Starting phenix.real_space_refine
on Tue Jul 29 00:37:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6k7h_9932/07_2025/6k7h_9932.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6k7h_9932/07_2025/6k7h_9932.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6k7h_9932/07_2025/6k7h_9932.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6k7h_9932/07_2025/6k7h_9932.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6k7h_9932/07_2025/6k7h_9932.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6k7h_9932/07_2025/6k7h_9932.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    6857      2.51       5
     N    1753      2.21       5
     O    1911      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10577
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 987, 7860
          Classifications: {'peptide': 987}
          Link IDs: {'PTRANS': 30, 'TRANS': 956}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 2615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2615
          Classifications: {'peptide': 325}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299}
    Chain: "B"
      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: "C"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 63
          Unusual residues: {'NAG': 2, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 6.33, per 1000 atoms: 0.60
  Number of scatterers: 10577
  At special positions: 0
  Unit cell: (67.23, 109.56, 170.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1911      8.00
     N    1753      7.00
     C    6857      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  91 " - pdb=" SG  CYS C 104 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 157 " - pdb=" SG  CYS C 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 B   2 " - " MAN B   3 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN C 180 "
      " NAG C 401 " - " ASN C 294 "
      " NAG C 402 " - " ASN C 107 "
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2470

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 13 sheets defined
      49.1% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 74
    Processing helix  chain 'A' and resid 76 through 88
    Processing helix  chain 'A' and resid 101 through 127
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 3.752A  pdb=" N   GLY A 141 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA A 142 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 138 through 142'
    Processing helix  chain 'A' and resid 149 through 151
      No H-bonds generated for 'chain 'A' and resid 149 through 151'
    Processing helix  chain 'A' and resid 200 through 205
    Processing helix  chain 'A' and resid 208 through 213
    Processing helix  chain 'A' and resid 270 through 274
      removed outlier: 3.693A  pdb=" N   ASP A 273 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR A 274 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 270 through 274'
    Processing helix  chain 'A' and resid 288 through 323
    Processing helix  chain 'A' and resid 339 through 351
    Processing helix  chain 'A' and resid 352 through 355
      removed outlier: 3.811A  pdb=" N   ILE A 355 " --> pdb=" O   ASN A 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 352 through 355'
    Processing helix  chain 'A' and resid 358 through 377
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.985A  pdb=" N   LEU A 396 " --> pdb=" O   THR A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 456
    Processing helix  chain 'A' and resid 458 through 472
      removed outlier: 5.090A  pdb=" N   GLU A 464 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   PHE A 465 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 503
    Processing helix  chain 'A' and resid 561 through 567
      removed outlier: 3.974A  pdb=" N   ARG A 566 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 588
      removed outlier: 4.499A  pdb=" N   GLU A 575 " --> pdb=" O   SER A 571 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ILE A 576 " --> pdb=" O   LYS A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 618
      removed outlier: 4.196A  pdb=" N   VAL A 610 " --> pdb=" O   GLU A 606 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR A 616 " --> pdb=" O   GLN A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 633
      removed outlier: 3.731A  pdb=" N   LYS A 624 " --> pdb=" O   ASN A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 662
    Processing helix  chain 'A' and resid 673 through 684
    Processing helix  chain 'A' and resid 730 through 737
    Processing helix  chain 'A' and resid 742 through 751
    Processing helix  chain 'A' and resid 762 through 778
      removed outlier: 4.198A  pdb=" N   GLN A 776 " --> pdb=" O   MET A 772 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LYS A 778 " --> pdb=" O   LYS A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 795
    Processing helix  chain 'A' and resid 809 through 815
    Processing helix  chain 'A' and resid 821 through 823
      No H-bonds generated for 'chain 'A' and resid 821 through 823'
    Processing helix  chain 'A' and resid 824 through 831
    Processing helix  chain 'A' and resid 832 through 856
      removed outlier: 4.011A  pdb=" N   ASN A 851 " --> pdb=" O   CYS A 847 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU A 854 " --> pdb=" O   LYS A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 862
    Processing helix  chain 'A' and resid 874 through 880
      removed outlier: 3.515A  pdb=" N   ILE A 878 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 896
      removed outlier: 4.005A  pdb=" N   LEU A 891 " --> pdb=" O   ALA A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 908
    Processing helix  chain 'A' and resid 909 through 919
      removed outlier: 4.293A  pdb=" N   LYS A 913 " --> pdb=" O   PRO A 909 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLN A 916 " --> pdb=" O   TYR A 912 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASN A 917 " --> pdb=" O   LYS A 913 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 919 " --> pdb=" O   SER A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 948
      Proline residue:  A 944  - end of helix
    Processing helix  chain 'A' and resid 961 through 985
      removed outlier: 4.059A  pdb=" N   LEU A 965 " --> pdb=" O   ASP A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1011
    Processing helix  chain 'A' and resid 1025 through 1033
    Processing helix  chain 'A' and resid 1033 through 1062
      removed outlier: 3.975A  pdb=" N   TRP A1037 " --> pdb=" O   SER A1033 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   MET A1038 " --> pdb=" O   GLY A1034 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   LEU A1041 " --> pdb=" O   TRP A1037 " (cutoff:3.500A)
      Proline residue:  A1044  - end of helix
      removed outlier: 4.990A  pdb=" N   LEU A1050 " --> pdb=" O   ALA A1046 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ASP A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 74
      Proline residue:  C  52  - end of helix
      removed outlier: 3.985A  pdb=" N   LEU C  59 " --> pdb=" O   PHE C  55 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ILE C  62 " --> pdb=" O   GLY C  58 " (cutoff:3.500A)
      Proline residue:  C  63  - end of helix
    Processing helix  chain 'C' and resid 91 through 95
      removed outlier: 3.721A  pdb=" N   LEU C  95 " --> pdb=" O   ASN C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 136
    Processing helix  chain 'C' and resid 139 through 145
    Processing helix  chain 'C' and resid 146 through 151
    Processing helix  chain 'C' and resid 157 through 161
      removed outlier: 4.171A  pdb=" N   ARG C 161 " --> pdb=" O   GLU C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 177
    Processing helix  chain 'C' and resid 206 through 212
    Processing helix  chain 'C' and resid 222 through 227
    Processing helix  chain 'C' and resid 239 through 243
    Processing helix  chain 'C' and resid 254 through 262
    Processing helix  chain 'C' and resid 301 through 305
      removed outlier: 3.839A  pdb=" N   PHE C 304 " --> pdb=" O   VAL C 301 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASP C 305 " --> pdb=" O   HIS C 302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 301 through 305'
    Processing helix  chain 'C' and resid 323 through 350
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 137
    Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160
      removed outlier: 6.811A  pdb=" N   TRP A 262 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   SER A 174 " --> pdb=" O   TRP A 262 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   HIS A 264 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ASP A 168 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164
    Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 185
      removed outlier: 4.843A  pdb=" N   THR A 185 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   ASN A 193 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 221
    Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382
    Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391
      removed outlier: 6.723A  pdb=" N   GLY A 800 " --> pdb=" O   TYR A 817 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   ILE A 819 " --> pdb=" O   GLY A 800 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLY A 802 " --> pdb=" O   ILE A 819 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   THR A 781 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   VAL A 801 " --> pdb=" O   THR A 781 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   ALA A 783 " --> pdb=" O   VAL A 801 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   ILE A 803 " --> pdb=" O   ALA A 783 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   GLY A 785 " --> pdb=" O   ILE A 803 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   VAL A 403 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   LEU A 782 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   TYR A 405 " --> pdb=" O   LEU A 782 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ILE A 784 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   PHE A 407 " --> pdb=" O   ILE A 784 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   LYS A 404 " --> pdb=" O   LYS A 665 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   TRP A 667 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ILE A 406 " --> pdb=" O   TRP A 667 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   LEU A 669 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   SER A 408 " --> pdb=" O   LEU A 669 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 429 through 431
      removed outlier: 3.681A  pdb=" N   VAL A 429 " --> pdb=" O   ILE A 426 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE A 426 " --> pdb=" O   VAL A 429 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   ALA A 643 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507
    Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 545
    Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 81
      removed outlier: 7.247A  pdb=" N   VAL C 118 " --> pdb=" O   LEU C 275 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   LEU C 275 " --> pdb=" O   VAL C 118 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   MET C 120 " --> pdb=" O   TYR C 273 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103
      removed outlier: 4.030A  pdb=" N   CYS C 102 " --> pdb=" O   TYR C 297 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 109
      removed outlier: 5.078A  pdb=" N   ARG C 290 " --> pdb=" O   ILE C 188 " (cutoff:3.500A)

    473 hydrogen bonds defined for protein.
    1371 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.86

  Time building geometry restraints manager: 2.87 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: 1752
        1.32 -     1.44: 2903
        1.44 -     1.57: 6085
        1.57 -     1.69: 1
        1.69 -     1.81: 85
  Bond restraints: 10826
  Sorted by residual:
  bond pdb=" CB  VAL A 969 "
       pdb=" CG2 VAL A 969 "
    ideal  model  delta    sigma   weight residual
    1.521  1.434  0.087 3.30e-02 9.18e+02 6.99e+00
  bond pdb=" CB  PRO C 170 "
       pdb=" CG  PRO C 170 "
    ideal  model  delta    sigma   weight residual
    1.506  1.417  0.089 3.90e-02 6.57e+02 5.23e+00
  bond pdb=" CD  LYS C 308 "
       pdb=" CE  LYS C 308 "
    ideal  model  delta    sigma   weight residual
    1.520  1.458  0.062 3.00e-02 1.11e+03 4.30e+00
  bond pdb=" CB  ARG C 262 "
       pdb=" CG  ARG C 262 "
    ideal  model  delta    sigma   weight residual
    1.520  1.459  0.061 3.00e-02 1.11e+03 4.10e+00
  bond pdb=" CG1 ILE A 996 "
       pdb=" CD1 ILE A 996 "
    ideal  model  delta    sigma   weight residual
    1.513  1.436  0.077 3.90e-02 6.57e+02 3.94e+00
  ... (remaining 10821 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 14227
        2.76 -     5.52: 410
        5.52 -     8.28: 45
        8.28 -    11.04: 11
       11.04 -    13.80: 3
  Bond angle restraints: 14696
  Sorted by residual:
  angle pdb=" C   ARG A  75 "
        pdb=" N   ALA A  76 "
        pdb=" CA  ALA A  76 "
      ideal   model   delta    sigma   weight residual
     121.54  130.50   -8.96 1.91e+00 2.74e-01 2.20e+01
  angle pdb=" CA  MET C 318 "
        pdb=" CB  MET C 318 "
        pdb=" CG  MET C 318 "
      ideal   model   delta    sigma   weight residual
     114.10  123.09   -8.99 2.00e+00 2.50e-01 2.02e+01
  angle pdb=" C   MET A 830 "
        pdb=" N   ILE A 831 "
        pdb=" CA  ILE A 831 "
      ideal   model   delta    sigma   weight residual
     122.76  116.22    6.54 1.57e+00 4.06e-01 1.74e+01
  angle pdb=" C   GLY C 251 "
        pdb=" N   PHE C 252 "
        pdb=" CA  PHE C 252 "
      ideal   model   delta    sigma   weight residual
     121.54  129.35   -7.81 1.91e+00 2.74e-01 1.67e+01
  angle pdb=" C   THR A 281 "
        pdb=" N   SER A 282 "
        pdb=" CA  SER A 282 "
      ideal   model   delta    sigma   weight residual
     120.97  132.40  -11.43 2.84e+00 1.24e-01 1.62e+01
  ... (remaining 14691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.15: 5614
       16.15 -    32.31: 724
       32.31 -    48.46: 166
       48.46 -    64.62: 41
       64.62 -    80.77: 13
  Dihedral angle restraints: 6558
    sinusoidal: 2729
      harmonic: 3829
  Sorted by residual:
  dihedral pdb=" CA  LYS A 483 "
           pdb=" C   LYS A 483 "
           pdb=" N   ILE A 484 "
           pdb=" CA  ILE A 484 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.56  -49.44     0      5.00e+00 4.00e-02 9.78e+01
  dihedral pdb=" CB  CYS C 157 "
           pdb=" SG  CYS C 157 "
           pdb=" SG  CYS C 171 "
           pdb=" CB  CYS C 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.09   56.91     1      1.00e+01 1.00e-02 4.36e+01
  dihedral pdb=" CA  SER C 316 "
           pdb=" C   SER C 316 "
           pdb=" N   TRP C 317 "
           pdb=" CA  TRP C 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.98   27.02     0      5.00e+00 4.00e-02 2.92e+01
  ... (remaining 6555 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1175
       0.063 -    0.125: 414
       0.125 -    0.188: 80
       0.188 -    0.251: 11
       0.251 -    0.314: 2
  Chirality restraints: 1682
  Sorted by residual:
  chirality pdb=" C4  NAG B   2 "
            pdb=" C3  NAG B   2 "
            pdb=" C5  NAG B   2 "
            pdb=" O4  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.22   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" CB  ILE A 108 "
            pdb=" CA  ILE A 108 "
            pdb=" CG1 ILE A 108 "
            pdb=" CG2 ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CB  VAL A 545 "
            pdb=" CA  VAL A 545 "
            pdb=" CG1 VAL A 545 "
            pdb=" CG2 VAL A 545 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1679 not shown)

  Planarity restraints: 1839
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 402 "   -0.317 2.00e-02 2.50e+03   2.77e-01 9.59e+02
        pdb=" C7  NAG C 402 "    0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG C 402 "   -0.114 2.00e-02 2.50e+03
        pdb=" N2  NAG C 402 "    0.497 2.00e-02 2.50e+03
        pdb=" O7  NAG C 402 "   -0.134 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 401 "    0.238 2.00e-02 2.50e+03   1.97e-01 4.86e+02
        pdb=" C7  NAG C 401 "   -0.064 2.00e-02 2.50e+03
        pdb=" C8  NAG C 401 "    0.166 2.00e-02 2.50e+03
        pdb=" N2  NAG C 401 "   -0.325 2.00e-02 2.50e+03
        pdb=" O7  NAG C 401 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "   -0.132 2.00e-02 2.50e+03   1.15e-01 1.65e+02
        pdb=" C7  NAG B   1 "    0.026 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "    0.022 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "    0.190 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.106 2.00e-02 2.50e+03
  ... (remaining 1836 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2801
        2.80 -     3.32: 9424
        3.32 -     3.85: 17748
        3.85 -     4.37: 21002
        4.37 -     4.90: 36217
  Nonbonded interactions: 87192
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 400 "
            pdb=" OH  TYR A 912 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER A 490 "
            pdb=" OD1 ASP A 492 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" OE2 GLU A 897 "
            pdb=" OG  SER A 986 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   SER A 814 "
            pdb=" OG  SER A 814 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" ND2 ASN C 176 "
            pdb=" OD1 ASN C 235 "
     model   vdw
     2.333 3.120
  ... (remaining 87187 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.320
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
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      :  0.011   0.089  10834  Z= 0.443
  Angle     :  1.116  13.796  14717  Z= 0.592
  Chirality :  0.065   0.314   1682
  Planarity :  0.012   0.277   1836
  Dihedral  : 15.571  80.770   4079
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.94 %
    Favored  : 87.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.19), residues: 1302
  helix: -2.60 (0.15), residues: 594
  sheet: -1.24 (0.38), residues: 173
  loop : -2.75 (0.23), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A1003 
 HIS   0.008   0.002   HIS A 124 
 PHE   0.035   0.003   PHE C 179 
 TYR   0.029   0.003   TYR C 122 
 ARG   0.008   0.001   ARG A  37 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01152 (    3)
  link_NAG-ASN         : angle       3.25687 (    9)
  link_ALPHA1-4        : bond        0.00426 (    1)
  link_ALPHA1-4        : angle       5.60951 (    3)
  link_BETA1-4         : bond        0.00083 (    1)
  link_BETA1-4         : angle       3.28438 (    3)
  hydrogen bonds       : bond        0.11682 (  473)
  hydrogen bonds       : angle       6.60536 ( 1371)
  SS BOND              : bond        0.00765 (    3)
  SS BOND              : angle       1.68030 (    6)
  covalent geometry    : bond        0.01089 (10826)
  covalent geometry    : angle       1.10920 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 LYS cc_start: 0.8754 (mttt) cc_final: 0.8185 (mtmt)
REVERT: A  535 THR cc_start: 0.2267 (OUTLIER) cc_final: 0.1901 (t)
REVERT: A  599 ILE cc_start: -0.1456 (OUTLIER) cc_final: -0.1895 (tp)
REVERT: A  753 CYS cc_start: 0.7243 (m) cc_final: 0.6792 (m)
REVERT: A  852 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8388 (mp)
REVERT: C  146 ASP cc_start: 0.7661 (m-30) cc_final: 0.7333 (m-30)
REVERT: C  201 LYS cc_start: 0.9085 (pttt) cc_final: 0.8829 (ptmt)
REVERT: C  315 ILE cc_start: 0.8013 (pt) cc_final: 0.7719 (pt)
  outliers start: 13
  outliers final: 2
  residues processed: 144
  average time/residue: 0.3146
  time to fit residues: 61.7887
Evaluate side-chains
  93 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain C residue   50 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 66 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 39 optimal weight:   20.0000
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 134 GLN
A 140 ASN
A 147 HIS
A 234 ASN
A 320 ASN
A 323 HIS
A 397 ASN
A 453 GLN
A 522 GLN
A 583 GLN
A 605 GLN
A 679 ASN
A 682 HIS
A 744 GLN
A 810 GLN
A 949 GLN
A 993 HIS
C  92 ASN
C 131 HIS
C 142 GLN
C 190 ASN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.190412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.135421 restraints weight = 10907.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 3.67
r_work: 0.2856 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.094  10834  Z= 0.136
  Angle     :  0.643   8.096  14717  Z= 0.331
  Chirality :  0.044   0.177   1682
  Planarity :  0.005   0.051   1836
  Dihedral  :  7.044  58.067   1597
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.19 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.21), residues: 1302
  helix: -0.84 (0.20), residues: 592
  sheet: -0.89 (0.39), residues: 180
  loop : -2.19 (0.24), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A1003 
 HIS   0.003   0.001   HIS A 993 
 PHE   0.017   0.001   PHE C 108 
 TYR   0.019   0.001   TYR A 555 
 ARG   0.003   0.000   ARG A 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00279 (    3)
  link_NAG-ASN         : angle       2.36510 (    9)
  link_ALPHA1-4        : bond        0.00249 (    1)
  link_ALPHA1-4        : angle       4.45636 (    3)
  link_BETA1-4         : bond        0.00239 (    1)
  link_BETA1-4         : angle       2.97347 (    3)
  hydrogen bonds       : bond        0.04740 (  473)
  hydrogen bonds       : angle       5.22997 ( 1371)
  SS BOND              : bond        0.00560 (    3)
  SS BOND              : angle       1.33165 (    6)
  covalent geometry    : bond        0.00305 (10826)
  covalent geometry    : angle       0.63524 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 LYS cc_start: 0.8885 (mttt) cc_final: 0.8355 (mtmt)
REVERT: A  535 THR cc_start: 0.2169 (OUTLIER) cc_final: 0.1838 (t)
REVERT: A  599 ILE cc_start: -0.0513 (OUTLIER) cc_final: -0.1311 (tp)
REVERT: A  693 MET cc_start: 0.3500 (mpp) cc_final: 0.2628 (ttt)
REVERT: A  753 CYS cc_start: 0.7710 (m) cc_final: 0.7375 (m)
REVERT: A  852 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8767 (mp)
REVERT: A  905 MET cc_start: 0.8461 (mtp) cc_final: 0.8241 (mtp)
REVERT: A 1059 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6864 (tpt-90)
REVERT: C   92 ASN cc_start: 0.8776 (t0) cc_final: 0.8522 (t0)
REVERT: C  146 ASP cc_start: 0.7893 (m-30) cc_final: 0.7603 (m-30)
REVERT: C  201 LYS cc_start: 0.9041 (pttt) cc_final: 0.8829 (ptpt)
REVERT: C  315 ILE cc_start: 0.8009 (pt) cc_final: 0.7742 (pt)
  outliers start: 26
  outliers final: 9
  residues processed: 127
  average time/residue: 0.2913
  time to fit residues: 52.3076
Evaluate side-chains
  109 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 1.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 50 optimal weight:   40.0000
   chunk 125 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 51 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 124 HIS
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 HIS
C 117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.190848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.133705 restraints weight = 11043.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 3.55
r_work: 0.2800 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  10834  Z= 0.239
  Angle     :  0.690  11.920  14717  Z= 0.349
  Chirality :  0.047   0.202   1682
  Planarity :  0.005   0.045   1836
  Dihedral  :  6.810  57.831   1597
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.58 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.22), residues: 1302
  helix: -0.31 (0.21), residues: 593
  sheet: -0.81 (0.38), residues: 181
  loop : -2.05 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A1003 
 HIS   0.015   0.002   HIS A 682 
 PHE   0.019   0.002   PHE C 179 
 TYR   0.022   0.002   TYR C 122 
 ARG   0.004   0.000   ARG C 290 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00626 (    3)
  link_NAG-ASN         : angle       2.58279 (    9)
  link_ALPHA1-4        : bond        0.00233 (    1)
  link_ALPHA1-4        : angle       4.50674 (    3)
  link_BETA1-4         : bond        0.00221 (    1)
  link_BETA1-4         : angle       3.34216 (    3)
  hydrogen bonds       : bond        0.05210 (  473)
  hydrogen bonds       : angle       5.16978 ( 1371)
  SS BOND              : bond        0.00440 (    3)
  SS BOND              : angle       1.44968 (    6)
  covalent geometry    : bond        0.00582 (10826)
  covalent geometry    : angle       0.68265 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.5671 (ptm) cc_final: 0.5405 (ptp)
REVERT: A  326 LYS cc_start: 0.8915 (mttt) cc_final: 0.8365 (mtmt)
REVERT: A  535 THR cc_start: 0.2443 (OUTLIER) cc_final: 0.2100 (t)
REVERT: A  599 ILE cc_start: -0.0286 (OUTLIER) cc_final: -0.1170 (tp)
REVERT: A  693 MET cc_start: 0.3765 (mpp) cc_final: 0.2931 (ttt)
REVERT: A  727 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7610 (mp)
REVERT: A  753 CYS cc_start: 0.7780 (m) cc_final: 0.7115 (m)
REVERT: A  772 MET cc_start: 0.8752 (tmm) cc_final: 0.8508 (tmm)
REVERT: A  874 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8160 (tt0)
REVERT: A  900 CYS cc_start: 0.7628 (OUTLIER) cc_final: 0.6870 (t)
REVERT: A 1059 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6876 (tpt-90)
REVERT: C   92 ASN cc_start: 0.8805 (t0) cc_final: 0.8518 (t0)
REVERT: C  146 ASP cc_start: 0.7892 (m-30) cc_final: 0.7569 (m-30)
REVERT: C  262 ARG cc_start: 0.8858 (mmt-90) cc_final: 0.8595 (ttm-80)
REVERT: C  315 ILE cc_start: 0.8094 (pt) cc_final: 0.7808 (pt)
  outliers start: 34
  outliers final: 20
  residues processed: 123
  average time/residue: 0.2955
  time to fit residues: 53.8388
Evaluate side-chains
  118 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 1.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  831 ILE
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  884 MET
Chi-restraints excluded: chain A residue  900 CYS
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 46 optimal weight:   20.0000
   chunk 124 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   chunk 128 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.191726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.136335 restraints weight = 10893.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 3.44
r_work: 0.2873 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10834  Z= 0.149
  Angle     :  0.609  10.022  14717  Z= 0.310
  Chirality :  0.045   0.178   1682
  Planarity :  0.004   0.045   1836
  Dihedral  :  6.374  58.230   1595
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.28 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.23), residues: 1302
  helix:  0.14 (0.22), residues: 591
  sheet: -0.66 (0.38), residues: 181
  loop : -1.82 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 927 
 HIS   0.009   0.001   HIS A 682 
 PHE   0.013   0.001   PHE A 368 
 TYR   0.016   0.001   TYR C 122 
 ARG   0.003   0.000   ARG A 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00399 (    3)
  link_NAG-ASN         : angle       2.22284 (    9)
  link_ALPHA1-4        : bond        0.00068 (    1)
  link_ALPHA1-4        : angle       4.29666 (    3)
  link_BETA1-4         : bond        0.00307 (    1)
  link_BETA1-4         : angle       3.16466 (    3)
  hydrogen bonds       : bond        0.04455 (  473)
  hydrogen bonds       : angle       4.91586 ( 1371)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       0.97995 (    6)
  covalent geometry    : bond        0.00352 (10826)
  covalent geometry    : angle       0.60217 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.5525 (ptm) cc_final: 0.5257 (ptp)
REVERT: A  326 LYS cc_start: 0.8915 (mttt) cc_final: 0.8391 (mtmt)
REVERT: A  535 THR cc_start: 0.2443 (OUTLIER) cc_final: 0.2062 (t)
REVERT: A  599 ILE cc_start: -0.0158 (OUTLIER) cc_final: -0.0987 (tp)
REVERT: A  693 MET cc_start: 0.3857 (mpp) cc_final: 0.2985 (ttt)
REVERT: A  727 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7666 (mp)
REVERT: A  742 VAL cc_start: 0.5797 (OUTLIER) cc_final: 0.5517 (t)
REVERT: A  753 CYS cc_start: 0.7856 (m) cc_final: 0.7143 (m)
REVERT: A  874 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8140 (tt0)
REVERT: A  900 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6916 (t)
REVERT: A 1059 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6896 (tpt-90)
REVERT: C   92 ASN cc_start: 0.8740 (t0) cc_final: 0.8485 (t0)
REVERT: C  146 ASP cc_start: 0.7875 (m-30) cc_final: 0.7581 (m-30)
REVERT: C  223 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (tt)
REVERT: C  315 ILE cc_start: 0.8104 (pt) cc_final: 0.7871 (pt)
  outliers start: 37
  outliers final: 16
  residues processed: 131
  average time/residue: 0.2812
  time to fit residues: 55.2494
Evaluate side-chains
  117 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  884 MET
Chi-restraints excluded: chain A residue  899 SER
Chi-restraints excluded: chain A residue  900 CYS
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 113 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 6 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 HIS
C 117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.192719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.133910 restraints weight = 10908.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 3.98
r_work: 0.2847 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10834  Z= 0.114
  Angle     :  0.576   8.971  14717  Z= 0.293
  Chirality :  0.044   0.276   1682
  Planarity :  0.004   0.045   1836
  Dihedral  :  6.016  57.804   1595
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.97 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.23), residues: 1302
  helix:  0.42 (0.22), residues: 593
  sheet: -0.60 (0.39), residues: 182
  loop : -1.64 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 927 
 HIS   0.008   0.001   HIS A 682 
 PHE   0.012   0.001   PHE A 968 
 TYR   0.013   0.001   TYR C 273 
 ARG   0.007   0.000   ARG A 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00321 (    3)
  link_NAG-ASN         : angle       2.05401 (    9)
  link_ALPHA1-4        : bond        0.00113 (    1)
  link_ALPHA1-4        : angle       4.14060 (    3)
  link_BETA1-4         : bond        0.00289 (    1)
  link_BETA1-4         : angle       3.06144 (    3)
  hydrogen bonds       : bond        0.04030 (  473)
  hydrogen bonds       : angle       4.71222 ( 1371)
  SS BOND              : bond        0.00211 (    3)
  SS BOND              : angle       0.80237 (    6)
  covalent geometry    : bond        0.00253 (10826)
  covalent geometry    : angle       0.56939 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 1.724 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.7396 (mp10) cc_final: 0.7159 (mp10)
REVERT: A  180 MET cc_start: 0.5314 (mmt) cc_final: 0.4662 (mmt)
REVERT: A  213 MET cc_start: 0.5555 (ptm) cc_final: 0.5258 (ptp)
REVERT: A  326 LYS cc_start: 0.8851 (mttt) cc_final: 0.8265 (mtmt)
REVERT: A  535 THR cc_start: 0.2418 (OUTLIER) cc_final: 0.2020 (t)
REVERT: A  599 ILE cc_start: 0.0073 (OUTLIER) cc_final: -0.0779 (tp)
REVERT: A  693 MET cc_start: 0.3691 (mpp) cc_final: 0.2893 (ttt)
REVERT: A  727 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7356 (mp)
REVERT: A  742 VAL cc_start: 0.5820 (OUTLIER) cc_final: 0.5549 (t)
REVERT: A  753 CYS cc_start: 0.7723 (m) cc_final: 0.6970 (m)
REVERT: A  852 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8686 (mp)
REVERT: A  874 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8025 (tt0)
REVERT: A  900 CYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6694 (t)
REVERT: A 1059 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6824 (tpt-90)
REVERT: C   92 ASN cc_start: 0.8662 (t0) cc_final: 0.8360 (t0)
REVERT: C  146 ASP cc_start: 0.7765 (m-30) cc_final: 0.7510 (m-30)
REVERT: C  223 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8081 (tt)
REVERT: C  310 MET cc_start: 0.8751 (tmm) cc_final: 0.8548 (ttp)
REVERT: C  315 ILE cc_start: 0.8034 (pt) cc_final: 0.7821 (pt)
  outliers start: 33
  outliers final: 17
  residues processed: 123
  average time/residue: 0.3105
  time to fit residues: 58.3761
Evaluate side-chains
  119 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  884 MET
Chi-restraints excluded: chain A residue  899 SER
Chi-restraints excluded: chain A residue  900 CYS
Chi-restraints excluded: chain A residue  939 ILE
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   chunk 120 optimal weight:    4.9990
   chunk 52 optimal weight:   20.0000
   chunk 2 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 117 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 HIS
C 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.191139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.130223 restraints weight = 10951.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 4.16
r_work: 0.2844 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10834  Z= 0.148
  Angle     :  0.590   8.441  14717  Z= 0.300
  Chirality :  0.045   0.238   1682
  Planarity :  0.004   0.045   1836
  Dihedral  :  5.931  57.431   1595
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.23 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.24), residues: 1302
  helix:  0.51 (0.22), residues: 591
  sheet: -0.53 (0.39), residues: 182
  loop : -1.61 (0.27), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 927 
 HIS   0.005   0.001   HIS A 682 
 PHE   0.020   0.001   PHE A 368 
 TYR   0.017   0.001   TYR C 122 
 ARG   0.005   0.000   ARG A 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00436 (    3)
  link_NAG-ASN         : angle       2.13444 (    9)
  link_ALPHA1-4        : bond        0.00008 (    1)
  link_ALPHA1-4        : angle       4.05046 (    3)
  link_BETA1-4         : bond        0.00307 (    1)
  link_BETA1-4         : angle       3.18951 (    3)
  hydrogen bonds       : bond        0.04229 (  473)
  hydrogen bonds       : angle       4.73058 ( 1371)
  SS BOND              : bond        0.00292 (    3)
  SS BOND              : angle       0.97140 (    6)
  covalent geometry    : bond        0.00350 (10826)
  covalent geometry    : angle       0.58273 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 99
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.7376 (mp10) cc_final: 0.7118 (mp10)
REVERT: A  213 MET cc_start: 0.5564 (ptm) cc_final: 0.5343 (ptp)
REVERT: A  326 LYS cc_start: 0.8850 (mttt) cc_final: 0.8254 (mtmt)
REVERT: A  535 THR cc_start: 0.2435 (OUTLIER) cc_final: 0.2036 (t)
REVERT: A  599 ILE cc_start: -0.0078 (OUTLIER) cc_final: -0.0961 (tt)
REVERT: A  693 MET cc_start: 0.3697 (mpp) cc_final: 0.2912 (ttt)
REVERT: A  727 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7432 (mp)
REVERT: A  742 VAL cc_start: 0.5843 (OUTLIER) cc_final: 0.5571 (t)
REVERT: A  753 CYS cc_start: 0.7745 (m) cc_final: 0.6997 (m)
REVERT: A  852 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8701 (mp)
REVERT: A  874 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8060 (tt0)
REVERT: A 1059 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6815 (tpt-90)
REVERT: C   92 ASN cc_start: 0.8663 (t0) cc_final: 0.8358 (t0)
REVERT: C  223 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8129 (tt)
REVERT: C  315 ILE cc_start: 0.8066 (pt) cc_final: 0.7856 (pt)
REVERT: C  348 HIS cc_start: 0.7666 (t70) cc_final: 0.7416 (t-90)
  outliers start: 41
  outliers final: 22
  residues processed: 134
  average time/residue: 0.2223
  time to fit residues: 45.0712
Evaluate side-chains
  125 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  884 MET
Chi-restraints excluded: chain A residue  899 SER
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   chunk 30 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 127 optimal weight:    0.7980
   chunk 44 optimal weight:   20.0000
   chunk 114 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 117 ASN
C 254 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.188718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.133150 restraints weight = 11142.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 4.06
r_work: 0.2777 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  10834  Z= 0.232
  Angle     :  0.655   9.572  14717  Z= 0.331
  Chirality :  0.047   0.241   1682
  Planarity :  0.004   0.045   1836
  Dihedral  :  6.134  57.361   1595
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.58 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.23), residues: 1302
  helix:  0.37 (0.22), residues: 591
  sheet: -0.58 (0.39), residues: 182
  loop : -1.59 (0.27), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 143 
 HIS   0.005   0.001   HIS A 323 
 PHE   0.023   0.002   PHE A 368 
 TYR   0.021   0.002   TYR C 122 
 ARG   0.004   0.000   ARG A 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00643 (    3)
  link_NAG-ASN         : angle       2.32458 (    9)
  link_ALPHA1-4        : bond        0.00115 (    1)
  link_ALPHA1-4        : angle       4.22117 (    3)
  link_BETA1-4         : bond        0.00145 (    1)
  link_BETA1-4         : angle       3.34782 (    3)
  hydrogen bonds       : bond        0.04816 (  473)
  hydrogen bonds       : angle       4.90739 ( 1371)
  SS BOND              : bond        0.00467 (    3)
  SS BOND              : angle       1.35752 (    6)
  covalent geometry    : bond        0.00569 (10826)
  covalent geometry    : angle       0.64821 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 101
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  326 LYS cc_start: 0.8896 (mttt) cc_final: 0.8310 (mtmt)
REVERT: A  535 THR cc_start: 0.2527 (OUTLIER) cc_final: 0.2111 (t)
REVERT: A  599 ILE cc_start: -0.0365 (OUTLIER) cc_final: -0.1238 (tt)
REVERT: A  693 MET cc_start: 0.3806 (mpp) cc_final: 0.2952 (ttt)
REVERT: A  727 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7571 (mp)
REVERT: A  753 CYS cc_start: 0.7901 (m) cc_final: 0.7252 (m)
REVERT: A  852 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8823 (mp)
REVERT: A  874 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8178 (tt0)
REVERT: A 1059 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6879 (tpt-90)
REVERT: C   92 ASN cc_start: 0.8742 (t0) cc_final: 0.8415 (t0)
REVERT: C  223 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8279 (tt)
REVERT: C  315 ILE cc_start: 0.8075 (pt) cc_final: 0.7839 (pt)
REVERT: C  348 HIS cc_start: 0.7719 (t70) cc_final: 0.7476 (t-90)
  outliers start: 40
  outliers final: 27
  residues processed: 134
  average time/residue: 0.3621
  time to fit residues: 74.3033
Evaluate side-chains
  133 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  884 MET
Chi-restraints excluded: chain A residue  899 SER
Chi-restraints excluded: chain A residue  925 VAL
Chi-restraints excluded: chain A residue  939 ILE
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 73 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0170
   chunk 125 optimal weight:    0.7980
   chunk 116 optimal weight:    2.9990
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
A 264 HIS
A 352 ASN
C 117 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.192370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.133050 restraints weight = 10916.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 4.49
r_work: 0.2856 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10834  Z= 0.118
  Angle     :  0.591   8.835  14717  Z= 0.301
  Chirality :  0.044   0.221   1682
  Planarity :  0.004   0.045   1836
  Dihedral  :  5.807  57.354   1595
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.62 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.24), residues: 1302
  helix:  0.66 (0.22), residues: 593
  sheet: -0.48 (0.39), residues: 182
  loop : -1.52 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 927 
 HIS   0.002   0.001   HIS A 323 
 PHE   0.021   0.001   PHE A 368 
 TYR   0.015   0.001   TYR C 273 
 ARG   0.011   0.000   ARG A 743 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00299 (    3)
  link_NAG-ASN         : angle       1.87415 (    9)
  link_ALPHA1-4        : bond        0.00334 (    1)
  link_ALPHA1-4        : angle       3.94840 (    3)
  link_BETA1-4         : bond        0.00222 (    1)
  link_BETA1-4         : angle       3.01836 (    3)
  hydrogen bonds       : bond        0.04002 (  473)
  hydrogen bonds       : angle       4.69557 ( 1371)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       0.74790 (    6)
  covalent geometry    : bond        0.00265 (10826)
  covalent geometry    : angle       0.58497 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 2.041 
Fit side-chains
REVERT: A  136 GLN cc_start: 0.7458 (mp10) cc_final: 0.6819 (tm-30)
REVERT: A  326 LYS cc_start: 0.8812 (mttt) cc_final: 0.8219 (mtmt)
REVERT: A  599 ILE cc_start: 0.0013 (OUTLIER) cc_final: -0.0860 (tt)
REVERT: A  693 MET cc_start: 0.3668 (mpp) cc_final: 0.2797 (ttt)
REVERT: A  727 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7460 (mp)
REVERT: A  753 CYS cc_start: 0.7753 (m) cc_final: 0.6995 (m)
REVERT: A  831 ILE cc_start: 0.8862 (pt) cc_final: 0.8567 (mp)
REVERT: A  852 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8684 (mp)
REVERT: A  874 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8050 (tt0)
REVERT: A 1059 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6791 (tpt-90)
REVERT: C   92 ASN cc_start: 0.8642 (t0) cc_final: 0.8319 (t0)
REVERT: C  223 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8006 (tt)
REVERT: C  348 HIS cc_start: 0.7651 (t70) cc_final: 0.7414 (t-90)
  outliers start: 36
  outliers final: 19
  residues processed: 126
  average time/residue: 0.3792
  time to fit residues: 72.2039
Evaluate side-chains
  117 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 1.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  884 MET
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  939 ILE
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0970
   chunk 46 optimal weight:   50.0000
   chunk 113 optimal weight:    2.9990
   chunk 108 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
C 117 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.191048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.131161 restraints weight = 11058.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 4.35
r_work: 0.2803 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10834  Z= 0.125
  Angle     :  0.600  11.047  14717  Z= 0.302
  Chirality :  0.044   0.198   1682
  Planarity :  0.004   0.044   1836
  Dihedral  :  5.643  56.792   1594
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.45 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.24), residues: 1302
  helix:  0.76 (0.22), residues: 593
  sheet: -0.47 (0.39), residues: 180
  loop : -1.48 (0.27), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 143 
 HIS   0.003   0.001   HIS A 936 
 PHE   0.021   0.001   PHE A 368 
 TYR   0.021   0.001   TYR A 849 
 ARG   0.013   0.000   ARG A 743 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00380 (    3)
  link_NAG-ASN         : angle       1.92629 (    9)
  link_ALPHA1-4        : bond        0.00154 (    1)
  link_ALPHA1-4        : angle       3.80897 (    3)
  link_BETA1-4         : bond        0.00254 (    1)
  link_BETA1-4         : angle       3.09466 (    3)
  hydrogen bonds       : bond        0.04018 (  473)
  hydrogen bonds       : angle       4.70314 ( 1371)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       0.81348 (    6)
  covalent geometry    : bond        0.00288 (10826)
  covalent geometry    : angle       0.59368 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 99
  time to evaluate  : 1.119 
Fit side-chains
REVERT: A  136 GLN cc_start: 0.7356 (mp10) cc_final: 0.6695 (tm-30)
REVERT: A  180 MET cc_start: 0.5419 (mmt) cc_final: 0.4734 (mmt)
REVERT: A  326 LYS cc_start: 0.8823 (mttt) cc_final: 0.8230 (mtmt)
REVERT: A  693 MET cc_start: 0.3609 (mpp) cc_final: 0.2750 (ttt)
REVERT: A  727 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7416 (mp)
REVERT: A  743 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7407 (ttm-80)
REVERT: A  753 CYS cc_start: 0.7849 (m) cc_final: 0.7121 (m)
REVERT: A  852 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8658 (mp)
REVERT: A  874 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8082 (tt0)
REVERT: A 1059 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6703 (tpt170)
REVERT: C   92 ASN cc_start: 0.8639 (t0) cc_final: 0.8300 (t0)
REVERT: C  223 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7972 (tt)
  outliers start: 36
  outliers final: 26
  residues processed: 130
  average time/residue: 0.1965
  time to fit residues: 38.4893
Evaluate side-chains
  126 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  884 MET
Chi-restraints excluded: chain A residue  899 SER
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  939 ILE
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 115 optimal weight:    0.1980
   chunk 40 optimal weight:    6.9990
   chunk 110 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 114 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.188758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.134003 restraints weight = 10959.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 3.56
r_work: 0.2812 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10834  Z= 0.180
  Angle     :  0.641  10.350  14717  Z= 0.323
  Chirality :  0.046   0.208   1682
  Planarity :  0.004   0.044   1836
  Dihedral  :  5.839  57.002   1594
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.71 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.24), residues: 1302
  helix:  0.63 (0.22), residues: 593
  sheet: -0.57 (0.39), residues: 180
  loop : -1.45 (0.27), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 927 
 HIS   0.004   0.001   HIS A 323 
 PHE   0.021   0.001   PHE A 368 
 TYR   0.019   0.002   TYR C 122 
 ARG   0.011   0.000   ARG A 743 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00554 (    3)
  link_NAG-ASN         : angle       2.11670 (    9)
  link_ALPHA1-4        : bond        0.00124 (    1)
  link_ALPHA1-4        : angle       3.95740 (    3)
  link_BETA1-4         : bond        0.00166 (    1)
  link_BETA1-4         : angle       3.27071 (    3)
  hydrogen bonds       : bond        0.04532 (  473)
  hydrogen bonds       : angle       4.86202 ( 1371)
  SS BOND              : bond        0.00375 (    3)
  SS BOND              : angle       1.19494 (    6)
  covalent geometry    : bond        0.00435 (10826)
  covalent geometry    : angle       0.63443 (14696)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 93
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.7372 (mp10) cc_final: 0.6814 (tm-30)
REVERT: A  326 LYS cc_start: 0.8872 (mttt) cc_final: 0.8314 (mtmt)
REVERT: A  599 ILE cc_start: -0.0357 (OUTLIER) cc_final: -0.1052 (tt)
REVERT: A  693 MET cc_start: 0.3911 (mpp) cc_final: 0.3009 (ttt)
REVERT: A  727 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7665 (mp)
REVERT: A  753 CYS cc_start: 0.7975 (m) cc_final: 0.7288 (m)
REVERT: A  852 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8787 (mp)
REVERT: A  874 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8145 (tt0)
REVERT: A 1059 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6804 (tpt170)
REVERT: C   92 ASN cc_start: 0.8734 (t0) cc_final: 0.8422 (t0)
REVERT: C  223 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8244 (tt)
  outliers start: 35
  outliers final: 26
  residues processed: 124
  average time/residue: 0.2097
  time to fit residues: 39.1594
Evaluate side-chains
  122 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  884 MET
Chi-restraints excluded: chain A residue  899 SER
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  939 ILE
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1059 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  302 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 55 optimal weight:    9.9990
   chunk 122 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 118 optimal weight:    0.8980
   chunk 125 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 117 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.192154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.134472 restraints weight = 10884.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 4.14
r_work: 0.2872 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10834  Z= 0.121
  Angle     :  0.600  13.232  14717  Z= 0.301
  Chirality :  0.044   0.209   1682
  Planarity :  0.004   0.044   1836
  Dihedral  :  5.587  56.680   1594
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.40 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.24), residues: 1302
  helix:  0.85 (0.22), residues: 588
  sheet: -0.44 (0.39), residues: 182
  loop : -1.34 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 473 
 PHE   0.022   0.001   PHE A 368 
 TYR   0.013   0.001   TYR C 273 
 ARG   0.010   0.000   ARG A 743 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00325 (    3)
  link_NAG-ASN         : angle       1.75377 (    9)
  link_ALPHA1-4        : bond        0.00040 (    1)
  link_ALPHA1-4        : angle       3.89414 (    3)
  link_BETA1-4         : bond        0.00268 (    1)
  link_BETA1-4         : angle       2.99377 (    3)
  hydrogen bonds       : bond        0.03938 (  473)
  hydrogen bonds       : angle       4.70268 ( 1371)
  SS BOND              : bond        0.00222 (    3)
  SS BOND              : angle       0.75812 (    6)
  covalent geometry    : bond        0.00278 (10826)
  covalent geometry    : angle       0.59498 (14696)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6227.94 seconds
wall clock time: 117 minutes 35.59 seconds (7055.59 seconds total)