues: 163
  loop : -2.02 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 323 
 HIS   0.005   0.001   HIS C 302 
 PHE   0.017   0.002   PHE A 221 
 TYR   0.015   0.002   TYR A 722 
 ARG   0.004   0.000   ARG A 135 

*********************** 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
  183 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 144
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  111 TRP cc_start: 0.8151 (t60) cc_final: 0.7779 (t-100)
REVERT: A  145 ASP cc_start: 0.8230 (p0) cc_final: 0.7935 (p0)
REVERT: A  174 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9292 (t)
REVERT: A  399 GLU cc_start: 0.8762 (tt0) cc_final: 0.8312 (mt-10)
REVERT: A  877 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8019 (t80)
REVERT: A  910 MET cc_start: 0.8760 (mmm) cc_final: 0.8531 (mmm)
REVERT: A  950 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8037 (mtm)
REVERT: A 1014 ASP cc_start: 0.8661 (m-30) cc_final: 0.8346 (t0)
REVERT: A 1050 GLN cc_start: 0.9101 (pp30) cc_final: 0.8720 (pp30)
  outliers start: 39
  outliers final: 31
  residues processed: 168
  average time/residue: 0.2019
  time to fit residues: 49.0323
Evaluate side-chains
  174 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 140
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
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  174 THR
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  680 THR
Chi-restraints excluded: chain A residue  717 GLU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  822 SER
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 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  212 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 54 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0060
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
A  59 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 = 0.3787 r_free = 0.3787 target = 0.163348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.151825 restraints weight = 10832.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.139569 restraints weight = 17355.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.137809 restraints weight = 15957.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   9559  Z= 0.217
  Angle     :  0.612   9.878  12961  Z= 0.303
  Chirality :  0.043   0.185   1465
  Planarity :  0.004   0.054   1611
  Dihedral  :  7.458  80.606   1376
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.24), residues: 1129
  helix: -0.49 (0.24), residues: 473
  sheet: -2.31 (0.39), residues: 163
  loop : -1.88 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 260 
 HIS   0.005   0.001   HIS C 302 
 PHE   0.021   0.001   PHE A1039 
 TYR   0.021   0.001   TYR A 722 
 ARG   0.003   0.000   ARG A 135 

*********************** 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
  188 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  145 ASP cc_start: 0.8255 (p0) cc_final: 0.7925 (p0)
REVERT: A  174 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9130 (t)
REVERT: A  366 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7927 (tm-30)
REVERT: A  747 TYR cc_start: 0.7006 (m-80) cc_final: 0.6435 (m-80)
REVERT: A  877 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8082 (t80)
REVERT: A  910 MET cc_start: 0.8782 (mmm) cc_final: 0.8566 (mmm)
REVERT: A  950 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7871 (mtm)
REVERT: A 1014 ASP cc_start: 0.8531 (m-30) cc_final: 0.8201 (t0)
REVERT: A 1050 GLN cc_start: 0.9013 (pp30) cc_final: 0.8629 (pp30)
REVERT: C  310 MET cc_start: 0.8926 (tmm) cc_final: 0.8529 (tmm)
  outliers start: 38
  outliers final: 31
  residues processed: 176
  average time/residue: 0.1949
  time to fit residues: 49.9459
Evaluate side-chains
  175 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
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  127 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  174 THR
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  680 THR
Chi-restraints excluded: chain A residue  717 GLU
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 1019 THR
Chi-restraints excluded: chain A residue 1044 ILE
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  208 THR
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  336 SER
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 111 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3813 r_free = 0.3813 target = 0.165850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.154676 restraints weight = 10817.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.142108 restraints weight = 18198.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.139331 restraints weight = 16890.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9559  Z= 0.186
  Angle     :  0.575   8.912  12961  Z= 0.286
  Chirality :  0.042   0.195   1465
  Planarity :  0.004   0.040   1611
  Dihedral  :  6.920  79.406   1376
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 21.53 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.25), residues: 1129
  helix: -0.23 (0.24), residues: 479
  sheet: -2.10 (0.40), residues: 162
  loop : -1.68 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 260 
 HIS   0.004   0.001   HIS C 302 
 PHE   0.020   0.001   PHE A1039 
 TYR   0.013   0.001   TYR C 350 
 ARG   0.006   0.000   ARG A 206 

*********************** 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
  184 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 150
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  145 ASP cc_start: 0.8280 (p0) cc_final: 0.7878 (p0)
REVERT: A  747 TYR cc_start: 0.7212 (m-80) cc_final: 0.6916 (m-80)
REVERT: A  851 LYS cc_start: 0.7839 (mmtm) cc_final: 0.7222 (mmmm)
REVERT: A  877 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8002 (t80)
REVERT: A  882 LEU cc_start: 0.8783 (tp) cc_final: 0.8305 (tt)
REVERT: A  910 MET cc_start: 0.8747 (mmm) cc_final: 0.8545 (mmm)
REVERT: A  927 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8044 (tm-30)
REVERT: A 1050 GLN cc_start: 0.9080 (pp30) cc_final: 0.8779 (pp30)
REVERT: C  310 MET cc_start: 0.8920 (tmm) cc_final: 0.8502 (tmm)
REVERT: C  322 ASN cc_start: 0.8154 (t0) cc_final: 0.6521 (p0)
REVERT: C  343 LEU cc_start: 0.7697 (mp) cc_final: 0.7240 (mp)
  outliers start: 34
  outliers final: 31
  residues processed: 177
  average time/residue: 0.1986
  time to fit residues: 50.5423
Evaluate side-chains
  172 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
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  141 ILE
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  717 GLU
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 1019 THR
Chi-restraints excluded: chain A residue 1044 ILE
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  208 THR
Chi-restraints excluded: chain C residue  212 VAL
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 110 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 109 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  92 ASN
C 131 HIS
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.159966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.150515 restraints weight = 10746.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.138931 restraints weight = 21419.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.134822 restraints weight = 18469.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   9559  Z= 0.354
  Angle     :  0.687   9.473  12961  Z= 0.341
  Chirality :  0.046   0.172   1465
  Planarity :  0.004   0.048   1611
  Dihedral  :  7.157  79.858   1376
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 21.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.25), residues: 1129
  helix: -0.41 (0.23), residues: 473
  sheet: -2.05 (0.39), residues: 167
  loop : -1.74 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 323 
 HIS   0.005   0.002   HIS A1023 
 PHE   0.022   0.002   PHE A1039 
 TYR   0.021   0.002   TYR A 722 
 ARG   0.005   0.000   ARG A 206 

*********************** 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
  177 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 137
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  111 TRP cc_start: 0.8175 (t60) cc_final: 0.7872 (t-100)
REVERT: A  145 ASP cc_start: 0.8302 (p0) cc_final: 0.7974 (p0)
REVERT: A  399 GLU cc_start: 0.8756 (tt0) cc_final: 0.8147 (mt-10)
REVERT: A  747 TYR cc_start: 0.6919 (m-80) cc_final: 0.6548 (m-80)
REVERT: A  790 MET cc_start: 0.9061 (mmm) cc_final: 0.8145 (mmm)
REVERT: A  877 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8101 (t80)
REVERT: A  910 MET cc_start: 0.8780 (mmm) cc_final: 0.8545 (mmm)
REVERT: A  950 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7984 (mtm)
REVERT: A 1014 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7454 (t0)
REVERT: A 1050 GLN cc_start: 0.9167 (pp30) cc_final: 0.8777 (pp30)
REVERT: C  310 MET cc_start: 0.8992 (tmm) cc_final: 0.8509 (tmm)
  outliers start: 40
  outliers final: 33
  residues processed: 164
  average time/residue: 0.1960
  time to fit residues: 46.5099
Evaluate side-chains
  168 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 132
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
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  184 CYS
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  337 VAL
Chi-restraints excluded: chain A residue  391 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  717 GLU
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  860 LEU
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  879 TYR
Chi-restraints excluded: chain A residue  899 GLN
Chi-restraints excluded: chain A residue  936 THR
Chi-restraints excluded: chain A residue  950 MET
Chi-restraints excluded: chain A residue  978 PHE
Chi-restraints excluded: chain A residue 1014 ASP
Chi-restraints excluded: chain A residue 1044 ILE
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  208 THR
Chi-restraints excluded: chain C residue  212 VAL
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 34 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0470
   chunk 111 optimal weight:    5.9990
   chunk 62 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.1084

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

Flipped N/Q/H residues before XYZ refinement:
A 872 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 = 0.3772 r_free = 0.3772 target = 0.161769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.152535 restraints weight = 10983.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.140534 restraints weight = 21331.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.136758 restraints weight = 17921.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9559  Z= 0.286
  Angle     :  0.641   8.958  12961  Z= 0.319
  Chirality :  0.045   0.181   1465
  Planarity :  0.004   0.045   1611
  Dihedral  :  7.014  79.098   1376
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 22.12 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.25), residues: 1129
  helix: -0.28 (0.24), residues: 472
  sheet: -1.96 (0.39), residues: 167
  loop : -1.73 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 323 
 HIS   0.005   0.001   HIS C 302 
 PHE   0.020   0.001   PHE A1039 
 TYR   0.013   0.001   TYR C 350 
 ARG   0.005   0.000   ARG A 206 

********************** 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
  183 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  111 TRP cc_start: 0.8198 (t60) cc_final: 0.7832 (t-100)
REVERT: A  145 ASP cc_start: 0.8273 (p0) cc_final: 0.7906 (p0)
REVERT: A  747 TYR cc_start: 0.6919 (m-80) cc_final: 0.6716 (m-80)
REVERT: A  776 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.7654 (mp)
REVERT: A  790 MET cc_start: 0.9034 (mmm) cc_final: 0.8170 (mmm)
REVERT: A  819 ASN cc_start: 0.9510 (p0) cc_final: 0.9284 (p0)
REVERT: A  877 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8148 (t80)
REVERT: A  910 MET cc_start: 0.8767 (mmm) cc_final: 0.8527 (mmm)
REVERT: A  950 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7972 (mtm)
REVERT: A 1014 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7783 (t0)
REVERT: A 1050 GLN cc_start: 0.9159 (pp30) cc_final: 0.8791 (pp30)
REVERT: C  310 MET cc_start: 0.8971 (tmm) cc_final: 0.8503 (tmm)
  outliers start: 38
  outliers final: 30
  residues processed: 169
  average time/residue: 0.2015
  time to fit residues: 48.7524
Evaluate side-chains
  175 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
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  127 ILE
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  295 TYR
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  717 GLU
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  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  978 PHE
Chi-restraints excluded: chain A residue 1014 ASP
Chi-restraints excluded: chain A residue 1044 ILE
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  208 THR
Chi-restraints excluded: chain C residue  212 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 87 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 777 GLN
** 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 = 0.3743 r_free = 0.3743 target = 0.158705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.149523 restraints weight = 10947.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.136791 restraints weight = 20778.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.132496 restraints weight = 17801.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9559  Z= 0.390
  Angle     :  0.718   9.321  12961  Z= 0.358
  Chirality :  0.047   0.175   1465
  Planarity :  0.004   0.047   1611
  Dihedral  :  7.204  79.218   1376
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.22 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.25), residues: 1129
  helix: -0.49 (0.23), residues: 476
  sheet: -2.13 (0.38), residues: 167
  loop : -1.78 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 323 
 HIS   0.006   0.002   HIS A1023 
 PHE   0.021   0.002   PHE A1039 
 TYR   0.013   0.002   TYR A 879 
 ARG   0.004   0.000   ARG A 133 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2600.96 seconds
wall clock time: 47 minutes 34.43 seconds (2854.43 seconds total)