Starting phenix.real_space_refine
on Thu Jul  2 02:56:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7m22_23629/07_2026/7m22_23629_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7m22_23629/07_2026/7m22_23629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7m22_23629/07_2026/7m22_23629_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7m22_23629/07_2026/7m22_23629_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7m22_23629/07_2026/7m22_23629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7m22_23629/07_2026/7m22_23629.map"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      35      5.16       5
     C    3819      2.51       5
     N    1069      2.21       5
     O    1118      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6042
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 852
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 905
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "E"
      Number of atoms: 893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 893
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 3, 'TRANS': 104}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 3363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3363
          Classifications: {'peptide': 422}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 395}
          Chain breaks: 3
    Chain: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "N"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 14
          Ad-hoc single atom residues: {' CA': 1}
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.12, per 1000 atoms: 0.19
  Number of scatterers: 6042
  At special positions: 0
  Unit cell: (94.424, 104.081, 120.176, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      35     16.00
     O    1118      8.00
     N    1069      7.00
     C    3819      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  30 " - pdb=" SG  CYS C  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  31 " - pdb=" SG  CYS C  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  96 " - pdb=" SG  CYS C 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 172 " - pdb=" SG  CYS D 207 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  20 " - pdb=" SG  CYS E  40 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 149 " - pdb=" SG  CYS N 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 208 " - pdb=" SG  CYS N 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 277 " - pdb=" SG  CYS N 427 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 434 " - pdb=" SG  CYS N 592 " 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
    NAG-ASN
      " NAG E 201 " - " ASN E  81 "
      " NAG N 701 " - " ASN N 157 "
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 152.9 milliseconds
  

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 10 sheets defined
      19.7% alpha, 41.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'C' and resid 71 through 81
      removed outlier: 4.203A  pdb=" N   GLY C  75 " --> pdb=" O   ALA C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 84
      No H-bonds generated for 'chain 'C' and resid 82 through 84'
    Processing helix  chain 'C' and resid 85 through 92
      removed outlier: 3.809A  pdb=" N   LYS C  92 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 97
    Processing helix  chain 'C' and resid 117 through 119
      No H-bonds generated for 'chain 'C' and resid 117 through 119'
    Processing helix  chain 'D' and resid 105 through 118
      removed outlier: 3.675A  pdb=" N   GLY D 116 " --> pdb=" O   TRP D 112 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG D 117 " --> pdb=" O   TYR D 113 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ASN D 118 " --> pdb=" O   LEU D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 129
      Proline residue:  D 126  - end of helix
    Processing helix  chain 'D' and resid 140 through 149
    Processing helix  chain 'E' and resid 21 through 26
    Processing helix  chain 'E' and resid 35 through 41
    Processing helix  chain 'E' and resid 45 through 69
      removed outlier: 3.587A  pdb=" N   GLN E  55 " --> pdb=" O   LYS E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 78
    Processing helix  chain 'E' and resid 81 through 95
    Processing helix  chain 'N' and resid 289 through 291
      No H-bonds generated for 'chain 'N' and resid 289 through 291'
    Processing helix  chain 'N' and resid 305 through 310
      removed outlier: 3.590A  pdb=" N   GLN N 308 " --> pdb=" O   THR N 305 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ARG N 310 " --> pdb=" O   GLN N 307 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 428 through 432
      removed outlier: 3.665A  pdb=" N   ALA N 432 " --> pdb=" O   VAL N 429 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 446 through 448
      No H-bonds generated for 'chain 'N' and resid 446 through 448'
    Processing helix  chain 'N' and resid 461 through 466
    Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48
    Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 111
    Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 133
      removed outlier: 4.362A  pdb=" N   ARG D 160 " --> pdb=" O   ILE C 133 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG E 118 " --> pdb=" O   PHE D 196 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'N' and resid 152 through 153
      removed outlier: 3.638A  pdb=" N   LEU N 180 " --> pdb=" O   PHE N 153 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU N 213 " --> pdb=" O   LYS N 228 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LYS N 228 " --> pdb=" O   LEU N 213 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE N 215 " --> pdb=" O   ILE N 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'N' and resid 158 through 161
      removed outlier: 6.641A  pdb=" N   GLY N 259 " --> pdb=" O   PHE N 194 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE N 194 " --> pdb=" O   GLY N 259 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   SER N 261 " --> pdb=" O   LEU N 192 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL N 267 " --> pdb=" O   GLU N 186 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'N' and resid 279 through 280
      removed outlier: 6.587A  pdb=" N   CYS N 427 " --> pdb=" O   LEU N 339 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   LEU N 339 " --> pdb=" O   CYS N 427 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   GLN N 330 " --> pdb=" O   ARG N 408 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   ARG N 408 " --> pdb=" O   GLN N 330 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASP N 332 " --> pdb=" O   PHE N 406 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   PHE N 406 " --> pdb=" O   ASP N 332 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   ARG N 334 " --> pdb=" O   THR N 404 " (cutoff:3.500A)
      removed outlier: 10.024A  pdb=" N   THR N 404 " --> pdb=" O   ARG N 334 " (cutoff:3.500A)
      removed outlier: 9.748A  pdb=" N   LEU N 336 " --> pdb=" O   LEU N 402 " (cutoff:3.500A)
      removed outlier: 10.964A  pdb=" N   LEU N 402 " --> pdb=" O   LEU N 336 " (cutoff:3.500A)
      removed outlier: 9.959A  pdb=" N   MET N 338 " --> pdb=" O   ALA N 400 " (cutoff:3.500A)
      removed outlier: 10.897A  pdb=" N   ALA N 400 " --> pdb=" O   MET N 338 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   THR N 340 " --> pdb=" O   LEU N 398 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   SER N 360 " --> pdb=" O   GLN N 412 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   TRP N 414 " --> pdb=" O   VAL N 358 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   VAL N 358 " --> pdb=" O   TRP N 414 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'N' and resid 293 through 295
      removed outlier: 6.698A  pdb=" N   GLN N 330 " --> pdb=" O   ARG N 408 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   ARG N 408 " --> pdb=" O   GLN N 330 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASP N 332 " --> pdb=" O   PHE N 406 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   PHE N 406 " --> pdb=" O   ASP N 332 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   ARG N 334 " --> pdb=" O   THR N 404 " (cutoff:3.500A)
      removed outlier: 10.024A  pdb=" N   THR N 404 " --> pdb=" O   ARG N 334 " (cutoff:3.500A)
      removed outlier: 9.748A  pdb=" N   LEU N 336 " --> pdb=" O   LEU N 402 " (cutoff:3.500A)
      removed outlier: 10.964A  pdb=" N   LEU N 402 " --> pdb=" O   LEU N 336 " (cutoff:3.500A)
      removed outlier: 9.959A  pdb=" N   MET N 338 " --> pdb=" O   ALA N 400 " (cutoff:3.500A)
      removed outlier: 10.897A  pdb=" N   ALA N 400 " --> pdb=" O   MET N 338 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   THR N 340 " --> pdb=" O   LEU N 398 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   SER N 360 " --> pdb=" O   GLN N 412 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   TRP N 414 " --> pdb=" O   VAL N 358 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   VAL N 358 " --> pdb=" O   TRP N 414 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 347 through 348
    Processing sheet with id=AA9, first strand: chain 'N' and resid 436 through 437
      removed outlier: 6.513A  pdb=" N   CYS N 592 " --> pdb=" O   VAL N 498 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   VAL N 498 " --> pdb=" O   CYS N 592 " (cutoff:3.500A)
      removed outlier: 13.427A  pdb=" N   LEU N 488 " --> pdb=" O   GLU N 576 " (cutoff:3.500A)
      removed outlier: 11.526A  pdb=" N   GLU N 576 " --> pdb=" O   LEU N 488 " (cutoff:3.500A)
      removed outlier: 12.666A  pdb=" N   VAL N 490 " --> pdb=" O   TYR N 574 " (cutoff:3.500A)
      removed outlier: 11.314A  pdb=" N   TYR N 574 " --> pdb=" O   VAL N 490 " (cutoff:3.500A)
      removed outlier: 11.439A  pdb=" N   LEU N 492 " --> pdb=" O   ARG N 572 " (cutoff:3.500A)
      removed outlier: 12.351A  pdb=" N   ARG N 572 " --> pdb=" O   LEU N 492 " (cutoff:3.500A)
      removed outlier: 10.069A  pdb=" N   THR N 494 " --> pdb=" O   TYR N 570 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   TYR N 570 " --> pdb=" O   THR N 494 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLY N 500 " --> pdb=" O   ASP N 564 " (cutoff:3.500A)
      removed outlier: 9.477A  pdb=" N   ASP N 564 " --> pdb=" O   GLY N 500 " (cutoff:3.500A)
      removed outlier: 9.922A  pdb=" N   ILE N 502 " --> pdb=" O   ARG N 562 " (cutoff:3.500A)
      removed outlier: 9.891A  pdb=" N   ARG N 562 " --> pdb=" O   ILE N 502 " (cutoff:3.500A)
      removed outlier: 9.721A  pdb=" N   GLN N 504 " --> pdb=" O   ILE N 560 " (cutoff:3.500A)
      removed outlier: 10.227A  pdb=" N   ILE N 560 " --> pdb=" O   GLN N 504 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   LYS N 523 " --> pdb=" O   GLU N 576 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TRP N 578 " --> pdb=" O   VAL N 521 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL N 521 " --> pdb=" O   TRP N 578 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 450 through 452
      removed outlier: 13.427A  pdb=" N   LEU N 488 " --> pdb=" O   GLU N 576 " (cutoff:3.500A)
      removed outlier: 11.526A  pdb=" N   GLU N 576 " --> pdb=" O   LEU N 488 " (cutoff:3.500A)
      removed outlier: 12.666A  pdb=" N   VAL N 490 " --> pdb=" O   TYR N 574 " (cutoff:3.500A)
      removed outlier: 11.314A  pdb=" N   TYR N 574 " --> pdb=" O   VAL N 490 " (cutoff:3.500A)
      removed outlier: 11.439A  pdb=" N   LEU N 492 " --> pdb=" O   ARG N 572 " (cutoff:3.500A)
      removed outlier: 12.351A  pdb=" N   ARG N 572 " --> pdb=" O   LEU N 492 " (cutoff:3.500A)
      removed outlier: 10.069A  pdb=" N   THR N 494 " --> pdb=" O   TYR N 570 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   TYR N 570 " --> pdb=" O   THR N 494 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLY N 500 " --> pdb=" O   ASP N 564 " (cutoff:3.500A)
      removed outlier: 9.477A  pdb=" N   ASP N 564 " --> pdb=" O   GLY N 500 " (cutoff:3.500A)
      removed outlier: 9.922A  pdb=" N   ILE N 502 " --> pdb=" O   ARG N 562 " (cutoff:3.500A)
      removed outlier: 9.891A  pdb=" N   ARG N 562 " --> pdb=" O   ILE N 502 " (cutoff:3.500A)
      removed outlier: 9.721A  pdb=" N   GLN N 504 " --> pdb=" O   ILE N 560 " (cutoff:3.500A)
      removed outlier: 10.227A  pdb=" N   ILE N 560 " --> pdb=" O   GLN N 504 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   LYS N 523 " --> pdb=" O   GLU N 576 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TRP N 578 " --> pdb=" O   VAL N 521 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL N 521 " --> pdb=" O   TRP N 578 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    597 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: 0.56

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1984
        1.34 -     1.46: 1481
        1.46 -     1.58: 2674
        1.58 -     1.70: 0
        1.70 -     1.83: 50
  Bond restraints: 6189
  Sorted by residual:
  bond pdb=" C5  NAG N 701 "
       pdb=" O5  NAG N 701 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.44e+00
  bond pdb=" N   ILE N 538 "
       pdb=" CA  ILE N 538 "
    ideal  model  delta    sigma   weight residual
    1.474  1.456  0.019 1.57e-02 4.06e+03 1.43e+00
  bond pdb=" CB  ASP N 540 "
       pdb=" CG  ASP N 540 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.37e+00
  bond pdb=" CB  CYS C  30 "
       pdb=" SG  CYS C  30 "
    ideal  model  delta    sigma   weight residual
    1.808  1.772  0.036 3.30e-02 9.18e+02 1.18e+00
  bond pdb=" CB  CYS N 230 "
       pdb=" SG  CYS N 230 "
    ideal  model  delta    sigma   weight residual
    1.808  1.772  0.036 3.30e-02 9.18e+02 1.16e+00
  ... (remaining 6184 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 7777
        1.48 -     2.97: 522
        2.97 -     4.45: 74
        4.45 -     5.94: 16
        5.94 -     7.42: 4
  Bond angle restraints: 8393
  Sorted by residual:
  angle pdb=" C   GLN N 544 "
        pdb=" N   GLN N 545 "
        pdb=" CA  GLN N 545 "
      ideal   model   delta    sigma   weight residual
     122.26  115.25    7.01 1.60e+00 3.91e-01 1.92e+01
  angle pdb=" N   LEU N 467 "
        pdb=" CA  LEU N 467 "
        pdb=" C   LEU N 467 "
      ideal   model   delta    sigma   weight residual
     111.28  116.02   -4.74 1.09e+00 8.42e-01 1.89e+01
  angle pdb=" N   GLN N 544 "
        pdb=" CA  GLN N 544 "
        pdb=" C   GLN N 544 "
      ideal   model   delta    sigma   weight residual
     111.28  114.80   -3.52 1.09e+00 8.42e-01 1.04e+01
  angle pdb=" C   LEU N 467 "
        pdb=" N   VAL N 468 "
        pdb=" CA  VAL N 468 "
      ideal   model   delta    sigma   weight residual
     121.97  116.89    5.08 1.80e+00 3.09e-01 7.95e+00
  angle pdb=" C   ARG N 466 "
        pdb=" N   LEU N 467 "
        pdb=" CA  LEU N 467 "
      ideal   model   delta    sigma   weight residual
     120.28  123.93   -3.65 1.34e+00 5.57e-01 7.40e+00
  ... (remaining 8388 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 3405
       17.89 -    35.78: 274
       35.78 -    53.67: 47
       53.67 -    71.56: 13
       71.56 -    89.44: 8
  Dihedral angle restraints: 3747
    sinusoidal: 1567
      harmonic: 2180
  Sorted by residual:
  dihedral pdb=" CB  CYS C  96 "
           pdb=" SG  CYS C  96 "
           pdb=" SG  CYS C 111 "
           pdb=" CB  CYS C 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.30  -69.30     1      1.00e+01 1.00e-02 6.21e+01
  dihedral pdb=" CA  ARG N 421 "
           pdb=" C   ARG N 421 "
           pdb=" N   LEU N 422 "
           pdb=" CA  LEU N 422 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.37  -27.63     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  LEU N 420 "
           pdb=" C   LEU N 420 "
           pdb=" N   ARG N 421 "
           pdb=" CA  ARG N 421 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.39   27.61     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 3744 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 509
       0.037 -    0.074: 245
       0.074 -    0.111: 119
       0.111 -    0.149: 33
       0.149 -    0.186: 4
  Chirality restraints: 910
  Sorted by residual:
  chirality pdb=" CB  THR N 154 "
            pdb=" CA  THR N 154 "
            pdb=" OG1 THR N 154 "
            pdb=" CG2 THR N 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.62e-01
  chirality pdb=" CA  CYS C  49 "
            pdb=" N   CYS C  49 "
            pdb=" C   CYS C  49 "
            pdb=" CB  CYS C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CB  VAL N 468 "
            pdb=" CA  VAL N 468 "
            pdb=" CG1 VAL N 468 "
            pdb=" CG2 VAL N 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 907 not shown)

  Planarity restraints: 1084
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N 561 "   -0.092 9.50e-02 1.11e+02   5.41e-02 1.64e+01
        pdb=" NE  ARG N 561 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ  ARG N 561 "   -0.067 2.00e-02 2.50e+03
        pdb=" NH1 ARG N 561 "    0.024 2.00e-02 2.50e+03
        pdb=" NH2 ARG N 561 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N 350 "   -0.077 9.50e-02 1.11e+02   4.61e-02 1.22e+01
        pdb=" NE  ARG N 350 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG N 350 "   -0.058 2.00e-02 2.50e+03
        pdb=" NH1 ARG N 350 "    0.020 2.00e-02 2.50e+03
        pdb=" NH2 ARG N 350 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N 408 "    0.076 9.50e-02 1.11e+02   4.25e-02 8.92e+00
        pdb=" NE  ARG N 408 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG N 408 "    0.049 2.00e-02 2.50e+03
        pdb=" NH1 ARG N 408 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG N 408 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1081 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 281
        2.71 -     3.26: 6108
        3.26 -     3.81: 9313
        3.81 -     4.35: 11638
        4.35 -     4.90: 19539
  Nonbonded interactions: 46879
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C  47 "
            pdb=" OD2 ASP N 252 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" NZ  LYS D 154 "
            pdb=" OG1 THR D 156 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" O   VAL N 255 "
            pdb="CA    CA N 700 "
     model   vdw
     2.228 3.250
  nonbonded pdb=" OH  TYR N 169 "
            pdb=" OD2 ASP N 211 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OD2 ASP N 211 "
            pdb="CA    CA N 700 "
     model   vdw
     2.240 3.250
  ... (remaining 46874 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.160
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.260
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6201  Z= 0.206
  Angle     :  0.838   7.819   8419  Z= 0.488
  Chirality :  0.052   0.186    910
  Planarity :  0.006   0.054   1082
  Dihedral  : 14.155  89.444   2311
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.16 %
    Favored  : 94.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.28), residues: 732
  helix: -1.78 (0.39), residues: 111
  sheet:  1.09 (0.35), residues: 186
  loop : -0.91 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.068   0.008   ARG N 561 
 TYR   0.025   0.005   TYR N 357 
 PHE   0.012   0.002   PHE D 190 
 TRP   0.023   0.003   TRP N 535 
 HIS   0.006   0.001   HIS C  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.21 ( 6189)
  covalent geometry    : angle       0.82728 /  0.49 ( 8393)
  SS BOND              : bond        0.00416 /  0.25 (   10)
  SS BOND              : angle       2.33297 /  1.37 (   20)
  hydrogen bonds       : bond        0.17122 / 11.51 (  206)
  hydrogen bonds       : angle       7.79682 /  5.47 (  597)
  link_NAG-ASN         : bond        0.00648 /  0.34 (    2)
  link_NAG-ASN         : angle       3.04091 /  1.65 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 221
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7380 (p90) cc_final: 0.6664 (p90)
REVERT: C   48 MET cc_start: 0.7326 (pmm) cc_final: 0.7013 (pmm)
REVERT: C  116 ASP cc_start: 0.7754 (m-30) cc_final: 0.7193 (m-30)
REVERT: D  111 ILE cc_start: 0.8318 (mm) cc_final: 0.7917 (mm)
REVERT: D  125 MET cc_start: 0.8095 (ttm) cc_final: 0.7784 (ttm)
REVERT: D  154 LYS cc_start: 0.8140 (tptp) cc_final: 0.7707 (tptp)
REVERT: D  178 SER cc_start: 0.8348 (p) cc_final: 0.8052 (p)
REVERT: D  188 VAL cc_start: 0.8545 (m) cc_final: 0.8200 (p)
REVERT: E   51 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7476 (mmmt)
REVERT: E   91 ASP cc_start: 0.7903 (t0) cc_final: 0.7695 (t0)
REVERT: N  151 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8240 (mtmt)
REVERT: N  160 ILE cc_start: 0.8071 (tp) cc_final: 0.7680 (pt)
REVERT: N  161 GLU cc_start: 0.7323 (pm20) cc_final: 0.6998 (pm20)
REVERT: N  174 ASP cc_start: 0.7712 (t0) cc_final: 0.7315 (t0)
REVERT: N  186 GLU cc_start: 0.6908 (tp30) cc_final: 0.6252 (tp30)
REVERT: N  188 ILE cc_start: 0.8164 (mp) cc_final: 0.7821 (mt)
REVERT: N  212 TRP cc_start: 0.8535 (p90) cc_final: 0.8323 (p90)
REVERT: N  226 ILE cc_start: 0.8829 (mt) cc_final: 0.8504 (mm)
REVERT: N  229 TYR cc_start: 0.7965 (m-80) cc_final: 0.7622 (m-80)
REVERT: N  238 LEU cc_start: 0.8468 (pt) cc_final: 0.8201 (pp)
REVERT: N  239 ARG cc_start: 0.7441 (mtt90) cc_final: 0.7063 (mtt-85)
REVERT: N  278 ASN cc_start: 0.6584 (m-40) cc_final: 0.6321 (m-40)
REVERT: N  339 LEU cc_start: 0.7946 (tp) cc_final: 0.7725 (mp)
REVERT: N  364 GLU cc_start: 0.6716 (tp30) cc_final: 0.6425 (tp30)
REVERT: N  373 MET cc_start: 0.6995 (tmm) cc_final: 0.6703 (tmm)
REVERT: N  376 ARG cc_start: 0.8098 (ptp-170) cc_final: 0.7844 (ptp-110)
REVERT: N  423 GLU cc_start: 0.6904 (tp30) cc_final: 0.6686 (tp30)
REVERT: N  456 GLN cc_start: 0.7737 (tm-30) cc_final: 0.6616 (tm-30)
REVERT: N  457 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6735 (mm-30)
REVERT: N  460 TRP cc_start: 0.7725 (t-100) cc_final: 0.7108 (t-100)
REVERT: N  498 VAL cc_start: 0.8365 (t) cc_final: 0.7955 (m)
REVERT: N  535 TRP cc_start: 0.7304 (m100) cc_final: 0.6626 (m100)
REVERT: N  555 TYR cc_start: 0.7522 (p90) cc_final: 0.7283 (p90)
REVERT: N  559 ASP cc_start: 0.7477 (t0) cc_final: 0.7238 (t0)
REVERT: N  572 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6364 (mtt180)
  outliers start: 4
  outliers final: 2
  residues processed: 225
  average time/residue: 0.0764
  time to fit residues: 21.5764
Evaluate side-chains
  211 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 209
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain N residue  542 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0370
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   overall best weight:    0.4858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  37 ASN
C  90 HIS
C  91 ASN
D 119 GLN
D 138 GLN
D 181 HIS
D 211 ASN
N 171 HIS
N 172 ASN
N 250 HIS
N 292 GLN
N 385 GLN
N 396 ASN
N 415 HIS
N 436 ASN
N 480 GLN
** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.130719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.113303 restraints weight = 10383.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.117128 restraints weight = 5304.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.119682 restraints weight = 3219.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.121344 restraints weight = 2190.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.122575 restraints weight = 1639.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6201  Z= 0.192
  Angle     :  0.712   6.520   8419  Z= 0.380
  Chirality :  0.048   0.141    910
  Planarity :  0.005   0.052   1082
  Dihedral  :  7.395  54.989    872
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 10.93 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.29), residues: 732
  helix: -0.60 (0.44), residues: 111
  sheet:  1.50 (0.37), residues: 173
  loop : -0.80 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N 263 
 TYR   0.028   0.002   TYR C 130 
 PHE   0.011   0.002   PHE N 549 
 TRP   0.016   0.002   TRP N 535 
 HIS   0.010   0.001   HIS C  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.19 ( 6189)
  covalent geometry    : angle       0.70631 /  0.38 ( 8393)
  SS BOND              : bond        0.00499 /  0.29 (   10)
  SS BOND              : angle       1.47221 /  0.94 (   20)
  hydrogen bonds       : bond        0.04861 /  3.23 (  206)
  hydrogen bonds       : angle       5.84447 /  4.18 (  597)
  link_NAG-ASN         : bond        0.00611 /  0.32 (    2)
  link_NAG-ASN         : angle       2.68805 /  1.47 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7679 (p90) cc_final: 0.7059 (p90)
REVERT: C   48 MET cc_start: 0.7374 (pmm) cc_final: 0.6958 (pmm)
REVERT: C  108 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7593 (mtm110)
REVERT: D  111 ILE cc_start: 0.8357 (mm) cc_final: 0.7953 (mm)
REVERT: D  124 ARG cc_start: 0.6828 (mpp80) cc_final: 0.6594 (mtt90)
REVERT: D  125 MET cc_start: 0.7808 (ttm) cc_final: 0.7464 (ttp)
REVERT: D  174 MET cc_start: 0.7996 (ttp) cc_final: 0.7751 (ttp)
REVERT: D  178 SER cc_start: 0.8352 (p) cc_final: 0.8127 (p)
REVERT: E   32 ARG cc_start: 0.8585 (mmt90) cc_final: 0.8384 (mmt90)
REVERT: E   77 LEU cc_start: 0.8583 (tp) cc_final: 0.8274 (tp)
REVERT: E   91 ASP cc_start: 0.7898 (t0) cc_final: 0.7671 (t0)
REVERT: N  151 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8270 (mtmt)
REVERT: N  160 ILE cc_start: 0.8153 (tp) cc_final: 0.7780 (pt)
REVERT: N  161 GLU cc_start: 0.7284 (pm20) cc_final: 0.7046 (pm20)
REVERT: N  174 ASP cc_start: 0.7767 (t0) cc_final: 0.7244 (t0)
REVERT: N  186 GLU cc_start: 0.6616 (tp30) cc_final: 0.5989 (tp30)
REVERT: N  188 ILE cc_start: 0.8269 (mp) cc_final: 0.8039 (mt)
REVERT: N  212 TRP cc_start: 0.8505 (p90) cc_final: 0.8056 (p90)
REVERT: N  228 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7493 (mtpt)
REVERT: N  229 TYR cc_start: 0.8084 (m-80) cc_final: 0.7443 (m-80)
REVERT: N  233 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7516 (mtpp)
REVERT: N  288 ILE cc_start: 0.8295 (mt) cc_final: 0.8084 (mt)
REVERT: N  332 ASP cc_start: 0.7685 (t0) cc_final: 0.7427 (t0)
REVERT: N  339 LEU cc_start: 0.8235 (tp) cc_final: 0.7922 (mp)
REVERT: N  362 LYS cc_start: 0.7940 (mtmt) cc_final: 0.7680 (mtmm)
REVERT: N  364 GLU cc_start: 0.6721 (tp30) cc_final: 0.6320 (tp30)
REVERT: N  373 MET cc_start: 0.6937 (tmm) cc_final: 0.6594 (tmm)
REVERT: N  376 ARG cc_start: 0.8095 (ptp-170) cc_final: 0.7745 (ptp-110)
REVERT: N  456 GLN cc_start: 0.8018 (tm-30) cc_final: 0.6774 (tm-30)
REVERT: N  457 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7023 (mm-30)
REVERT: N  535 TRP cc_start: 0.7413 (m100) cc_final: 0.6809 (m100)
REVERT: N  542 ARG cc_start: 0.5581 (OUTLIER) cc_final: 0.4389 (mmm160)
REVERT: N  559 ASP cc_start: 0.7754 (t0) cc_final: 0.7415 (t0)
REVERT: N  572 ARG cc_start: 0.7033 (mtt180) cc_final: 0.6272 (mtt180)
REVERT: N  576 GLU cc_start: 0.6712 (mp0) cc_final: 0.6408 (mp0)
  outliers start: 27
  outliers final: 20
  residues processed: 202
  average time/residue: 0.0794
  time to fit residues: 19.9835
Evaluate side-chains
  215 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 194
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  200 ASN
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  488 LEU
Chi-restraints excluded: chain N residue  542 ARG
Chi-restraints excluded: chain N residue  550 GLU
Chi-restraints excluded: chain N residue  585 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0870
   chunk 32 optimal weight:    0.4980
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 211 ASN
** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.129870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112900 restraints weight = 10301.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116553 restraints weight = 5335.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.118943 restraints weight = 3285.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.120591 restraints weight = 2255.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.121740 restraints weight = 1697.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6201  Z= 0.192
  Angle     :  0.668   6.964   8419  Z= 0.354
  Chirality :  0.048   0.213    910
  Planarity :  0.005   0.052   1082
  Dihedral  :  6.974  59.578    872
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 12.90 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.30), residues: 732
  helix: -0.63 (0.46), residues: 117
  sheet:  1.40 (0.38), residues: 173
  loop : -0.88 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N 562 
 TYR   0.029   0.002   TYR C 130 
 PHE   0.011   0.002   PHE E 122 
 TRP   0.014   0.002   TRP N 535 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00430 /  0.19 ( 6189)
  covalent geometry    : angle       0.66160 /  0.35 ( 8393)
  SS BOND              : bond        0.00476 /  0.29 (   10)
  SS BOND              : angle       1.43899 /  0.89 (   20)
  hydrogen bonds       : bond        0.04708 /  3.09 (  206)
  hydrogen bonds       : angle       5.60704 /  4.03 (  597)
  link_NAG-ASN         : bond        0.00635 /  0.33 (    2)
  link_NAG-ASN         : angle       2.52858 /  1.39 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7812 (p90) cc_final: 0.7325 (p90)
REVERT: C   48 MET cc_start: 0.7341 (pmm) cc_final: 0.6953 (pmm)
REVERT: C  108 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7610 (mtm110)
REVERT: D  111 ILE cc_start: 0.8388 (mm) cc_final: 0.7978 (mm)
REVERT: E   51 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7563 (mmmt)
REVERT: E   91 ASP cc_start: 0.7861 (t0) cc_final: 0.7625 (t0)
REVERT: N  151 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8183 (mtmt)
REVERT: N  153 PHE cc_start: 0.7452 (m-80) cc_final: 0.7213 (m-80)
REVERT: N  174 ASP cc_start: 0.7849 (t0) cc_final: 0.7288 (t0)
REVERT: N  186 GLU cc_start: 0.6552 (tp30) cc_final: 0.6023 (tp30)
REVERT: N  188 ILE cc_start: 0.8318 (mp) cc_final: 0.7960 (mt)
REVERT: N  229 TYR cc_start: 0.8017 (m-80) cc_final: 0.7556 (m-80)
REVERT: N  233 LYS cc_start: 0.7721 (mtpp) cc_final: 0.7507 (mtpp)
REVERT: N  239 ARG cc_start: 0.7399 (mtt90) cc_final: 0.6995 (mtt-85)
REVERT: N  278 ASN cc_start: 0.6242 (m110) cc_final: 0.6014 (m-40)
REVERT: N  332 ASP cc_start: 0.7742 (t0) cc_final: 0.7530 (t0)
REVERT: N  339 LEU cc_start: 0.8196 (tp) cc_final: 0.7944 (mp)
REVERT: N  362 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7705 (mtmm)
REVERT: N  364 GLU cc_start: 0.6778 (tp30) cc_final: 0.6355 (tp30)
REVERT: N  373 MET cc_start: 0.6881 (tmm) cc_final: 0.6625 (tmm)
REVERT: N  376 ARG cc_start: 0.8040 (ptp-170) cc_final: 0.7655 (ptp-110)
REVERT: N  456 GLN cc_start: 0.8020 (tm-30) cc_final: 0.6715 (tm-30)
REVERT: N  457 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7143 (mm-30)
REVERT: N  498 VAL cc_start: 0.8436 (t) cc_final: 0.8023 (m)
REVERT: N  535 TRP cc_start: 0.7498 (m100) cc_final: 0.6964 (m100)
REVERT: N  542 ARG cc_start: 0.5576 (OUTLIER) cc_final: 0.4457 (mmm160)
REVERT: N  570 TYR cc_start: 0.6419 (m-80) cc_final: 0.6165 (m-80)
REVERT: N  572 ARG cc_start: 0.7037 (mtt180) cc_final: 0.6275 (mtt180)
REVERT: N  576 GLU cc_start: 0.6807 (mp0) cc_final: 0.6525 (mp0)
  outliers start: 36
  outliers final: 21
  residues processed: 207
  average time/residue: 0.1003
  time to fit residues: 25.8034
Evaluate side-chains
  213 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 191
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  171 MET
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  337 THR
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  488 LEU
Chi-restraints excluded: chain N residue  542 ARG
Chi-restraints excluded: chain N residue  557 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0010
   chunk 22 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0000
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    0.2980
   chunk 57 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.3790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 164 ASN
** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 396 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.130549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.113437 restraints weight = 10330.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.117208 restraints weight = 5240.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119686 restraints weight = 3155.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.121362 restraints weight = 2138.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.122504 restraints weight = 1595.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6201  Z= 0.154
  Angle     :  0.632   6.975   8419  Z= 0.332
  Chirality :  0.047   0.196    910
  Planarity :  0.005   0.049   1082
  Dihedral  :  6.579  57.410    872
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 14.87 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.30), residues: 732
  helix: -0.50 (0.47), residues: 117
  sheet:  1.23 (0.37), residues: 187
  loop : -0.98 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N 562 
 TYR   0.028   0.002   TYR C 130 
 PHE   0.010   0.001   PHE E 122 
 TRP   0.012   0.002   TRP D 179 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 6189)
  covalent geometry    : angle       0.62663 /  0.33 ( 8393)
  SS BOND              : bond        0.00485 /  0.27 (   10)
  SS BOND              : angle       1.32441 /  0.85 (   20)
  hydrogen bonds       : bond        0.04235 /  2.76 (  206)
  hydrogen bonds       : angle       5.43505 /  3.90 (  597)
  link_NAG-ASN         : bond        0.00427 /  0.22 (    2)
  link_NAG-ASN         : angle       2.26822 /  1.25 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 190
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7810 (p90) cc_final: 0.7414 (p90)
REVERT: C   48 MET cc_start: 0.7347 (pmm) cc_final: 0.6938 (pmm)
REVERT: C  101 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6995 (pp)
REVERT: D  111 ILE cc_start: 0.8367 (mm) cc_final: 0.7956 (mm)
REVERT: E   91 ASP cc_start: 0.7889 (t0) cc_final: 0.7620 (t0)
REVERT: N  151 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8136 (mtmt)
REVERT: N  153 PHE cc_start: 0.7409 (m-80) cc_final: 0.7209 (m-80)
REVERT: N  174 ASP cc_start: 0.7812 (t0) cc_final: 0.7269 (t0)
REVERT: N  188 ILE cc_start: 0.8333 (mp) cc_final: 0.8090 (mt)
REVERT: N  190 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7199 (mm-40)
REVERT: N  228 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7788 (mtpp)
REVERT: N  229 TYR cc_start: 0.7980 (m-80) cc_final: 0.7393 (m-80)
REVERT: N  233 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7523 (mtpp)
REVERT: N  237 GLU cc_start: 0.6821 (mp0) cc_final: 0.6371 (mp0)
REVERT: N  239 ARG cc_start: 0.7355 (mtt90) cc_final: 0.7057 (mtt90)
REVERT: N  332 ASP cc_start: 0.7865 (t0) cc_final: 0.7663 (t0)
REVERT: N  339 LEU cc_start: 0.8174 (tp) cc_final: 0.7933 (mp)
REVERT: N  362 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7696 (mtmm)
REVERT: N  364 GLU cc_start: 0.6770 (tp30) cc_final: 0.6282 (tp30)
REVERT: N  373 MET cc_start: 0.6834 (tmm) cc_final: 0.6582 (tmm)
REVERT: N  376 ARG cc_start: 0.8050 (ptp-170) cc_final: 0.7572 (ptp-110)
REVERT: N  456 GLN cc_start: 0.8063 (tm-30) cc_final: 0.6815 (tm-30)
REVERT: N  457 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7199 (mm-30)
REVERT: N  498 VAL cc_start: 0.8351 (t) cc_final: 0.7951 (m)
REVERT: N  535 TRP cc_start: 0.7483 (m100) cc_final: 0.6957 (m100)
REVERT: N  542 ARG cc_start: 0.5579 (OUTLIER) cc_final: 0.4311 (mmm160)
REVERT: N  570 TYR cc_start: 0.6498 (m-80) cc_final: 0.6228 (m-80)
REVERT: N  572 ARG cc_start: 0.6995 (mtt180) cc_final: 0.6253 (mtt180)
REVERT: N  576 GLU cc_start: 0.6794 (mp0) cc_final: 0.6426 (mp0)
  outliers start: 36
  outliers final: 22
  residues processed: 204
  average time/residue: 0.1042
  time to fit residues: 26.2315
Evaluate side-chains
  211 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 187
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain E residue   20 CYS
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  337 THR
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  444 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  542 ARG
Chi-restraints excluded: chain N residue  557 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    0.2980
   chunk 30 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 164 ASN
** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.129170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112329 restraints weight = 10534.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.115994 restraints weight = 5425.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.118395 restraints weight = 3298.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.120012 restraints weight = 2256.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.121156 restraints weight = 1691.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6201  Z= 0.210
  Angle     :  0.672   7.893   8419  Z= 0.350
  Chirality :  0.048   0.198    910
  Planarity :  0.005   0.052   1082
  Dihedral  :  6.469  48.590    872
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 18.36 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.30), residues: 732
  helix: -0.63 (0.46), residues: 117
  sheet:  1.02 (0.38), residues: 183
  loop : -1.06 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG N 562 
 TYR   0.033   0.002   TYR C 130 
 PHE   0.013   0.002   PHE E 122 
 TRP   0.015   0.002   TRP N 372 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00469 /  0.21 ( 6189)
  covalent geometry    : angle       0.66711 /  0.35 ( 8393)
  SS BOND              : bond        0.00453 /  0.27 (   10)
  SS BOND              : angle       1.22935 /  0.80 (   20)
  hydrogen bonds       : bond        0.04673 /  2.99 (  206)
  hydrogen bonds       : angle       5.53251 /  3.96 (  597)
  link_NAG-ASN         : bond        0.00748 /  0.39 (    2)
  link_NAG-ASN         : angle       2.40089 /  1.32 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 190
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7915 (p90) cc_final: 0.7470 (p90)
REVERT: C   48 MET cc_start: 0.7339 (pmm) cc_final: 0.6965 (pmm)
REVERT: C  108 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7647 (mtm110)
REVERT: D  111 ILE cc_start: 0.8482 (mm) cc_final: 0.8054 (mm)
REVERT: E   32 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8069 (mmt90)
REVERT: E   91 ASP cc_start: 0.7849 (t0) cc_final: 0.7600 (t0)
REVERT: N  151 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8205 (mtmt)
REVERT: N  174 ASP cc_start: 0.7814 (t0) cc_final: 0.7269 (t0)
REVERT: N  188 ILE cc_start: 0.8384 (mp) cc_final: 0.8132 (mt)
REVERT: N  190 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7354 (mm-40)
REVERT: N  229 TYR cc_start: 0.7963 (m-80) cc_final: 0.7507 (m-80)
REVERT: N  237 GLU cc_start: 0.6711 (mp0) cc_final: 0.6421 (mp0)
REVERT: N  252 ASP cc_start: 0.7487 (p0) cc_final: 0.7284 (p0)
REVERT: N  339 LEU cc_start: 0.8174 (tp) cc_final: 0.7939 (mp)
REVERT: N  362 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7756 (mtmm)
REVERT: N  364 GLU cc_start: 0.6908 (tp30) cc_final: 0.6406 (tp30)
REVERT: N  376 ARG cc_start: 0.8054 (ptp-170) cc_final: 0.7546 (ptp-110)
REVERT: N  456 GLN cc_start: 0.8013 (tm-30) cc_final: 0.6776 (tm-30)
REVERT: N  457 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7197 (mm-30)
REVERT: N  498 VAL cc_start: 0.8552 (t) cc_final: 0.8159 (m)
REVERT: N  535 TRP cc_start: 0.7555 (m100) cc_final: 0.7038 (m100)
REVERT: N  542 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.4723 (mmm160)
REVERT: N  555 TYR cc_start: 0.7834 (p90) cc_final: 0.7612 (p90)
REVERT: N  570 TYR cc_start: 0.6483 (m-80) cc_final: 0.6199 (m-80)
REVERT: N  572 ARG cc_start: 0.6965 (mtt180) cc_final: 0.6230 (mtt180)
REVERT: N  576 GLU cc_start: 0.6795 (mp0) cc_final: 0.6446 (mp0)
  outliers start: 33
  outliers final: 27
  residues processed: 204
  average time/residue: 0.0995
  time to fit residues: 25.3322
Evaluate side-chains
  217 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  172 ASN
Chi-restraints excluded: chain N residue  238 LEU
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  279 VAL
Chi-restraints excluded: chain N residue  296 SER
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  337 THR
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  444 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  542 ARG
Chi-restraints excluded: chain N residue  557 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0980
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0030
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.3790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 164 ASN
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.130577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.113678 restraints weight = 10334.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.117298 restraints weight = 5334.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119707 restraints weight = 3253.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.121215 restraints weight = 2225.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.122418 restraints weight = 1696.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6201  Z= 0.156
  Angle     :  0.659  10.846   8419  Z= 0.335
  Chirality :  0.047   0.223    910
  Planarity :  0.005   0.052   1082
  Dihedral  :  6.167  44.080    872
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 19.58 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.30), residues: 732
  helix: -0.48 (0.47), residues: 117
  sheet:  1.05 (0.38), residues: 184
  loop : -1.12 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  32 
 TYR   0.032   0.002   TYR C 130 
 PHE   0.009   0.001   PHE N 153 
 TRP   0.011   0.002   TRP D 179 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.16 ( 6189)
  covalent geometry    : angle       0.65539 /  0.33 ( 8393)
  SS BOND              : bond        0.00386 /  0.22 (   10)
  SS BOND              : angle       1.04039 /  0.64 (   20)
  hydrogen bonds       : bond        0.04277 /  2.74 (  206)
  hydrogen bonds       : angle       5.38860 /  3.86 (  597)
  link_NAG-ASN         : bond        0.00406 /  0.21 (    2)
  link_NAG-ASN         : angle       2.09019 /  1.14 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7935 (p90) cc_final: 0.7435 (p90)
REVERT: C   48 MET cc_start: 0.7349 (pmm) cc_final: 0.6959 (pmm)
REVERT: C   78 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6942 (t)
REVERT: D  111 ILE cc_start: 0.8442 (mm) cc_final: 0.8014 (mm)
REVERT: D  154 LYS cc_start: 0.8343 (tptp) cc_final: 0.8067 (tptp)
REVERT: D  170 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8213 (mt0)
REVERT: E   91 ASP cc_start: 0.7875 (t0) cc_final: 0.7652 (t0)
REVERT: N  151 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8188 (mtmt)
REVERT: N  174 ASP cc_start: 0.7802 (t0) cc_final: 0.7279 (t0)
REVERT: N  188 ILE cc_start: 0.8351 (mp) cc_final: 0.8107 (mt)
REVERT: N  229 TYR cc_start: 0.7960 (m-80) cc_final: 0.7371 (m-80)
REVERT: N  339 LEU cc_start: 0.8163 (tp) cc_final: 0.7924 (mp)
REVERT: N  362 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7730 (mtmm)
REVERT: N  364 GLU cc_start: 0.6943 (tp30) cc_final: 0.6311 (tp30)
REVERT: N  373 MET cc_start: 0.6926 (tmm) cc_final: 0.6520 (tmm)
REVERT: N  376 ARG cc_start: 0.7949 (ptp-170) cc_final: 0.7473 (ptp-110)
REVERT: N  456 GLN cc_start: 0.8038 (tm-30) cc_final: 0.6852 (tm-30)
REVERT: N  457 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7198 (mm-30)
REVERT: N  535 TRP cc_start: 0.7576 (m100) cc_final: 0.6967 (m100)
REVERT: N  542 ARG cc_start: 0.5650 (OUTLIER) cc_final: 0.4777 (mmm160)
REVERT: N  555 TYR cc_start: 0.7878 (p90) cc_final: 0.7616 (p90)
REVERT: N  572 ARG cc_start: 0.6950 (mtt180) cc_final: 0.6218 (mtt180)
REVERT: N  576 GLU cc_start: 0.6833 (mp0) cc_final: 0.6469 (mp0)
  outliers start: 33
  outliers final: 23
  residues processed: 200
  average time/residue: 0.1007
  time to fit residues: 24.9904
Evaluate side-chains
  217 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 191
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  170 GLN
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  238 LEU
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  279 VAL
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  337 THR
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  444 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  501 VAL
Chi-restraints excluded: chain N residue  542 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.112006 restraints weight = 10475.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.115612 restraints weight = 5459.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.118048 restraints weight = 3343.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.119705 restraints weight = 2292.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.120748 restraints weight = 1719.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6201  Z= 0.232
  Angle     :  0.696   9.008   8419  Z= 0.360
  Chirality :  0.049   0.177    910
  Planarity :  0.005   0.052   1082
  Dihedral  :  6.360  42.988    872
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 20.18 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.30), residues: 732
  helix: -0.50 (0.48), residues: 111
  sheet:  1.08 (0.38), residues: 178
  loop : -1.23 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  32 
 TYR   0.039   0.002   TYR C 130 
 PHE   0.013   0.002   PHE E 122 
 TRP   0.026   0.002   TRP N 372 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00520 /  0.23 ( 6189)
  covalent geometry    : angle       0.69104 /  0.36 ( 8393)
  SS BOND              : bond        0.00453 /  0.28 (   10)
  SS BOND              : angle       1.23342 /  0.79 (   20)
  hydrogen bonds       : bond        0.04785 /  3.10 (  206)
  hydrogen bonds       : angle       5.51962 /  3.94 (  597)
  link_NAG-ASN         : bond        0.00882 /  0.46 (    2)
  link_NAG-ASN         : angle       2.48026 /  1.36 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 194
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7929 (p90) cc_final: 0.7462 (p90)
REVERT: C   48 MET cc_start: 0.7347 (pmm) cc_final: 0.7074 (pmm)
REVERT: C   78 THR cc_start: 0.7201 (OUTLIER) cc_final: 0.6938 (t)
REVERT: D  111 ILE cc_start: 0.8513 (mm) cc_final: 0.8076 (mm)
REVERT: E   32 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8117 (mmt90)
REVERT: E   91 ASP cc_start: 0.7859 (t0) cc_final: 0.7632 (t0)
REVERT: N  151 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8188 (mtmt)
REVERT: N  174 ASP cc_start: 0.7787 (t0) cc_final: 0.7172 (t0)
REVERT: N  188 ILE cc_start: 0.8366 (mp) cc_final: 0.8138 (mt)
REVERT: N  190 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7366 (mm-40)
REVERT: N  229 TYR cc_start: 0.7864 (m-80) cc_final: 0.7338 (m-80)
REVERT: N  237 GLU cc_start: 0.6797 (mp0) cc_final: 0.6359 (mp0)
REVERT: N  339 LEU cc_start: 0.8174 (tp) cc_final: 0.7971 (mp)
REVERT: N  362 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7731 (mtmm)
REVERT: N  364 GLU cc_start: 0.6916 (tp30) cc_final: 0.6361 (tp30)
REVERT: N  373 MET cc_start: 0.6974 (tmm) cc_final: 0.6395 (tmm)
REVERT: N  376 ARG cc_start: 0.8047 (ptp-170) cc_final: 0.7661 (ptp-110)
REVERT: N  405 ARG cc_start: 0.8103 (ttt180) cc_final: 0.7881 (ttt-90)
REVERT: N  456 GLN cc_start: 0.7946 (tm-30) cc_final: 0.6675 (tm-30)
REVERT: N  457 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7250 (mm-30)
REVERT: N  535 TRP cc_start: 0.7577 (m100) cc_final: 0.7005 (m100)
REVERT: N  542 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5681 (mmm160)
REVERT: N  555 TYR cc_start: 0.7837 (p90) cc_final: 0.7603 (p90)
REVERT: N  572 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6311 (mtt180)
REVERT: N  576 GLU cc_start: 0.6786 (mp0) cc_final: 0.6466 (mp0)
  outliers start: 34
  outliers final: 24
  residues processed: 210
  average time/residue: 0.1084
  time to fit residues: 28.0142
Evaluate side-chains
  216 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 190
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  195 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  172 ASN
Chi-restraints excluded: chain N residue  193 ILE
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  279 VAL
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  444 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  501 VAL
Chi-restraints excluded: chain N residue  542 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0010
   chunk 45 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0020
   overall best weight:    0.4394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.130106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.113270 restraints weight = 10511.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116913 restraints weight = 5441.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.119320 restraints weight = 3313.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.120990 restraints weight = 2279.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.122004 restraints weight = 1698.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6201  Z= 0.172
  Angle     :  0.659   8.655   8419  Z= 0.340
  Chirality :  0.047   0.182    910
  Planarity :  0.005   0.054   1082
  Dihedral  :  6.023  42.781    871
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 21.09 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.30), residues: 732
  helix: -0.48 (0.48), residues: 111
  sheet:  1.10 (0.38), residues: 184
  loop : -1.35 (0.27), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  32 
 TYR   0.038   0.002   TYR C 130 
 PHE   0.024   0.002   PHE N 260 
 TRP   0.019   0.002   TRP N 372 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.17 ( 6189)
  covalent geometry    : angle       0.65488 /  0.34 ( 8393)
  SS BOND              : bond        0.00424 /  0.26 (   10)
  SS BOND              : angle       1.18827 /  0.77 (   20)
  hydrogen bonds       : bond        0.04262 /  2.77 (  206)
  hydrogen bonds       : angle       5.36701 /  3.83 (  597)
  link_NAG-ASN         : bond        0.00583 /  0.31 (    2)
  link_NAG-ASN         : angle       2.23345 /  1.21 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7896 (p90) cc_final: 0.7457 (p90)
REVERT: C   48 MET cc_start: 0.7339 (pmm) cc_final: 0.6909 (pmm)
REVERT: C   78 THR cc_start: 0.7086 (OUTLIER) cc_final: 0.6870 (t)
REVERT: D  111 ILE cc_start: 0.8487 (mm) cc_final: 0.8069 (mm)
REVERT: D  154 LYS cc_start: 0.8306 (tptp) cc_final: 0.8034 (tptp)
REVERT: E   32 ARG cc_start: 0.8527 (mmt90) cc_final: 0.8063 (mmt90)
REVERT: E   65 TYR cc_start: 0.7941 (t80) cc_final: 0.7667 (t80)
REVERT: E   91 ASP cc_start: 0.7837 (t0) cc_final: 0.7624 (t0)
REVERT: N  151 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8118 (mtmt)
REVERT: N  174 ASP cc_start: 0.7783 (t0) cc_final: 0.7222 (t0)
REVERT: N  188 ILE cc_start: 0.8361 (mp) cc_final: 0.8105 (mt)
REVERT: N  190 GLN cc_start: 0.7612 (mm-40) cc_final: 0.6829 (mm110)
REVERT: N  229 TYR cc_start: 0.8035 (m-80) cc_final: 0.7470 (m-80)
REVERT: N  237 GLU cc_start: 0.6733 (mp0) cc_final: 0.5328 (mp0)
REVERT: N  339 LEU cc_start: 0.8212 (tp) cc_final: 0.7974 (mp)
REVERT: N  362 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7731 (mtmm)
REVERT: N  364 GLU cc_start: 0.6908 (tp30) cc_final: 0.6370 (tp30)
REVERT: N  373 MET cc_start: 0.6925 (tmm) cc_final: 0.6373 (tmm)
REVERT: N  376 ARG cc_start: 0.8031 (ptp-170) cc_final: 0.7658 (ptp-110)
REVERT: N  405 ARG cc_start: 0.8088 (ttt180) cc_final: 0.7860 (ttt180)
REVERT: N  456 GLN cc_start: 0.7939 (tm-30) cc_final: 0.6637 (tm-30)
REVERT: N  457 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7250 (mm-30)
REVERT: N  535 TRP cc_start: 0.7574 (m100) cc_final: 0.6978 (m100)
REVERT: N  555 TYR cc_start: 0.7820 (p90) cc_final: 0.7593 (p90)
REVERT: N  572 ARG cc_start: 0.6997 (mtt180) cc_final: 0.6360 (mtt180)
REVERT: N  576 GLU cc_start: 0.6811 (mp0) cc_final: 0.6497 (mp0)
  outliers start: 28
  outliers final: 21
  residues processed: 200
  average time/residue: 0.1083
  time to fit residues: 26.7251
Evaluate side-chains
  211 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  195 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  238 LEU
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  444 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  501 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    0.3980
   chunk 2 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0970
   chunk 56 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 55 optimal weight:    0.3980
   chunk 40 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0970
   overall best weight:    0.2976

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.131262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.114068 restraints weight = 10496.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.117713 restraints weight = 5428.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.120231 restraints weight = 3329.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.121858 restraints weight = 2274.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.123065 restraints weight = 1708.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6201  Z= 0.139
  Angle     :  0.645   8.778   8419  Z= 0.329
  Chirality :  0.045   0.146    910
  Planarity :  0.005   0.053   1082
  Dihedral  :  5.303  23.902    867
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.46 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.30), residues: 732
  helix: -0.34 (0.49), residues: 111
  sheet:  1.37 (0.38), residues: 181
  loop : -1.36 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  32 
 TYR   0.036   0.001   TYR C 130 
 PHE   0.024   0.001   PHE N 260 
 TRP   0.016   0.001   TRP N 372 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 6189)
  covalent geometry    : angle       0.64124 /  0.33 ( 8393)
  SS BOND              : bond        0.00373 /  0.21 (   10)
  SS BOND              : angle       1.17055 /  0.75 (   20)
  hydrogen bonds       : bond        0.03997 /  2.56 (  206)
  hydrogen bonds       : angle       5.19724 /  3.70 (  597)
  link_NAG-ASN         : bond        0.00423 /  0.22 (    2)
  link_NAG-ASN         : angle       2.07483 /  1.14 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7888 (p90) cc_final: 0.7435 (p90)
REVERT: C   48 MET cc_start: 0.7359 (pmm) cc_final: 0.6935 (pmm)
REVERT: C   78 THR cc_start: 0.7077 (OUTLIER) cc_final: 0.6873 (t)
REVERT: C  104 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6913 (mp0)
REVERT: D  111 ILE cc_start: 0.8443 (mm) cc_final: 0.8025 (mm)
REVERT: D  154 LYS cc_start: 0.8302 (tptp) cc_final: 0.7975 (tptp)
REVERT: E   79 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8098 (mtm-85)
REVERT: E   91 ASP cc_start: 0.7857 (t0) cc_final: 0.7616 (t0)
REVERT: N  151 LYS cc_start: 0.8352 (mtmt) cc_final: 0.8110 (mtmt)
REVERT: N  174 ASP cc_start: 0.7787 (t0) cc_final: 0.7207 (t0)
REVERT: N  188 ILE cc_start: 0.8348 (mp) cc_final: 0.8117 (mt)
REVERT: N  190 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7244 (mm-40)
REVERT: N  229 TYR cc_start: 0.8010 (m-80) cc_final: 0.7389 (m-80)
REVERT: N  237 GLU cc_start: 0.6796 (mp0) cc_final: 0.6198 (mp0)
REVERT: N  339 LEU cc_start: 0.8197 (tp) cc_final: 0.7946 (mp)
REVERT: N  362 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7571 (mtmm)
REVERT: N  364 GLU cc_start: 0.6894 (tp30) cc_final: 0.6297 (tp30)
REVERT: N  373 MET cc_start: 0.6896 (tmm) cc_final: 0.6311 (tmm)
REVERT: N  376 ARG cc_start: 0.8168 (ptp-170) cc_final: 0.7736 (ptp-110)
REVERT: N  405 ARG cc_start: 0.8027 (ttt180) cc_final: 0.7680 (ttt90)
REVERT: N  440 MET cc_start: 0.7862 (tpp) cc_final: 0.7652 (tpp)
REVERT: N  456 GLN cc_start: 0.7951 (tm-30) cc_final: 0.6648 (tm-30)
REVERT: N  457 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7227 (mm-30)
REVERT: N  555 TYR cc_start: 0.7866 (p90) cc_final: 0.7638 (p90)
REVERT: N  572 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6295 (mtt180)
REVERT: N  576 GLU cc_start: 0.6824 (mp0) cc_final: 0.6489 (mp0)
  outliers start: 23
  outliers final: 18
  residues processed: 206
  average time/residue: 0.0987
  time to fit residues: 24.9807
Evaluate side-chains
  212 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  238 LEU
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  279 VAL
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  501 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   chunk 47 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 53 optimal weight:    0.1980
   chunk 15 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  69 HIS
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.113501 restraints weight = 10283.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.117248 restraints weight = 5255.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.119772 restraints weight = 3184.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.121441 restraints weight = 2170.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122633 restraints weight = 1622.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6201  Z= 0.184
  Angle     :  0.696   8.770   8419  Z= 0.359
  Chirality :  0.047   0.163    910
  Planarity :  0.005   0.053   1082
  Dihedral  :  5.510  23.396    867
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.61 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.30), residues: 732
  helix: -0.48 (0.48), residues: 111
  sheet:  1.22 (0.37), residues: 195
  loop : -1.44 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E  32 
 TYR   0.038   0.002   TYR C 130 
 PHE   0.026   0.002   PHE N 260 
 TRP   0.019   0.002   TRP N 372 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.18 ( 6189)
  covalent geometry    : angle       0.68883 /  0.36 ( 8393)
  SS BOND              : bond        0.00384 /  0.23 (   10)
  SS BOND              : angle       1.84478 /  1.44 (   20)
  hydrogen bonds       : bond        0.04405 /  2.89 (  206)
  hydrogen bonds       : angle       5.31758 /  3.80 (  597)
  link_NAG-ASN         : bond        0.00651 /  0.34 (    2)
  link_NAG-ASN         : angle       2.33283 /  1.29 (    6)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 196
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7895 (p90) cc_final: 0.7433 (p90)
REVERT: C   48 MET cc_start: 0.7373 (pmm) cc_final: 0.6905 (pmm)
REVERT: C   78 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6920 (t)
REVERT: C   85 THR cc_start: 0.8727 (t) cc_final: 0.8464 (p)
REVERT: D  111 ILE cc_start: 0.8477 (mm) cc_final: 0.8043 (mm)
REVERT: D  154 LYS cc_start: 0.8294 (tptp) cc_final: 0.7959 (tptp)
REVERT: E   32 ARG cc_start: 0.8481 (mmt90) cc_final: 0.8087 (mmt90)
REVERT: E   91 ASP cc_start: 0.7885 (t0) cc_final: 0.7631 (t0)
REVERT: N  151 LYS cc_start: 0.8399 (mtmt) cc_final: 0.8056 (mtpp)
REVERT: N  174 ASP cc_start: 0.7796 (t0) cc_final: 0.7240 (t0)
REVERT: N  188 ILE cc_start: 0.8317 (mp) cc_final: 0.8086 (mt)
REVERT: N  190 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7186 (mm-40)
REVERT: N  229 TYR cc_start: 0.7990 (m-80) cc_final: 0.7465 (m-80)
REVERT: N  237 GLU cc_start: 0.6877 (mp0) cc_final: 0.6206 (mp0)
REVERT: N  339 LEU cc_start: 0.8230 (tp) cc_final: 0.7912 (mp)
REVERT: N  362 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7581 (mtmm)
REVERT: N  364 GLU cc_start: 0.6923 (tp30) cc_final: 0.6267 (tp30)
REVERT: N  373 MET cc_start: 0.6881 (tmm) cc_final: 0.6319 (tmm)
REVERT: N  376 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7707 (ptp-110)
REVERT: N  405 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7794 (ttt180)
REVERT: N  456 GLN cc_start: 0.7937 (tm-30) cc_final: 0.6578 (tm-30)
REVERT: N  457 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7253 (mm-30)
REVERT: N  536 GLU cc_start: 0.6511 (tp30) cc_final: 0.6168 (tp30)
REVERT: N  555 TYR cc_start: 0.7887 (p90) cc_final: 0.7634 (p90)
REVERT: N  559 ASP cc_start: 0.8050 (t0) cc_final: 0.7695 (t0)
REVERT: N  572 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6215 (mtt180)
REVERT: N  576 GLU cc_start: 0.6798 (mp0) cc_final: 0.6466 (mp0)
  outliers start: 20
  outliers final: 17
  residues processed: 205
  average time/residue: 0.1028
  time to fit residues: 25.9687
Evaluate side-chains
  213 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 195
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  195 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain N residue  238 LEU
Chi-restraints excluded: chain N residue  267 VAL
Chi-restraints excluded: chain N residue  312 HIS
Chi-restraints excluded: chain N residue  342 ILE
Chi-restraints excluded: chain N residue  438 LEU
Chi-restraints excluded: chain N residue  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  501 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 7 optimal weight:    0.2980
   chunk 68 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0870
   overall best weight:    0.4158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  69 HIS
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 116 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.131025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.114059 restraints weight = 10290.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.117681 restraints weight = 5369.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120136 restraints weight = 3284.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.121785 restraints weight = 2247.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.122942 restraints weight = 1687.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6201  Z= 0.171
  Angle     :  0.691   8.914   8419  Z= 0.353
  Chirality :  0.047   0.194    910
  Planarity :  0.005   0.053   1082
  Dihedral  :  5.402  21.387    867
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.76 %
    Favored  : 74.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.30), residues: 732
  helix: -0.38 (0.49), residues: 111
  sheet:  1.29 (0.37), residues: 195
  loop : -1.47 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E  32 
 TYR   0.038   0.002   TYR C 130 
 PHE   0.027   0.002   PHE N 260 
 TRP   0.030   0.002   TRP N 372 
 HIS   0.008   0.001   HIS C  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.17 ( 6189)
  covalent geometry    : angle       0.67933 /  0.35 ( 8393)
  SS BOND              : bond        0.00394 /  0.23 (   10)
  SS BOND              : angle       2.46667 /  2.00 (   20)
  hydrogen bonds       : bond        0.04263 /  2.77 (  206)
  hydrogen bonds       : angle       5.24934 /  3.74 (  597)
  link_NAG-ASN         : bond        0.00570 /  0.30 (    2)
  link_NAG-ASN         : angle       2.17976 /  1.20 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1322.50 seconds
wall clock time: 23 minutes 29.59 seconds (1409.59 seconds total)