Starting phenix.real_space_refine
on Wed Feb  4 07:07:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vsg_32110/02_2026/7vsg_32110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vsg_32110/02_2026/7vsg_32110.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vsg_32110/02_2026/7vsg_32110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vsg_32110/02_2026/7vsg_32110.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vsg_32110/02_2026/7vsg_32110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vsg_32110/02_2026/7vsg_32110.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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
     P       1      5.49       5
     S      45      5.16       5
     Be      1      3.05       5
     C    6072      2.51       5
     N    1503      2.21       5
     O    1699      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9324
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 815, 6600
          Classifications: {'peptide': 815}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 792}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
    Chain: "B"
      Number of atoms: 2604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2604
          Classifications: {'peptide': 324}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298}
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 54
          Unusual residues: {'17F': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 27
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.42, per 1000 atoms: 0.26
  Number of scatterers: 9324
  At special positions: 0
  Unit cell: (102.09, 99.6, 135.29, 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
     F       3      9.00
     O    1699      8.00
     N    1503      7.00
     C    6072      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  91 " - pdb=" SG  CYS B 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 157 " - pdb=" SG  CYS B 171 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-4
      " NAG D   2 " - " MAN D   3 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG B 401 " - " ASN B 107 "
      " NAG B 402 " - " ASN B 294 "
      " NAG D   1 " - " ASN B 180 "
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 520.7 milliseconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 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:
      45 helices and 10 sheets defined
      51.1% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 66
      removed outlier: 3.814A  pdb=" N   ARG A  66 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 82
    Processing helix  chain 'A' and resid 87 through 122
      removed outlier: 3.699A  pdb=" N   SER A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      Proline residue:  A  94  - end of helix
    Processing helix  chain 'A' and resid 137 through 141
    Processing helix  chain 'A' and resid 166 through 168
      No H-bonds generated for 'chain 'A' and resid 166 through 168'
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 282 through 315
    Processing helix  chain 'A' and resid 328 through 333
    Processing helix  chain 'A' and resid 335 through 351
    Processing helix  chain 'A' and resid 352 through 355
    Processing helix  chain 'A' and resid 356 through 371
      removed outlier: 3.969A  pdb=" N   TYR A 360 " --> pdb=" O   PRO A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 377
      removed outlier: 3.992A  pdb=" N   SER A 375 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 403
      removed outlier: 3.770A  pdb=" N   LEU A 400 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 403 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 666
    Processing helix  chain 'A' and resid 677 through 688
      removed outlier: 4.552A  pdb=" N   SER A 683 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   THR A 684 " --> pdb=" O   THR A 680 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   CYS A 685 " --> pdb=" O   ALA A 681 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TYR A 686 " --> pdb=" O   LYS A 682 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA A 687 " --> pdb=" O   SER A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 726
      removed outlier: 3.897A  pdb=" N   GLU A 712 " --> pdb=" O   SER A 708 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG A 723 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS A 724 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS A 725 " --> pdb=" O   GLU A 721 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU A 726 " --> pdb=" O   TYR A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 745
      No H-bonds generated for 'chain 'A' and resid 743 through 745'
    Processing helix  chain 'A' and resid 752 through 762
    Processing helix  chain 'A' and resid 763 through 766
      removed outlier: 3.532A  pdb=" N   SER A 766 " --> pdb=" O   SER A 763 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 763 through 766'
    Processing helix  chain 'A' and resid 770 through 780
    Processing helix  chain 'A' and resid 791 through 804
    Processing helix  chain 'A' and resid 820 through 827
    Processing helix  chain 'A' and resid 839 through 845
      removed outlier: 3.890A  pdb=" N   ASN A 844 " --> pdb=" O   GLN A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 895
      removed outlier: 4.190A  pdb=" N   LYS A 857 " --> pdb=" O   LYS A 853 " (cutoff:3.500A)
      Proline residue:  A 887  - end of helix
      removed outlier: 3.669A  pdb=" N   GLN A 892 " --> pdb=" O   GLN A 888 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   PHE A 893 " --> pdb=" O   PHE A 889 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   PHE A 894 " --> pdb=" O   LEU A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 914
      removed outlier: 4.697A  pdb=" N   ASN A 912 " --> pdb=" O   LEU A 908 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ILE A 913 " --> pdb=" O   THR A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 926
      removed outlier: 3.968A  pdb=" N   ILE A 920 " --> pdb=" O   THR A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 938
      removed outlier: 3.763A  pdb=" N   THR A 936 " --> pdb=" O   ILE A 932 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 944
      removed outlier: 3.554A  pdb=" N   TYR A 942 " --> pdb=" O   PRO A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 951
    Processing helix  chain 'A' and resid 952 through 978
    Processing helix  chain 'A' and resid 991 through 1015
    Processing helix  chain 'A' and resid 1019 through 1041
    Processing helix  chain 'A' and resid 1055 through 1062
    Processing helix  chain 'A' and resid 1063 through 1090
      Proline residue:  A1080  - end of helix
      removed outlier: 3.552A  pdb=" N   ASN A1089 " --> pdb=" O   ILE A1085 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   VAL A1090 " --> pdb=" O   VAL A1086 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 75
      Proline residue:  B  52  - end of helix
      removed outlier: 3.692A  pdb=" N   PHE B  55 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      Proline residue:  B  63  - end of helix
      removed outlier: 3.519A  pdb=" N   THR B  71 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 96
    Processing helix  chain 'B' and resid 131 through 136
    Processing helix  chain 'B' and resid 139 through 144
    Processing helix  chain 'B' and resid 146 through 152
      removed outlier: 3.690A  pdb=" N   LEU B 151 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASN B 152 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 177
    Processing helix  chain 'B' and resid 206 through 212
    Processing helix  chain 'B' and resid 222 through 227
      removed outlier: 3.570A  pdb=" N   ARG B 226 " --> pdb=" O   ASN B 222 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 222 through 227'
    Processing helix  chain 'B' and resid 239 through 243
      removed outlier: 4.185A  pdb=" N   LEU B 243 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 262
    Processing helix  chain 'B' and resid 322 through 349
      removed outlier: 4.227A  pdb=" N   GLY B 326 " --> pdb=" O   ASN B 322 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
    Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 136
      removed outlier: 4.549A  pdb=" N   TYR A 126 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   TYR A 258 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 188
    Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382
      removed outlier: 3.557A  pdb=" N   GLU A 387 " --> pdb=" O   ASP A 382 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391
      removed outlier: 3.507A  pdb=" N   LEU A 390 " --> pdb=" O   SER A 848 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 669 through 671
      removed outlier: 6.656A  pdb=" N   THR A 811 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   ILE A 831 " --> pdb=" O   THR A 811 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   SER A 813 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 696 through 700
      removed outlier: 9.042A  pdb=" N   LEU A 786 " --> pdb=" O   TYR A 747 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LEU A 749 " --> pdb=" O   LEU A 786 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 81
      removed outlier: 7.323A  pdb=" N   VAL B 118 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   LEU B 275 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   MET B 120 " --> pdb=" O   TYR B 273 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 109
      removed outlier: 4.766A  pdb=" N   ARG B 290 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE B 188 " --> pdb=" O   ARG B 290 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU B 184 " --> pdb=" O   ASN B 294 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 162 through 163

    431 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.16 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: 1547
        1.32 -     1.45: 2610
        1.45 -     1.57: 5323
        1.57 -     1.69: 2
        1.69 -     1.81: 71
  Bond restraints: 9553
  Sorted by residual:
  bond pdb=" F3  BFD A 409 "
       pdb="BE   BFD A 409 "
    ideal  model  delta    sigma   weight residual
    1.529  1.765 -0.236 2.00e-02 2.50e+03 1.39e+02
  bond pdb=" F2  BFD A 409 "
       pdb="BE   BFD A 409 "
    ideal  model  delta    sigma   weight residual
    1.535  1.752 -0.217 2.00e-02 2.50e+03 1.17e+02
  bond pdb=" F1  BFD A 409 "
       pdb="BE   BFD A 409 "
    ideal  model  delta    sigma   weight residual
    1.542  1.755 -0.213 2.00e-02 2.50e+03 1.14e+02
  bond pdb=" CG  BFD A 409 "
       pdb=" OD1 BFD A 409 "
    ideal  model  delta    sigma   weight residual
    1.269  1.454 -0.185 2.00e-02 2.50e+03 8.51e+01
  bond pdb=" C1  MAN D   3 "
       pdb=" O5  MAN D   3 "
    ideal  model  delta    sigma   weight residual
    1.399  1.445 -0.046 2.00e-02 2.50e+03 5.38e+00
  ... (remaining 9548 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.41: 12909
        3.41 -     6.81: 33
        6.81 -    10.22: 6
       10.22 -    13.63: 1
       13.63 -    17.03: 4
  Bond angle restraints: 12953
  Sorted by residual:
  angle pdb=" O   BFD A 409 "
        pdb=" C   BFD A 409 "
        pdb=" N   LYS A 410 "
      ideal   model   delta    sigma   weight residual
     123.00  134.67  -11.67 1.60e+00 3.91e-01 5.32e+01
  angle pdb=" F2  BFD A 409 "
        pdb="BE   BFD A 409 "
        pdb=" F3  BFD A 409 "
      ideal   model   delta    sigma   weight residual
     112.60   95.57   17.03 3.00e+00 1.11e-01 3.22e+01
  angle pdb=" CA  BFD A 409 "
        pdb=" C   BFD A 409 "
        pdb=" O   BFD A 409 "
      ideal   model   delta    sigma   weight residual
     120.80  111.22    9.58 1.70e+00 3.46e-01 3.18e+01
  angle pdb=" OD1 BFD A 409 "
        pdb="BE   BFD A 409 "
        pdb=" F1  BFD A 409 "
      ideal   model   delta    sigma   weight residual
     102.38  118.58  -16.20 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" F1  BFD A 409 "
        pdb="BE   BFD A 409 "
        pdb=" F3  BFD A 409 "
      ideal   model   delta    sigma   weight residual
     111.29   95.46   15.83 3.00e+00 1.11e-01 2.79e+01
  ... (remaining 12948 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.37: 5367
       24.37 -    48.74: 284
       48.74 -    73.12: 37
       73.12 -    97.49: 21
       97.49 -   121.86: 21
  Dihedral angle restraints: 5730
    sinusoidal: 2387
      harmonic: 3343
  Sorted by residual:
  dihedral pdb=" CB  CYS B  91 "
           pdb=" SG  CYS B  91 "
           pdb=" SG  CYS B 104 "
           pdb=" CB  CYS B 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.03  -63.03     1      1.00e+01 1.00e-02 5.25e+01
  dihedral pdb=" C6  17F A1101 "
           pdb=" C4  17F A1101 "
           pdb=" C5  17F A1101 "
           pdb=" O6  17F A1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      67.29 -170.85 -121.86     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" C2  NAG D   2 "
           pdb=" C3  NAG D   2 "
           pdb=" C4  NAG D   2 "
           pdb=" O4  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   61.42  113.69     1      3.00e+01 1.11e-03 1.50e+01
  ... (remaining 5727 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1297
       0.060 -    0.120: 158
       0.120 -    0.180: 8
       0.180 -    0.240: 1
       0.240 -    0.300: 2
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" C1  NAG B 401 "
            pdb=" ND2 ASN B 107 "
            pdb=" C2  NAG B 401 "
            pdb=" O5  NAG B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" C1  NAG B 402 "
            pdb=" ND2 ASN B 294 "
            pdb=" C2  NAG B 402 "
            pdb=" O5  NAG B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B 180 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.292 2.00e-02 2.50e+03   2.43e-01 7.41e+02
        pdb=" C7  NAG D   2 "   -0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.190 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.411 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.213 2.00e-02 2.50e+03   1.81e-01 4.08e+02
        pdb=" C7  NAG D   1 "    0.047 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.038 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.294 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.166 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 402 "    0.175 2.00e-02 2.50e+03   1.45e-01 2.62e+02
        pdb=" C7  NAG B 402 "   -0.049 2.00e-02 2.50e+03
        pdb=" C8  NAG B 402 "    0.129 2.00e-02 2.50e+03
        pdb=" N2  NAG B 402 "   -0.234 2.00e-02 2.50e+03
        pdb=" O7  NAG B 402 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1612 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1002
        2.75 -     3.29: 9576
        3.29 -     3.82: 15411
        3.82 -     4.36: 18766
        4.36 -     4.90: 31272
  Nonbonded interactions: 76027
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 763 "
            pdb=" NZ  LYS A 772 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   LEU A 983 "
            pdb=" OG  SER A1063 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR A 907 "
            pdb=" OG  SER A1037 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   LEU A 758 "
            pdb=" OG  SER A 762 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   PHE A 915 "
            pdb=" OG  SER A1029 "
     model   vdw
     2.268 3.040
  ... (remaining 76022 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:                  0.010
  Normalize map: mean=0, sd=1:             1.190
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.860
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
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   0.236   9561  Z= 0.269
  Angle     :  0.678  17.035  12974  Z= 0.339
  Chirality :  0.041   0.300   1466
  Planarity :  0.010   0.243   1612
  Dihedral  : 17.174 121.862   3565
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.39 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.24), residues: 1126
  helix:  0.59 (0.22), residues: 498
  sheet:  0.69 (0.45), residues: 137
  loop : -1.01 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 135 
 TYR   0.016   0.001   TYR A 318 
 PHE   0.014   0.001   PHE A1047 
 TRP   0.012   0.001   TRP A 313 
 HIS   0.004   0.001   HIS A 864 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 9553)
  covalent geometry    : angle       0.67359 (12953)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       0.64412 (    6)
  hydrogen bonds       : bond        0.25408 (  431)
  hydrogen bonds       : angle       7.97322 ( 1233)
  link_ALPHA1-4        : bond        0.01254 (    1)
  link_ALPHA1-4        : angle       2.49270 (    3)
  link_BETA1-4         : bond        0.00266 (    1)
  link_BETA1-4         : angle       0.94199 (    3)
  link_NAG-ASN         : bond        0.00549 (    3)
  link_NAG-ASN         : angle       2.56447 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   45 ILE cc_start: 0.6976 (pt) cc_final: 0.6121 (pt)
REVERT: A  145 ASP cc_start: 0.8244 (t70) cc_final: 0.7882 (t70)
REVERT: A  285 GLU cc_start: 0.7538 (tt0) cc_final: 0.7326 (tt0)
REVERT: A  395 ASP cc_start: 0.7834 (m-30) cc_final: 0.7477 (t0)
REVERT: A  816 ASP cc_start: 0.6971 (p0) cc_final: 0.6537 (p0)
REVERT: A  846 ASP cc_start: 0.8086 (m-30) cc_final: 0.7827 (m-30)
REVERT: B   31 THR cc_start: 0.8069 (m) cc_final: 0.7837 (p)
REVERT: B  197 ILE cc_start: 0.8262 (mp) cc_final: 0.7750 (tp)
REVERT: B  337 PHE cc_start: 0.7258 (t80) cc_final: 0.6943 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1029
  time to fit residues: 23.8996
Evaluate side-chains
  111 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    1.6182

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 126 ASN
B 131 HIS
B 347 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.161671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125944 restraints weight = 13201.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125336 restraints weight = 14530.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.127175 restraints weight = 12316.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.127423 restraints weight = 8725.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.127895 restraints weight = 8206.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9561  Z= 0.159
  Angle     :  0.638  10.775  12974  Z= 0.320
  Chirality :  0.044   0.270   1466
  Planarity :  0.004   0.044   1612
  Dihedral  : 15.355 125.743   1384
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  8.17 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.25), residues: 1126
  helix:  1.14 (0.23), residues: 501
  sheet:  0.31 (0.42), residues: 150
  loop : -0.97 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 133 
 TYR   0.013   0.002   TYR A 318 
 PHE   0.018   0.002   PHE A 775 
 TRP   0.013   0.001   TRP A 313 
 HIS   0.007   0.001   HIS A 862 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9553)
  covalent geometry    : angle       0.63030 (12953)
  SS BOND              : bond        0.00600 (    3)
  SS BOND              : angle       1.13740 (    6)
  hydrogen bonds       : bond        0.05628 (  431)
  hydrogen bonds       : angle       5.32545 ( 1233)
  link_ALPHA1-4        : bond        0.00347 (    1)
  link_ALPHA1-4        : angle       5.32867 (    3)
  link_BETA1-4         : bond        0.00217 (    1)
  link_BETA1-4         : angle       1.75044 (    3)
  link_NAG-ASN         : bond        0.00575 (    3)
  link_NAG-ASN         : angle       1.96063 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  145 ASP cc_start: 0.8289 (t70) cc_final: 0.7997 (t70)
REVERT: A  395 ASP cc_start: 0.7743 (m-30) cc_final: 0.7467 (t0)
REVERT: A  790 MET cc_start: 0.8640 (mmm) cc_final: 0.8293 (mtp)
REVERT: A  800 ARG cc_start: 0.6987 (ttm170) cc_final: 0.6520 (ttm110)
REVERT: A  816 ASP cc_start: 0.7096 (p0) cc_final: 0.6746 (p0)
REVERT: B  197 ILE cc_start: 0.8294 (mp) cc_final: 0.7791 (tp)
REVERT: B  337 PHE cc_start: 0.7298 (t80) cc_final: 0.6822 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 128
  average time/residue: 0.0894
  time to fit residues: 16.5552
Evaluate side-chains
  111 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  289 ASN
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 99 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 GLN
A 314 GLN
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 GLN
B 126 ASN
B 347 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.156710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.120283 restraints weight = 13407.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.118923 restraints weight = 13856.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.120422 restraints weight = 14929.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121341 restraints weight = 9088.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.121692 restraints weight = 8087.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   9561  Z= 0.256
  Angle     :  0.707  10.836  12974  Z= 0.354
  Chirality :  0.048   0.326   1466
  Planarity :  0.005   0.042   1612
  Dihedral  : 12.435 119.896   1384
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.30 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.24), residues: 1126
  helix:  0.80 (0.23), residues: 500
  sheet:  0.13 (0.43), residues: 146
  loop : -1.15 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 133 
 TYR   0.017   0.002   TYR A 311 
 PHE   0.018   0.002   PHE A1036 
 TRP   0.014   0.002   TRP A1067 
 HIS   0.010   0.002   HIS A1023 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 ( 9553)
  covalent geometry    : angle       0.70275 (12953)
  SS BOND              : bond        0.00543 (    3)
  SS BOND              : angle       1.15450 (    6)
  hydrogen bonds       : bond        0.05685 (  431)
  hydrogen bonds       : angle       5.23231 ( 1233)
  link_ALPHA1-4        : bond        0.00621 (    1)
  link_ALPHA1-4        : angle       3.53441 (    3)
  link_BETA1-4         : bond        0.00992 (    1)
  link_BETA1-4         : angle       1.46628 (    3)
  link_NAG-ASN         : bond        0.00448 (    3)
  link_NAG-ASN         : angle       2.10042 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ASP cc_start: 0.8307 (t70) cc_final: 0.7944 (t70)
REVERT: A  395 ASP cc_start: 0.7872 (m-30) cc_final: 0.7625 (t0)
REVERT: A  790 MET cc_start: 0.8693 (mmm) cc_final: 0.8334 (mtp)
REVERT: A  816 ASP cc_start: 0.7256 (p0) cc_final: 0.6795 (p0)
REVERT: A  844 ASN cc_start: 0.7576 (t0) cc_final: 0.7343 (t0)
REVERT: A  851 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7963 (mttm)
REVERT: B  126 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8362 (t0)
REVERT: B  197 ILE cc_start: 0.8370 (mp) cc_final: 0.7896 (tp)
REVERT: B  337 PHE cc_start: 0.7255 (t80) cc_final: 0.6752 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 128
  average time/residue: 0.0972
  time to fit residues: 17.9235
Evaluate side-chains
  120 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  289 ASN
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue 1045 TRP
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  126 ASN
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  329 TYR
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 73 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 2 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 126 ASN
B 130 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.160414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.123568 restraints weight = 13357.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123084 restraints weight = 14005.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124267 restraints weight = 14424.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.125178 restraints weight = 8669.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125512 restraints weight = 7599.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9561  Z= 0.123
  Angle     :  0.589  10.709  12974  Z= 0.287
  Chirality :  0.043   0.257   1466
  Planarity :  0.004   0.042   1612
  Dihedral  : 10.612 122.075   1384
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.88 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.25), residues: 1126
  helix:  1.10 (0.23), residues: 502
  sheet:  0.16 (0.43), residues: 149
  loop : -1.10 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  20 
 TYR   0.012   0.001   TYR A 324 
 PHE   0.017   0.001   PHE A 368 
 TRP   0.014   0.001   TRP A 313 
 HIS   0.004   0.001   HIS A 864 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9553)
  covalent geometry    : angle       0.58447 (12953)
  SS BOND              : bond        0.00408 (    3)
  SS BOND              : angle       0.86214 (    6)
  hydrogen bonds       : bond        0.04588 (  431)
  hydrogen bonds       : angle       4.86989 ( 1233)
  link_ALPHA1-4        : bond        0.01543 (    1)
  link_ALPHA1-4        : angle       3.38937 (    3)
  link_BETA1-4         : bond        0.00329 (    1)
  link_BETA1-4         : angle       1.99473 (    3)
  link_NAG-ASN         : bond        0.00535 (    3)
  link_NAG-ASN         : angle       1.57319 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 PHE cc_start: 0.7489 (m-80) cc_final: 0.7117 (m-80)
REVERT: A  145 ASP cc_start: 0.8345 (t70) cc_final: 0.7978 (t70)
REVERT: A  349 VAL cc_start: 0.8860 (p) cc_final: 0.8326 (m)
REVERT: A  395 ASP cc_start: 0.7866 (m-30) cc_final: 0.7579 (t0)
REVERT: A  790 MET cc_start: 0.8637 (mmm) cc_final: 0.8366 (mtp)
REVERT: A  816 ASP cc_start: 0.7101 (p0) cc_final: 0.6587 (p0)
REVERT: A  851 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7830 (mttm)
REVERT: B  197 ILE cc_start: 0.8307 (mp) cc_final: 0.7935 (tp)
REVERT: B  337 PHE cc_start: 0.7243 (t80) cc_final: 0.6730 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 125
  average time/residue: 0.0941
  time to fit residues: 16.6848
Evaluate side-chains
  110 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  289 ASN
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue 1045 TRP
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  329 TYR
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 881 ASN
B  42 GLN
B 126 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.157167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.120885 restraints weight = 13453.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118275 restraints weight = 15186.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120674 restraints weight = 13668.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121147 restraints weight = 8861.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.121456 restraints weight = 8712.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9561  Z= 0.176
  Angle     :  0.620  10.869  12974  Z= 0.307
  Chirality :  0.044   0.261   1466
  Planarity :  0.004   0.040   1612
  Dihedral  :  9.803 117.134   1384
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.26 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.25), residues: 1126
  helix:  1.06 (0.23), residues: 502
  sheet:  0.16 (0.47), residues: 132
  loop : -1.17 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 133 
 TYR   0.024   0.002   TYR A 879 
 PHE   0.018   0.002   PHE A  76 
 TRP   0.011   0.002   TRP A 313 
 HIS   0.008   0.001   HIS A 862 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 9553)
  covalent geometry    : angle       0.61533 (12953)
  SS BOND              : bond        0.00458 (    3)
  SS BOND              : angle       0.97847 (    6)
  hydrogen bonds       : bond        0.04868 (  431)
  hydrogen bonds       : angle       4.80495 ( 1233)
  link_ALPHA1-4        : bond        0.01256 (    1)
  link_ALPHA1-4        : angle       3.43689 (    3)
  link_BETA1-4         : bond        0.00397 (    1)
  link_BETA1-4         : angle       1.89020 (    3)
  link_NAG-ASN         : bond        0.00351 (    3)
  link_NAG-ASN         : angle       1.62609 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 102
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 PHE cc_start: 0.7486 (m-80) cc_final: 0.7052 (m-80)
REVERT: A  145 ASP cc_start: 0.8304 (t70) cc_final: 0.7947 (t70)
REVERT: A  395 ASP cc_start: 0.7930 (m-30) cc_final: 0.7637 (t0)
REVERT: A  790 MET cc_start: 0.8659 (mmm) cc_final: 0.8373 (mtp)
REVERT: A  800 ARG cc_start: 0.7439 (ttm170) cc_final: 0.6988 (ttm170)
REVERT: A  816 ASP cc_start: 0.7155 (p0) cc_final: 0.6825 (p0)
REVERT: A  851 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7886 (mttm)
REVERT: B  197 ILE cc_start: 0.8367 (mp) cc_final: 0.8024 (tp)
REVERT: B  337 PHE cc_start: 0.7248 (t80) cc_final: 0.6730 (t80)
  outliers start: 35
  outliers final: 26
  residues processed: 132
  average time/residue: 0.0940
  time to fit residues: 17.7419
Evaluate side-chains
  124 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  289 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain A residue 1045 TRP
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1091 ARG
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  329 TYR
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 58 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 844 ASN
B 126 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.160638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.123789 restraints weight = 13242.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.123888 restraints weight = 13928.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.124867 restraints weight = 14739.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125830 restraints weight = 8569.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.126104 restraints weight = 7472.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9561  Z= 0.113
  Angle     :  0.560  10.533  12974  Z= 0.274
  Chirality :  0.041   0.205   1466
  Planarity :  0.003   0.041   1612
  Dihedral  :  9.269 118.738   1384
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.63 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.25), residues: 1126
  helix:  1.30 (0.23), residues: 501
  sheet:  0.22 (0.45), residues: 147
  loop : -1.12 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 290 
 TYR   0.019   0.001   TYR A 879 
 PHE   0.018   0.001   PHE A 368 
 TRP   0.013   0.001   TRP A 313 
 HIS   0.003   0.001   HIS A 864 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9553)
  covalent geometry    : angle       0.55448 (12953)
  SS BOND              : bond        0.00364 (    3)
  SS BOND              : angle       0.79404 (    6)
  hydrogen bonds       : bond        0.04191 (  431)
  hydrogen bonds       : angle       4.58305 ( 1233)
  link_ALPHA1-4        : bond        0.01425 (    1)
  link_ALPHA1-4        : angle       3.95283 (    3)
  link_BETA1-4         : bond        0.00007 (    1)
  link_BETA1-4         : angle       2.15825 (    3)
  link_NAG-ASN         : bond        0.00457 (    3)
  link_NAG-ASN         : angle       1.35919 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 PHE cc_start: 0.7472 (m-80) cc_final: 0.7082 (m-80)
REVERT: A  145 ASP cc_start: 0.8329 (t70) cc_final: 0.7939 (t70)
REVERT: A  163 SER cc_start: 0.8128 (m) cc_final: 0.7721 (p)
REVERT: A  395 ASP cc_start: 0.7890 (m-30) cc_final: 0.7574 (t0)
REVERT: A  714 ARG cc_start: 0.7196 (mmm160) cc_final: 0.6828 (mmp80)
REVERT: A  790 MET cc_start: 0.8621 (mmm) cc_final: 0.8391 (mtp)
REVERT: A  816 ASP cc_start: 0.7053 (p0) cc_final: 0.6683 (p0)
REVERT: A  826 GLU cc_start: 0.7022 (tp30) cc_final: 0.6275 (tp30)
REVERT: A  851 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7840 (mttm)
REVERT: B   70 VAL cc_start: 0.8756 (p) cc_final: 0.8539 (m)
REVERT: B  197 ILE cc_start: 0.8421 (mp) cc_final: 0.8037 (tp)
REVERT: B  337 PHE cc_start: 0.7209 (t80) cc_final: 0.6684 (t80)
  outliers start: 24
  outliers final: 14
  residues processed: 132
  average time/residue: 0.0937
  time to fit residues: 17.6576
Evaluate side-chains
  124 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue 1045 TRP
Chi-restraints excluded: chain A residue 1091 ARG
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  329 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.161035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.124869 restraints weight = 13213.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124170 restraints weight = 14699.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125995 restraints weight = 12926.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.126359 restraints weight = 8668.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.126826 restraints weight = 8299.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9561  Z= 0.112
  Angle     :  0.557  10.089  12974  Z= 0.272
  Chirality :  0.041   0.194   1466
  Planarity :  0.003   0.040   1612
  Dihedral  :  8.818 120.404   1384
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.93 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.26), residues: 1126
  helix:  1.37 (0.23), residues: 508
  sheet:  0.44 (0.47), residues: 137
  loop : -1.08 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 290 
 TYR   0.021   0.001   TYR B 241 
 PHE   0.011   0.001   PHE A 995 
 TRP   0.012   0.001   TRP A 313 
 HIS   0.003   0.001   HIS A 862 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9553)
  covalent geometry    : angle       0.55165 (12953)
  SS BOND              : bond        0.00391 (    3)
  SS BOND              : angle       0.72597 (    6)
  hydrogen bonds       : bond        0.04031 (  431)
  hydrogen bonds       : angle       4.48490 ( 1233)
  link_ALPHA1-4        : bond        0.01282 (    1)
  link_ALPHA1-4        : angle       4.09866 (    3)
  link_BETA1-4         : bond        0.00095 (    1)
  link_BETA1-4         : angle       2.25722 (    3)
  link_NAG-ASN         : bond        0.00418 (    3)
  link_NAG-ASN         : angle       1.23429 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 PHE cc_start: 0.7399 (m-80) cc_final: 0.6995 (m-80)
REVERT: A  145 ASP cc_start: 0.8316 (t70) cc_final: 0.7951 (t70)
REVERT: A  395 ASP cc_start: 0.7920 (m-30) cc_final: 0.7508 (t0)
REVERT: A  714 ARG cc_start: 0.7088 (mmm160) cc_final: 0.6748 (mmp80)
REVERT: A  790 MET cc_start: 0.8584 (mmm) cc_final: 0.8363 (mtp)
REVERT: A  816 ASP cc_start: 0.7055 (p0) cc_final: 0.6785 (p0)
REVERT: A  820 ASP cc_start: 0.7220 (m-30) cc_final: 0.6996 (m-30)
REVERT: A  826 GLU cc_start: 0.6970 (tp30) cc_final: 0.6392 (tp30)
REVERT: A  851 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7882 (mttm)
REVERT: B  197 ILE cc_start: 0.8357 (mp) cc_final: 0.8019 (tp)
REVERT: B  337 PHE cc_start: 0.7188 (t80) cc_final: 0.6682 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 129
  average time/residue: 0.1026
  time to fit residues: 18.5388
Evaluate side-chains
  120 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1045 TRP
Chi-restraints excluded: chain A residue 1091 ARG
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  329 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 32 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.157344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.120951 restraints weight = 13285.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.119175 restraints weight = 12315.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121076 restraints weight = 11618.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.121299 restraints weight = 8348.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121689 restraints weight = 8716.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9561  Z= 0.176
  Angle     :  0.607   9.959  12974  Z= 0.303
  Chirality :  0.043   0.215   1466
  Planarity :  0.004   0.040   1612
  Dihedral  :  8.887 112.717   1384
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.93 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.25), residues: 1126
  helix:  1.18 (0.23), residues: 508
  sheet:  0.34 (0.51), residues: 120
  loop : -1.13 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 290 
 TYR   0.016   0.002   TYR A 879 
 PHE   0.022   0.002   PHE A 368 
 TRP   0.010   0.001   TRP A 959 
 HIS   0.007   0.001   HIS A 862 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9553)
  covalent geometry    : angle       0.60181 (12953)
  SS BOND              : bond        0.00399 (    3)
  SS BOND              : angle       0.97409 (    6)
  hydrogen bonds       : bond        0.04579 (  431)
  hydrogen bonds       : angle       4.60409 ( 1233)
  link_ALPHA1-4        : bond        0.01117 (    1)
  link_ALPHA1-4        : angle       4.22272 (    3)
  link_BETA1-4         : bond        0.00007 (    1)
  link_BETA1-4         : angle       2.13349 (    3)
  link_NAG-ASN         : bond        0.00329 (    3)
  link_NAG-ASN         : angle       1.24910 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 PHE cc_start: 0.7396 (m-80) cc_final: 0.6982 (m-80)
REVERT: A  145 ASP cc_start: 0.8371 (t70) cc_final: 0.7971 (t70)
REVERT: A  395 ASP cc_start: 0.7922 (m-30) cc_final: 0.7563 (t0)
REVERT: A  714 ARG cc_start: 0.7289 (mmm160) cc_final: 0.6921 (mmp80)
REVERT: A  790 MET cc_start: 0.8608 (mmm) cc_final: 0.8368 (mtp)
REVERT: A  816 ASP cc_start: 0.7196 (p0) cc_final: 0.6973 (p0)
REVERT: A  820 ASP cc_start: 0.7238 (m-30) cc_final: 0.6987 (m-30)
REVERT: B  197 ILE cc_start: 0.8396 (mp) cc_final: 0.8027 (tp)
REVERT: B  337 PHE cc_start: 0.7158 (t80) cc_final: 0.6663 (t80)
  outliers start: 31
  outliers final: 24
  residues processed: 122
  average time/residue: 0.0931
  time to fit residues: 16.6033
Evaluate side-chains
  118 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1045 TRP
Chi-restraints excluded: chain A residue 1050 GLN
Chi-restraints excluded: chain A residue 1091 ARG
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  329 TYR
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 36 optimal weight:    9.9990
   chunk 83 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0570
   chunk 76 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    1.2902

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

Flipped N/Q/H residues before XYZ refinement:
B 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.158768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.122352 restraints weight = 13149.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121807 restraints weight = 14518.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.123865 restraints weight = 13067.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124094 restraints weight = 8378.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.124469 restraints weight = 8131.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9561  Z= 0.130
  Angle     :  0.570   9.590  12974  Z= 0.282
  Chirality :  0.041   0.196   1466
  Planarity :  0.004   0.042   1612
  Dihedral  :  8.781 111.366   1384
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 18.01 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.25), residues: 1126
  helix:  1.28 (0.23), residues: 508
  sheet:  0.31 (0.47), residues: 137
  loop : -1.09 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 290 
 TYR   0.014   0.001   TYR A 879 
 PHE   0.013   0.001   PHE A1036 
 TRP   0.011   0.001   TRP A 313 
 HIS   0.004   0.001   HIS A1023 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9553)
  covalent geometry    : angle       0.56453 (12953)
  SS BOND              : bond        0.00400 (    3)
  SS BOND              : angle       1.05814 (    6)
  hydrogen bonds       : bond        0.04238 (  431)
  hydrogen bonds       : angle       4.51136 ( 1233)
  link_ALPHA1-4        : bond        0.01290 (    1)
  link_ALPHA1-4        : angle       4.32454 (    3)
  link_BETA1-4         : bond        0.00161 (    1)
  link_BETA1-4         : angle       1.97160 (    3)
  link_NAG-ASN         : bond        0.00362 (    3)
  link_NAG-ASN         : angle       1.15448 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 PHE cc_start: 0.7411 (m-80) cc_final: 0.6987 (m-80)
REVERT: A  145 ASP cc_start: 0.8324 (t70) cc_final: 0.7941 (t70)
REVERT: A  395 ASP cc_start: 0.7952 (m-30) cc_final: 0.7532 (t0)
REVERT: A  714 ARG cc_start: 0.7182 (mmm160) cc_final: 0.6868 (mmp80)
REVERT: A  790 MET cc_start: 0.8586 (mmm) cc_final: 0.8365 (mtp)
REVERT: A  816 ASP cc_start: 0.7138 (p0) cc_final: 0.6911 (p0)
REVERT: A  820 ASP cc_start: 0.7237 (m-30) cc_final: 0.7001 (m-30)
REVERT: A  851 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7853 (mmtt)
REVERT: B  197 ILE cc_start: 0.8377 (mp) cc_final: 0.8026 (tp)
REVERT: B  337 PHE cc_start: 0.7158 (t80) cc_final: 0.6666 (t80)
  outliers start: 21
  outliers final: 20
  residues processed: 119
  average time/residue: 0.0950
  time to fit residues: 16.2504
Evaluate side-chains
  116 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1045 TRP
Chi-restraints excluded: chain A residue 1091 ARG
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  126 ASN
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  329 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 29 optimal weight:    0.3980
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 32 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0470
   chunk 62 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
B 126 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.160718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.124314 restraints weight = 13181.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.122910 restraints weight = 14542.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125446 restraints weight = 12869.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.125652 restraints weight = 8446.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.126090 restraints weight = 7823.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9561  Z= 0.109
  Angle     :  0.561  10.036  12974  Z= 0.276
  Chirality :  0.041   0.187   1466
  Planarity :  0.003   0.044   1612
  Dihedral  :  8.659 113.429   1384
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 18.50 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.26), residues: 1126
  helix:  1.37 (0.23), residues: 508
  sheet:  0.40 (0.46), residues: 140
  loop : -1.03 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 290 
 TYR   0.013   0.001   TYR A 879 
 PHE   0.022   0.001   PHE A 368 
 TRP   0.012   0.001   TRP A 313 
 HIS   0.003   0.001   HIS A 864 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9553)
  covalent geometry    : angle       0.55566 (12953)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       0.89245 (    6)
  hydrogen bonds       : bond        0.03997 (  431)
  hydrogen bonds       : angle       4.43573 ( 1233)
  link_ALPHA1-4        : bond        0.01607 (    1)
  link_ALPHA1-4        : angle       4.35468 (    3)
  link_BETA1-4         : bond        0.00348 (    1)
  link_BETA1-4         : angle       1.95838 (    3)
  link_NAG-ASN         : bond        0.00377 (    3)
  link_NAG-ASN         : angle       1.13266 (    9)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 PHE cc_start: 0.7396 (m-80) cc_final: 0.7019 (m-80)
REVERT: A  145 ASP cc_start: 0.8411 (t70) cc_final: 0.8047 (t70)
REVERT: A  150 GLN cc_start: 0.6798 (mp-120) cc_final: 0.6581 (mp10)
REVERT: A  395 ASP cc_start: 0.7893 (m-30) cc_final: 0.7450 (t0)
REVERT: A  714 ARG cc_start: 0.7262 (mmm160) cc_final: 0.6869 (mmp80)
REVERT: A  820 ASP cc_start: 0.7247 (m-30) cc_final: 0.7019 (m-30)
REVERT: A  851 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7939 (mttm)
REVERT: B  197 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8057 (tp)
REVERT: B  337 PHE cc_start: 0.7057 (t80) cc_final: 0.6588 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1015
  time to fit residues: 16.5895
Evaluate side-chains
  114 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  823 MET
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1045 TRP
Chi-restraints excluded: chain A residue 1091 ARG
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  329 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.159456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.123336 restraints weight = 13108.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.123054 restraints weight = 14351.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.124415 restraints weight = 14186.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.124837 restraints weight = 9613.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.125280 restraints weight = 8589.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9561  Z= 0.132
  Angle     :  0.571   9.708  12974  Z= 0.282
  Chirality :  0.041   0.202   1466
  Planarity :  0.004   0.042   1612
  Dihedral  :  8.729 111.599   1384
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.31 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.25), residues: 1126
  helix:  1.36 (0.23), residues: 508
  sheet:  0.45 (0.50), residues: 121
  loop : -1.04 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 723 
 TYR   0.014   0.001   TYR A 879 
 PHE   0.013   0.001   PHE A1036 
 TRP   0.010   0.001   TRP A 313 
 HIS   0.004   0.001   HIS A 862 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9553)
  covalent geometry    : angle       0.56592 (12953)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       0.95777 (    6)
  hydrogen bonds       : bond        0.04134 (  431)
  hydrogen bonds       : angle       4.47286 ( 1233)
  link_ALPHA1-4        : bond        0.01348 (    1)
  link_ALPHA1-4        : angle       4.31122 (    3)
  link_BETA1-4         : bond        0.00158 (    1)
  link_BETA1-4         : angle       1.82467 (    3)
  link_NAG-ASN         : bond        0.00332 (    3)
  link_NAG-ASN         : angle       1.18849 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1398.04 seconds
wall clock time: 25 minutes 6.11 seconds (1506.11 seconds total)