Starting phenix.real_space_refine
on Tue Mar 11 15:05:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7m22_23629/03_2025/7m22_23629_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7m22_23629/03_2025/7m22_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7m22_23629/03_2025/7m22_23629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7m22_23629/03_2025/7m22_23629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7m22_23629/03_2025/7m22_23629_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7m22_23629/03_2025/7m22_23629_neut.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 15
          Unusual residues: {' CA': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 4.55, per 1000 atoms: 0.75
  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: 1.28
  Conformation dependent library (CDL) restraints added in 793.4 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: 0.70
  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: 1.86

  Time building geometry restraints manager: 1.58 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 2.510
  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 2.510
  ... (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:             2.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.770
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
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   6189  Z= 0.287
  Angle     :  0.827   7.420   8393  Z= 0.485
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (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
 TRP   0.023   0.003   TRP N 535 
 HIS   0.006   0.001   HIS C  90 
 PHE   0.012   0.002   PHE D 190 
 TYR   0.025   0.005   TYR N 357 
 ARG   0.068   0.008   ARG N 561 

*********************** 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  : 0.587 
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: 0.7899 (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: 0.7711 (t0) cc_final: 0.7315 (t0)
REVERT: N  186 GLU cc_start: 0.6907 (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: 0.8505 (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: 0.6704 (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: 0.7219 (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: 0.7237 (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: 0.2250
  time to fit residues: 62.5340
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  : 0.610 
-------------------------------------------------------------------------------
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 61 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0970
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.4980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
C  37 ASN
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: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.130192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.112857 restraints weight = 10285.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116581 restraints weight = 5271.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.119153 restraints weight = 3216.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6189  Z= 0.303
  Angle     :  0.714   6.480   8393  Z= 0.381
  Chirality :  0.049   0.140    910
  Planarity :  0.005   0.053   1082
  Dihedral  :  7.430  56.244    872
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 10.77 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.29), residues: 732
  helix: -0.67 (0.44), residues: 111
  sheet:  1.41 (0.37), residues: 173
  loop : -0.85 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N 535 
 HIS   0.010   0.002   HIS C  90 
 PHE   0.013   0.002   PHE N 549 
 TYR   0.029   0.002   TYR C 130 
 ARG   0.006   0.001   ARG N 263 

*********************** 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
  227 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 197
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7688 (p90) cc_final: 0.7112 (p90)
REVERT: C   48 MET cc_start: 0.7424 (pmm) cc_final: 0.7010 (pmm)
REVERT: D  111 ILE cc_start: 0.8383 (mm) cc_final: 0.7991 (mm)
REVERT: D  124 ARG cc_start: 0.6835 (mpp80) cc_final: 0.6570 (mtt90)
REVERT: D  174 MET cc_start: 0.7982 (ttp) cc_final: 0.7739 (ttp)
REVERT: D  178 SER cc_start: 0.8354 (p) cc_final: 0.8138 (p)
REVERT: E   77 LEU cc_start: 0.8592 (tp) cc_final: 0.8279 (tp)
REVERT: E   91 ASP cc_start: 0.7923 (t0) cc_final: 0.7689 (t0)
REVERT: N  151 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8292 (mtmt)
REVERT: N  160 ILE cc_start: 0.8139 (tp) cc_final: 0.7768 (pt)
REVERT: N  161 GLU cc_start: 0.7326 (pm20) cc_final: 0.7104 (pm20)
REVERT: N  174 ASP cc_start: 0.7763 (t0) cc_final: 0.7219 (t0)
REVERT: N  188 ILE cc_start: 0.8297 (mp) cc_final: 0.8059 (mt)
REVERT: N  212 TRP cc_start: 0.8513 (p90) cc_final: 0.8295 (p90)
REVERT: N  229 TYR cc_start: 0.8075 (m-80) cc_final: 0.7566 (m-80)
REVERT: N  233 LYS cc_start: 0.7780 (mtpp) cc_final: 0.7527 (mtpp)
REVERT: N  288 ILE cc_start: 0.8301 (mt) cc_final: 0.8100 (mt)
REVERT: N  332 ASP cc_start: 0.7739 (t0) cc_final: 0.7500 (t0)
REVERT: N  339 LEU cc_start: 0.8216 (tp) cc_final: 0.7959 (mp)
REVERT: N  362 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7672 (mtmm)
REVERT: N  364 GLU cc_start: 0.6771 (tp30) cc_final: 0.6330 (tp30)
REVERT: N  373 MET cc_start: 0.6966 (tmm) cc_final: 0.6641 (tmm)
REVERT: N  376 ARG cc_start: 0.8133 (ptp-170) cc_final: 0.7753 (ptp-110)
REVERT: N  440 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7475 (tpp)
REVERT: N  456 GLN cc_start: 0.8034 (tm-30) cc_final: 0.6752 (tm-30)
REVERT: N  457 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7050 (mm-30)
REVERT: N  535 TRP cc_start: 0.7421 (m100) cc_final: 0.6787 (m100)
REVERT: N  542 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.4379 (mmm160)
REVERT: N  559 ASP cc_start: 0.7806 (t0) cc_final: 0.7465 (t0)
REVERT: N  572 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6275 (mtt180)
REVERT: N  576 GLU cc_start: 0.6778 (mp0) cc_final: 0.6468 (mp0)
  outliers start: 30
  outliers final: 22
  residues processed: 205
  average time/residue: 0.2364
  time to fit residues: 59.7775
Evaluate side-chains
  217 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 193
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
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   78 THR
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   94 THR
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  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  440 MET
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  557 THR
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 28 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0980
   chunk 2 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3684 r_free = 0.3684 target = 0.129914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.113059 restraints weight = 10329.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.116715 restraints weight = 5328.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.119139 restraints weight = 3247.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6189  Z= 0.293
  Angle     :  0.662   7.029   8393  Z= 0.353
  Chirality :  0.048   0.225    910
  Planarity :  0.005   0.053   1082
  Dihedral  :  6.930  59.456    872
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 12.75 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.30), residues: 732
  helix: -0.62 (0.47), residues: 117
  sheet:  1.25 (0.38), residues: 176
  loop : -0.95 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N 535 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.012   0.002   PHE N 549 
 TYR   0.028   0.002   TYR C 130 
 ARG   0.005   0.000   ARG E  32 

*********************** 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
  233 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 197
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7835 (p90) cc_final: 0.7413 (p90)
REVERT: C   48 MET cc_start: 0.7383 (pmm) cc_final: 0.6985 (pmm)
REVERT: D  111 ILE cc_start: 0.8392 (mm) cc_final: 0.7985 (mm)
REVERT: D  125 MET cc_start: 0.7731 (ttm) cc_final: 0.7508 (ttm)
REVERT: E   51 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7624 (mmmt)
REVERT: E   91 ASP cc_start: 0.7948 (t0) cc_final: 0.7706 (t0)
REVERT: N  151 LYS cc_start: 0.8529 (mtmt) cc_final: 0.8190 (mtmt)
REVERT: N  153 PHE cc_start: 0.7443 (m-80) cc_final: 0.7214 (m-80)
REVERT: N  174 ASP cc_start: 0.7844 (t0) cc_final: 0.7262 (t0)
REVERT: N  186 GLU cc_start: 0.6603 (tp30) cc_final: 0.6124 (tp30)
REVERT: N  188 ILE cc_start: 0.8326 (mp) cc_final: 0.8102 (mt)
REVERT: N  228 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7698 (ttmm)
REVERT: N  229 TYR cc_start: 0.8030 (m-80) cc_final: 0.7513 (m-80)
REVERT: N  233 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7550 (mtpp)
REVERT: N  332 ASP cc_start: 0.7842 (t0) cc_final: 0.7632 (t0)
REVERT: N  339 LEU cc_start: 0.8205 (tp) cc_final: 0.7948 (mp)
REVERT: N  362 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7690 (mtmm)
REVERT: N  364 GLU cc_start: 0.6831 (tp30) cc_final: 0.6321 (tp30)
REVERT: N  372 TRP cc_start: 0.7795 (m100) cc_final: 0.7512 (m100)
REVERT: N  373 MET cc_start: 0.6923 (tmm) cc_final: 0.6650 (tmm)
REVERT: N  376 ARG cc_start: 0.8111 (ptp-170) cc_final: 0.7619 (ptp-110)
REVERT: N  456 GLN cc_start: 0.8044 (tm-30) cc_final: 0.6737 (tm-30)
REVERT: N  457 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7107 (mm-30)
REVERT: N  498 VAL cc_start: 0.8431 (t) cc_final: 0.8016 (m)
REVERT: N  535 TRP cc_start: 0.7472 (m100) cc_final: 0.7015 (m100)
REVERT: N  542 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.4534 (mmm160)
REVERT: N  559 ASP cc_start: 0.7807 (t0) cc_final: 0.7562 (t0)
REVERT: N  570 TYR cc_start: 0.6485 (m-80) cc_final: 0.6202 (m-80)
REVERT: N  572 ARG cc_start: 0.7001 (mtt180) cc_final: 0.6294 (mtt180)
REVERT: N  576 GLU cc_start: 0.6819 (mp0) cc_final: 0.6506 (mp0)
  outliers start: 36
  outliers final: 22
  residues processed: 209
  average time/residue: 0.2263
  time to fit residues: 58.4562
Evaluate side-chains
  215 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
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  141 VAL
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  172 ASN
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 63 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    0.3980
   chunk 29 optimal weight:    0.0570
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.2980
   chunk 5 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0980
   overall best weight:    0.3298

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3701 r_free = 0.3701 target = 0.131185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.114393 restraints weight = 10386.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.118079 restraints weight = 5321.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.120518 restraints weight = 3218.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6189  Z= 0.205
  Angle     :  0.620   7.024   8393  Z= 0.324
  Chirality :  0.046   0.194    910
  Planarity :  0.004   0.050   1082
  Dihedral  :  6.306  52.103    872
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 15.48 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.30), residues: 732
  helix: -0.47 (0.47), residues: 117
  sheet:  1.31 (0.38), residues: 179
  loop : -0.93 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 179 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.010   0.001   PHE D 190 
 TYR   0.027   0.001   TYR C 130 
 ARG   0.006   0.000   ARG E  32 

*********************** 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
  227 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 192
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7836 (p90) cc_final: 0.7431 (p90)
REVERT: C   48 MET cc_start: 0.7308 (pmm) cc_final: 0.6901 (pmm)
REVERT: C  101 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7079 (pp)
REVERT: D  111 ILE cc_start: 0.8387 (mm) cc_final: 0.7975 (mm)
REVERT: E   91 ASP cc_start: 0.7913 (t0) cc_final: 0.7650 (t0)
REVERT: N  151 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8163 (mtmt)
REVERT: N  153 PHE cc_start: 0.7407 (m-80) cc_final: 0.7192 (m-80)
REVERT: N  174 ASP cc_start: 0.7787 (t0) cc_final: 0.7263 (t0)
REVERT: N  186 GLU cc_start: 0.6582 (tp30) cc_final: 0.6133 (tp30)
REVERT: N  188 ILE cc_start: 0.8342 (mp) cc_final: 0.8107 (mt)
REVERT: N  229 TYR cc_start: 0.8031 (m-80) cc_final: 0.7468 (m-80)
REVERT: N  239 ARG cc_start: 0.7379 (mtt90) cc_final: 0.7059 (mtt90)
REVERT: N  339 LEU cc_start: 0.8205 (tp) cc_final: 0.7966 (mp)
REVERT: N  362 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7684 (mtmm)
REVERT: N  364 GLU cc_start: 0.6816 (tp30) cc_final: 0.6254 (tp30)
REVERT: N  372 TRP cc_start: 0.7726 (m100) cc_final: 0.7406 (m100)
REVERT: N  373 MET cc_start: 0.6906 (tmm) cc_final: 0.6617 (tmm)
REVERT: N  376 ARG cc_start: 0.8066 (ptp-170) cc_final: 0.7570 (ptp-110)
REVERT: N  456 GLN cc_start: 0.8071 (tm-30) cc_final: 0.6815 (tm-30)
REVERT: N  457 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7205 (mm-30)
REVERT: N  498 VAL cc_start: 0.8426 (t) cc_final: 0.8031 (m)
REVERT: N  535 TRP cc_start: 0.7474 (m100) cc_final: 0.6938 (m100)
REVERT: N  542 ARG cc_start: 0.5613 (OUTLIER) cc_final: 0.5313 (mmm160)
REVERT: N  559 ASP cc_start: 0.7879 (t0) cc_final: 0.7561 (t0)
REVERT: N  570 TYR cc_start: 0.6481 (m-80) cc_final: 0.6207 (m-80)
REVERT: N  572 ARG cc_start: 0.6982 (mtt180) cc_final: 0.6236 (mtt180)
REVERT: N  576 GLU cc_start: 0.6861 (mp0) cc_final: 0.6476 (mp0)
  outliers start: 35
  outliers final: 20
  residues processed: 204
  average time/residue: 0.2478
  time to fit residues: 62.1421
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  : 0.669 
-------------------------------------------------------------------------------
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   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  200 ASN
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  585 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3667 r_free = 0.3667 target = 0.129195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.112425 restraints weight = 10337.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116068 restraints weight = 5350.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.118475 restraints weight = 3261.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6189  Z= 0.332
  Angle     :  0.676   8.052   8393  Z= 0.354
  Chirality :  0.049   0.235    910
  Planarity :  0.005   0.052   1082
  Dihedral  :  6.404  47.078    872
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 19.12 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.30), residues: 732
  helix: -0.63 (0.46), residues: 117
  sheet:  1.01 (0.38), residues: 178
  loop : -1.09 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP N 535 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.013   0.002   PHE E 122 
 TYR   0.035   0.002   TYR C 130 
 ARG   0.007   0.001   ARG N 562 

*********************** 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
  222 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7950 (p90) cc_final: 0.7468 (p90)
REVERT: C   48 MET cc_start: 0.7424 (pmm) cc_final: 0.7064 (pmm)
REVERT: D  111 ILE cc_start: 0.8474 (mm) cc_final: 0.8059 (mm)
REVERT: D  125 MET cc_start: 0.7718 (ttp) cc_final: 0.7195 (ttp)
REVERT: E   91 ASP cc_start: 0.7934 (t0) cc_final: 0.7686 (t0)
REVERT: N  151 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8250 (mtmt)
REVERT: N  174 ASP cc_start: 0.7782 (t0) cc_final: 0.7231 (t0)
REVERT: N  188 ILE cc_start: 0.8374 (mp) cc_final: 0.8119 (mt)
REVERT: N  228 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7551 (mtpp)
REVERT: N  229 TYR cc_start: 0.8141 (m-80) cc_final: 0.7584 (m-80)
REVERT: N  339 LEU cc_start: 0.8201 (tp) cc_final: 0.7947 (mp)
REVERT: N  362 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7737 (mtmm)
REVERT: N  364 GLU cc_start: 0.6958 (tp30) cc_final: 0.6324 (tp30)
REVERT: N  376 ARG cc_start: 0.8137 (ptp-170) cc_final: 0.7576 (ptp-110)
REVERT: N  456 GLN cc_start: 0.8059 (tm-30) cc_final: 0.6835 (tm-30)
REVERT: N  457 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7224 (mm-30)
REVERT: N  498 VAL cc_start: 0.8520 (t) cc_final: 0.8118 (m)
REVERT: N  535 TRP cc_start: 0.7565 (m100) cc_final: 0.6909 (m100)
REVERT: N  542 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5326 (mmm160)
REVERT: N  555 TYR cc_start: 0.7879 (p90) cc_final: 0.7648 (p90)
REVERT: N  559 ASP cc_start: 0.7806 (t0) cc_final: 0.7499 (t0)
REVERT: N  570 TYR cc_start: 0.6532 (m-80) cc_final: 0.6209 (m-80)
REVERT: N  572 ARG cc_start: 0.6920 (mtt180) cc_final: 0.6203 (mtt180)
REVERT: N  576 GLU cc_start: 0.6836 (mp0) cc_final: 0.6466 (mp0)
  outliers start: 32
  outliers final: 25
  residues processed: 201
  average time/residue: 0.2438
  time to fit residues: 61.0848
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  : 0.670 
-------------------------------------------------------------------------------
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  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  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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0970
   chunk 67 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0870
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3687 r_free = 0.3687 target = 0.130459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.113660 restraints weight = 10226.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.117312 restraints weight = 5295.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.119673 restraints weight = 3229.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6189  Z= 0.240
  Angle     :  0.646  10.839   8393  Z= 0.334
  Chirality :  0.047   0.159    910
  Planarity :  0.005   0.051   1082
  Dihedral  :  6.102  42.590    872
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 20.03 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.30), residues: 732
  helix: -0.58 (0.47), residues: 117
  sheet:  0.95 (0.38), residues: 184
  loop : -1.13 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 179 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.010   0.001   PHE N 153 
 TYR   0.032   0.001   TYR C 130 
 ARG   0.008   0.000   ARG E  32 

*********************** 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
  222 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 191
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7945 (p90) cc_final: 0.7418 (p90)
REVERT: C   48 MET cc_start: 0.7348 (pmm) cc_final: 0.7083 (pmm)
REVERT: C   78 THR cc_start: 0.7105 (OUTLIER) cc_final: 0.6904 (t)
REVERT: D  111 ILE cc_start: 0.8504 (mm) cc_final: 0.8080 (mm)
REVERT: D  154 LYS cc_start: 0.8350 (tptp) cc_final: 0.8064 (tptp)
REVERT: D  170 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8203 (mt0)
REVERT: E   32 ARG cc_start: 0.8552 (mmt90) cc_final: 0.8190 (mmt90)
REVERT: E   91 ASP cc_start: 0.7856 (t0) cc_final: 0.7637 (t0)
REVERT: N  151 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8233 (mtmt)
REVERT: N  174 ASP cc_start: 0.7731 (t0) cc_final: 0.7192 (t0)
REVERT: N  188 ILE cc_start: 0.8359 (mp) cc_final: 0.8124 (mt)
REVERT: N  228 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7442 (mtpp)
REVERT: N  229 TYR cc_start: 0.8073 (m-80) cc_final: 0.7501 (m-80)
REVERT: N  339 LEU cc_start: 0.8210 (tp) cc_final: 0.7984 (mp)
REVERT: N  362 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7717 (mtmm)
REVERT: N  364 GLU cc_start: 0.6895 (tp30) cc_final: 0.6283 (tp30)
REVERT: N  373 MET cc_start: 0.7050 (tmm) cc_final: 0.6603 (tmm)
REVERT: N  376 ARG cc_start: 0.7946 (ptp-170) cc_final: 0.7472 (ptp-110)
REVERT: N  440 MET cc_start: 0.7908 (tpp) cc_final: 0.7413 (tpp)
REVERT: N  456 GLN cc_start: 0.8023 (tm-30) cc_final: 0.6820 (tm-30)
REVERT: N  457 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7216 (mm-30)
REVERT: N  498 VAL cc_start: 0.8584 (t) cc_final: 0.8172 (m)
REVERT: N  535 TRP cc_start: 0.7603 (m100) cc_final: 0.6983 (m100)
REVERT: N  542 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5378 (mmm160)
REVERT: N  555 TYR cc_start: 0.7848 (p90) cc_final: 0.7610 (p90)
REVERT: N  572 ARG cc_start: 0.6961 (mtt180) cc_final: 0.6220 (mtt180)
REVERT: N  576 GLU cc_start: 0.6871 (mp0) cc_final: 0.6533 (mp0)
  outliers start: 31
  outliers final: 22
  residues processed: 204
  average time/residue: 0.2565
  time to fit residues: 64.0956
Evaluate side-chains
  213 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 188
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
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   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  170 GLN
Chi-restraints excluded: chain D residue  195 THR
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  238 LEU
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  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 16 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 35 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0980
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0980
   chunk 28 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0770
   overall best weight:    0.2138

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3708 r_free = 0.3708 target = 0.131910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.115139 restraints weight = 10328.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.118792 restraints weight = 5310.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.121125 restraints weight = 3224.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6189  Z= 0.181
  Angle     :  0.621   8.878   8393  Z= 0.319
  Chirality :  0.045   0.154    910
  Planarity :  0.004   0.049   1082
  Dihedral  :  5.601  41.007    871
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 19.58 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.30), residues: 732
  helix: -0.39 (0.49), residues: 111
  sheet:  1.11 (0.38), residues: 184
  loop : -1.11 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP N 372 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.009   0.001   PHE D 190 
 TYR   0.032   0.001   TYR C 130 
 ARG   0.007   0.001   ARG E  32 

*********************** 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
  221 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 193
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7929 (p90) cc_final: 0.7381 (p90)
REVERT: C   48 MET cc_start: 0.7333 (pmm) cc_final: 0.6987 (pmm)
REVERT: C  101 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7061 (pp)
REVERT: D  111 ILE cc_start: 0.8478 (mm) cc_final: 0.8036 (mm)
REVERT: D  154 LYS cc_start: 0.8312 (tptp) cc_final: 0.7991 (tptp)
REVERT: D  170 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8182 (mt0)
REVERT: E   32 ARG cc_start: 0.8513 (mmt90) cc_final: 0.8174 (mmt90)
REVERT: E   91 ASP cc_start: 0.7835 (t0) cc_final: 0.7618 (t0)
REVERT: N  151 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8130 (mtmt)
REVERT: N  174 ASP cc_start: 0.7699 (t0) cc_final: 0.7159 (t0)
REVERT: N  188 ILE cc_start: 0.8352 (mp) cc_final: 0.8118 (mt)
REVERT: N  229 TYR cc_start: 0.8037 (m-80) cc_final: 0.7447 (m-80)
REVERT: N  263 ARG cc_start: 0.7365 (mmt90) cc_final: 0.7097 (mmt90)
REVERT: N  339 LEU cc_start: 0.8210 (tp) cc_final: 0.7995 (mp)
REVERT: N  362 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7695 (mtmm)
REVERT: N  364 GLU cc_start: 0.6861 (tp30) cc_final: 0.6299 (tp30)
REVERT: N  373 MET cc_start: 0.7015 (tmm) cc_final: 0.6419 (tmm)
REVERT: N  376 ARG cc_start: 0.8090 (ptp-170) cc_final: 0.7683 (ptp-110)
REVERT: N  440 MET cc_start: 0.7796 (tpp) cc_final: 0.7317 (tpp)
REVERT: N  456 GLN cc_start: 0.7999 (tm-30) cc_final: 0.6805 (tm-30)
REVERT: N  457 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7212 (mm-30)
REVERT: N  555 TYR cc_start: 0.7881 (p90) cc_final: 0.7650 (p90)
REVERT: N  572 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6293 (mtt180)
REVERT: N  576 GLU cc_start: 0.6898 (mp0) cc_final: 0.6542 (mp0)
  outliers start: 28
  outliers final: 17
  residues processed: 206
  average time/residue: 0.2578
  time to fit residues: 64.3951
Evaluate side-chains
  209 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 190
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 HIS
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  122 LEU
Chi-restraints excluded: chain D residue  170 GLN
Chi-restraints excluded: chain D residue  200 ASN
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   87 LEU
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  450 ILE
Chi-restraints excluded: chain N residue  469 SER
Chi-restraints excluded: chain N residue  501 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3666 r_free = 0.3666 target = 0.129051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.112474 restraints weight = 10351.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.116042 restraints weight = 5338.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.118375 restraints weight = 3240.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   6189  Z= 0.393
  Angle     :  0.706   8.362   8393  Z= 0.369
  Chirality :  0.050   0.207    910
  Planarity :  0.005   0.051   1082
  Dihedral  :  5.704  21.886    867
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 20.94 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.30), residues: 732
  helix: -0.66 (0.47), residues: 111
  sheet:  1.04 (0.39), residues: 179
  loop : -1.34 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP N 372 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.016   0.002   PHE D 190 
 TYR   0.043   0.002   TYR C 130 
 ARG   0.007   0.001   ARG E  32 

*********************** 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
  218 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7953 (p90) cc_final: 0.7425 (p90)
REVERT: C   48 MET cc_start: 0.7430 (pmm) cc_final: 0.7106 (pmm)
REVERT: C   85 THR cc_start: 0.8801 (t) cc_final: 0.8529 (p)
REVERT: D  111 ILE cc_start: 0.8568 (mm) cc_final: 0.8136 (mm)
REVERT: E   32 ARG cc_start: 0.8567 (mmt90) cc_final: 0.8180 (mmt90)
REVERT: E   91 ASP cc_start: 0.7906 (t0) cc_final: 0.7671 (t0)
REVERT: N  151 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8127 (mtpp)
REVERT: N  174 ASP cc_start: 0.7739 (t0) cc_final: 0.7174 (t0)
REVERT: N  188 ILE cc_start: 0.8365 (mp) cc_final: 0.8127 (mt)
REVERT: N  229 TYR cc_start: 0.8000 (m-80) cc_final: 0.7627 (m-80)
REVERT: N  339 LEU cc_start: 0.8218 (tp) cc_final: 0.7998 (mp)
REVERT: N  362 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7598 (mtmm)
REVERT: N  364 GLU cc_start: 0.6913 (tp30) cc_final: 0.6455 (tp30)
REVERT: N  373 MET cc_start: 0.6965 (tmm) cc_final: 0.6421 (tmm)
REVERT: N  376 ARG cc_start: 0.8095 (ptp-170) cc_final: 0.7678 (ptp-110)
REVERT: N  440 MET cc_start: 0.7887 (tpp) cc_final: 0.7668 (tpp)
REVERT: N  456 GLN cc_start: 0.7967 (tm-30) cc_final: 0.6652 (tm-30)
REVERT: N  457 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7290 (mm-30)
REVERT: N  498 VAL cc_start: 0.8692 (t) cc_final: 0.8247 (m)
REVERT: N  535 TRP cc_start: 0.7588 (m100) cc_final: 0.6954 (m100)
REVERT: N  555 TYR cc_start: 0.7862 (p90) cc_final: 0.7628 (p90)
REVERT: N  572 ARG cc_start: 0.6968 (mtt180) cc_final: 0.6285 (mtt180)
REVERT: N  576 GLU cc_start: 0.6823 (mp0) cc_final: 0.6488 (mp0)
  outliers start: 27
  outliers final: 22
  residues processed: 199
  average time/residue: 0.2424
  time to fit residues: 59.1767
Evaluate side-chains
  210 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
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   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  122 LEU
Chi-restraints excluded: chain D residue  195 THR
Chi-restraints excluded: chain D residue  200 ASN
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  342 ILE
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  550 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0670
   chunk 70 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 67 optimal weight:    0.4980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3678 r_free = 0.3678 target = 0.130057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.113310 restraints weight = 10281.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116891 restraints weight = 5325.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.119279 restraints weight = 3248.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6189  Z= 0.281
  Angle     :  0.675   9.597   8393  Z= 0.351
  Chirality :  0.047   0.158    910
  Planarity :  0.005   0.053   1082
  Dihedral  :  5.510  21.921    867
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.40 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.30), residues: 732
  helix: -0.60 (0.48), residues: 111
  sheet:  1.02 (0.38), residues: 193
  loop : -1.38 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP N 372 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.010   0.002   PHE E 122 
 TYR   0.040   0.002   TYR C 130 
 ARG   0.007   0.001   ARG E  32 

*********************** 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
  220 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7917 (p90) cc_final: 0.7358 (p90)
REVERT: C   48 MET cc_start: 0.7395 (pmm) cc_final: 0.6969 (pmm)
REVERT: C   53 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7330 (t)
REVERT: D  111 ILE cc_start: 0.8509 (mm) cc_final: 0.8066 (mm)
REVERT: D  154 LYS cc_start: 0.8296 (tptp) cc_final: 0.8003 (tptp)
REVERT: E   32 ARG cc_start: 0.8545 (mmt90) cc_final: 0.8112 (mmt90)
REVERT: E   61 LEU cc_start: 0.7685 (mt) cc_final: 0.7081 (mt)
REVERT: E   91 ASP cc_start: 0.7871 (t0) cc_final: 0.7637 (t0)
REVERT: N  151 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8056 (mtpp)
REVERT: N  174 ASP cc_start: 0.7717 (t0) cc_final: 0.7138 (t0)
REVERT: N  188 ILE cc_start: 0.8345 (mp) cc_final: 0.8117 (mt)
REVERT: N  229 TYR cc_start: 0.7976 (m-80) cc_final: 0.7526 (m-80)
REVERT: N  339 LEU cc_start: 0.8235 (tp) cc_final: 0.7986 (mp)
REVERT: N  362 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7592 (mtmm)
REVERT: N  364 GLU cc_start: 0.6964 (tp30) cc_final: 0.6465 (tp30)
REVERT: N  373 MET cc_start: 0.6953 (tmm) cc_final: 0.6401 (tmm)
REVERT: N  376 ARG cc_start: 0.8117 (ptp-170) cc_final: 0.7699 (ptp-110)
REVERT: N  405 ARG cc_start: 0.8190 (ttt180) cc_final: 0.7890 (ttt90)
REVERT: N  440 MET cc_start: 0.7851 (tpp) cc_final: 0.7280 (tpp)
REVERT: N  456 GLN cc_start: 0.7954 (tm-30) cc_final: 0.6562 (tm-30)
REVERT: N  457 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7287 (mm-30)
REVERT: N  535 TRP cc_start: 0.7575 (m100) cc_final: 0.6976 (m100)
REVERT: N  555 TYR cc_start: 0.7836 (p90) cc_final: 0.7611 (p90)
REVERT: N  572 ARG cc_start: 0.6965 (mtt180) cc_final: 0.6265 (mtt180)
REVERT: N  576 GLU cc_start: 0.6860 (mp0) cc_final: 0.6541 (mp0)
  outliers start: 27
  outliers final: 22
  residues processed: 203
  average time/residue: 0.2517
  time to fit residues: 62.2068
Evaluate side-chains
  215 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   53 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  122 LEU
Chi-restraints excluded: chain D residue  195 THR
Chi-restraints excluded: chain D residue  200 ASN
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  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  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 7 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0980
   chunk 66 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 55 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 292 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 = 0.3685 r_free = 0.3685 target = 0.130355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.113520 restraints weight = 10422.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.117181 restraints weight = 5350.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119613 restraints weight = 3238.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6189  Z= 0.260
  Angle     :  0.674   9.991   8393  Z= 0.348
  Chirality :  0.047   0.231    910
  Planarity :  0.005   0.053   1082
  Dihedral  :  5.430  22.021    867
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.15 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.30), residues: 732
  helix: -0.78 (0.46), residues: 111
  sheet:  1.05 (0.38), residues: 193
  loop : -1.41 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP N 372 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.009   0.001   PHE E 122 
 TYR   0.039   0.002   TYR C 130 
 ARG   0.006   0.001   ARG E  32 

********************** 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: 22
    poor density    : 194
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 TYR cc_start: 0.7924 (p90) cc_final: 0.7440 (p90)
REVERT: C   48 MET cc_start: 0.7434 (pmm) cc_final: 0.7133 (pmm)
REVERT: D  111 ILE cc_start: 0.8497 (mm) cc_final: 0.8071 (mm)
REVERT: D  154 LYS cc_start: 0.8295 (tptp) cc_final: 0.7974 (tptp)
REVERT: E   32 ARG cc_start: 0.8527 (mmt90) cc_final: 0.8050 (mmt90)
REVERT: E   65 TYR cc_start: 0.7948 (t80) cc_final: 0.7430 (t80)
REVERT: E   91 ASP cc_start: 0.7914 (t0) cc_final: 0.7665 (t0)
REVERT: N  151 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8008 (mtpp)
REVERT: N  174 ASP cc_start: 0.7718 (t0) cc_final: 0.7170 (t0)
REVERT: N  188 ILE cc_start: 0.8322 (mp) cc_final: 0.8085 (mt)
REVERT: N  229 TYR cc_start: 0.8012 (m-80) cc_final: 0.7543 (m-80)
REVERT: N  339 LEU cc_start: 0.8209 (tp) cc_final: 0.7956 (mp)
REVERT: N  362 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7564 (mtmm)
REVERT: N  364 GLU cc_start: 0.6921 (tp30) cc_final: 0.6400 (tp30)
REVERT: N  373 MET cc_start: 0.6921 (tmm) cc_final: 0.6377 (tmm)
REVERT: N  376 ARG cc_start: 0.8158 (ptp-170) cc_final: 0.7706 (ptp-110)
REVERT: N  405 ARG cc_start: 0.8183 (ttt180) cc_final: 0.7858 (ttt90)
REVERT: N  440 MET cc_start: 0.7922 (tpp) cc_final: 0.7306 (tpp)
REVERT: N  456 GLN cc_start: 0.7964 (tm-30) cc_final: 0.6531 (tm-30)
REVERT: N  457 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7249 (mm-30)
REVERT: N  498 VAL cc_start: 0.8583 (t) cc_final: 0.8125 (m)
REVERT: N  555 TYR cc_start: 0.7865 (p90) cc_final: 0.7646 (p90)
REVERT: N  572 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6164 (mtt180)
REVERT: N  576 GLU cc_start: 0.6851 (mp0) cc_final: 0.6521 (mp0)
  outliers start: 22
  outliers final: 21
  residues processed: 202
  average time/residue: 0.2508
  time to fit residues: 61.7752
Evaluate side-chains
  213 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   42 ARG
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 D residue  200 ASN
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  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  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 13 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0970
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0770
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 116 HIS
** N 292 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 = 0.3689 r_free = 0.3689 target = 0.130599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.113789 restraints weight = 10451.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.117348 restraints weight = 5371.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.119766 restraints weight = 3262.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6189  Z= 0.242
  Angle     :  0.662  10.237   8393  Z= 0.341
  Chirality :  0.046   0.146    910
  Planarity :  0.005   0.052   1082
  Dihedral  :  5.347  21.523    867
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 21.70 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.30), residues: 732
  helix: -0.63 (0.47), residues: 111
  sheet:  1.10 (0.38), residues: 193
  loop : -1.39 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP N 372 
 HIS   0.010   0.001   HIS C  38 
 PHE   0.009   0.001   PHE E 122 
 TYR   0.037   0.002   TYR C 130 
 ARG   0.006   0.001   ARG E  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2599.55 seconds
wall clock time: 45 minutes 37.94 seconds (2737.94 seconds total)