Starting phenix.real_space_refine
on Sat Aug 23 00:49:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6waz_21582/08_2025/6waz_21582.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6waz_21582/08_2025/6waz_21582.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6waz_21582/08_2025/6waz_21582.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6waz_21582/08_2025/6waz_21582.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6waz_21582/08_2025/6waz_21582.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6waz_21582/08_2025/6waz_21582.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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
     P      51      5.49       5
     S       8      5.16       5
     C    5338      2.51       5
     N    1453      2.21       5
     O    1687      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8537
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4222
          Classifications: {'peptide': 550}
          Incomplete info: {'truncation_to_alanine': 67}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 512}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 261
          Unresolved non-hydrogen angles: 321
          Unresolved non-hydrogen dihedrals: 219
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 21, 'TRP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 170
    Chain: "B"
      Number of atoms: 3177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 405, 3177
          Classifications: {'peptide': 405}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 30, 'TRANS': 374}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 167
          Unresolved non-hydrogen angles: 195
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 94
    Chain: "C"
      Number of atoms: 493
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 493
          Classifications: {'RNA': 23}
          Modifications used: {'5*END': 1, 'rna3p_pur': 13, 'rna3p_pyr': 9}
          Link IDs: {'rna3p': 22}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 645
          Inner-chain residues flagged as termini: ['pdbres="  G D  51 "']
          Classifications: {'DNA': 2, 'RNA': 29}
          Modifications used: {'5*END': 2, 'rna3p_pur': 10, 'rna3p_pyr': 17}
          Link IDs: {'rna3p': 30}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.24, per 1000 atoms: 0.26
  Number of scatterers: 8537
  At special positions: 0
  Unit cell: (103.88, 116.6, 110.24, 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)
     S       8     16.00
     P      51     15.00
     O    1687      8.00
     N    1453      7.00
     C    5338      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 355.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1798

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      37.9% alpha, 9.0% beta
      26 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 44
      removed outlier: 4.367A  pdb=" N   LYS A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ALA A  33 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 114 through 118
      removed outlier: 3.903A  pdb=" N   VAL A 118 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 128
      removed outlier: 3.715A  pdb=" N   THR A 128 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 194 through 211
    Processing helix  chain 'A' and resid 253 through 269
      removed outlier: 4.039A  pdb=" N   GLN A 269 " --> pdb=" O   ASN A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 284
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 4.283A  pdb=" N   GLU A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 383
      removed outlier: 3.764A  pdb=" N   GLN A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 404
      removed outlier: 3.552A  pdb=" N   TRP A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 489
    Processing helix  chain 'A' and resid 499 through 507
      removed outlier: 3.935A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 526
      removed outlier: 3.610A  pdb=" N   ASN A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 554
      removed outlier: 3.824A  pdb=" N   GLN A 547 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 44
      removed outlier: 3.934A  pdb=" N   ALA B  33 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLU B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 90
      removed outlier: 6.184A  pdb=" N   ASP B  86 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   PHE B  87 " --> pdb=" O   ARG B  83 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   TRP B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 103
    Processing helix  chain 'B' and resid 113 through 118
      removed outlier: 3.742A  pdb=" N   VAL B 118 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 127
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 155 through 175
      removed outlier: 4.884A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   SER B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS B 166 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
      removed outlier: 3.896A  pdb=" N   LYS B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 211
    Processing helix  chain 'B' and resid 253 through 268
    Processing helix  chain 'B' and resid 276 through 282
      removed outlier: 3.549A  pdb=" N   LEU B 282 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 311
      removed outlier: 3.564A  pdb=" N   LYS B 311 " --> pdb=" O   ARG B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 384
    Processing helix  chain 'B' and resid 394 through 406
      removed outlier: 4.094A  pdb=" N   TRP B 398 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   THR B 403 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 5.766A  pdb=" N   GLU B 404 " --> pdb=" O   THR B 400 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   TYR B 405 " --> pdb=" O   TRP B 401 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TRP B 406 " --> pdb=" O   TRP B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 427
      removed outlier: 3.754A  pdb=" N   TYR B 427 " --> pdb=" O   LYS B 424 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48
    Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 108
      removed outlier: 3.682A  pdb=" N   VAL A 189 " --> pdb=" O   THR A 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234
    Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328
      removed outlier: 7.098A  pdb=" N   ILE A 341 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   GLN A 343 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   LYS A 347 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 468
      removed outlier: 3.624A  pdb=" N   GLY A 456 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASP A 443 " --> pdb=" O   GLY A 456 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   PHE A 440 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL A 493 " --> pdb=" O   TYR A 532 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 48
      removed outlier: 3.991A  pdb=" N   ILE B 132 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR B 144 " --> pdb=" O   PHE B 130 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   PHE B 130 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 62
      removed outlier: 3.680A  pdb=" N   PHE B  61 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU B  74 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110
      removed outlier: 3.652A  pdb=" N   TYR B 188 " --> pdb=" O   TYR B 181 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TYR B 181 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 109 through 110
      removed outlier: 3.570A  pdb=" N   VAL B 189 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR B 107 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER B 105 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU B 234 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 351
      removed outlier: 7.327A  pdb=" N   ILE B 341 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LYS B 390 " --> pdb=" O   ALA B 327 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 331 through 333
      removed outlier: 3.801A  pdb=" N   GLY B 333 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)

    261 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      70 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1771
        1.33 -     1.45: 2201
        1.45 -     1.57: 4786
        1.57 -     1.69: 102
        1.69 -     1.81: 13
  Bond restraints: 8873
  Sorted by residual:
  bond pdb=" CB  THR B 131 "
       pdb=" CG2 THR B 131 "
    ideal  model  delta    sigma   weight residual
    1.521  1.451  0.070 3.30e-02 9.18e+02 4.50e+00
  bond pdb=" CG  GLU A 194 "
       pdb=" CD  GLU A 194 "
    ideal  model  delta    sigma   weight residual
    1.516  1.470  0.046 2.50e-02 1.60e+03 3.36e+00
  bond pdb=" CG1 ILE B 380 "
       pdb=" CD1 ILE B 380 "
    ideal  model  delta    sigma   weight residual
    1.513  1.447  0.066 3.90e-02 6.57e+02 2.89e+00
  bond pdb=" CG  ASP A  86 "
       pdb=" OD2 ASP A  86 "
    ideal  model  delta    sigma   weight residual
    1.249  1.217  0.032 1.90e-02 2.77e+03 2.80e+00
  bond pdb=" CB  THR A 216 "
       pdb=" CG2 THR A 216 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.70e+00
  ... (remaining 8868 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 11809
        1.67 -     3.33: 442
        3.33 -     5.00: 90
        5.00 -     6.66: 19
        6.66 -     8.33: 7
  Bond angle restraints: 12367
  Sorted by residual:
  angle pdb=" N   ASP B 177 "
        pdb=" CA  ASP B 177 "
        pdb=" C   ASP B 177 "
      ideal   model   delta    sigma   weight residual
     110.80  119.08   -8.28 2.13e+00 2.20e-01 1.51e+01
  angle pdb=" N   LYS A 431 "
        pdb=" CA  LYS A 431 "
        pdb=" C   LYS A 431 "
      ideal   model   delta    sigma   weight residual
     112.92  108.63    4.29 1.23e+00 6.61e-01 1.21e+01
  angle pdb=" CA  GLU B  42 "
        pdb=" CB  GLU B  42 "
        pdb=" CG  GLU B  42 "
      ideal   model   delta    sigma   weight residual
     114.10  121.05   -6.95 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" CA  THR A 240 "
        pdb=" CB  THR A 240 "
        pdb=" CG2 THR A 240 "
      ideal   model   delta    sigma   weight residual
     110.50  116.09   -5.59 1.70e+00 3.46e-01 1.08e+01
  angle pdb=" N   ASP A 256 "
        pdb=" CA  ASP A 256 "
        pdb=" CB  ASP A 256 "
      ideal   model   delta    sigma   weight residual
     110.16  105.33    4.83 1.48e+00 4.57e-01 1.07e+01
  ... (remaining 12362 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 4666
       17.43 -    34.87: 445
       34.87 -    52.30: 128
       52.30 -    69.73: 86
       69.73 -    87.16: 32
  Dihedral angle restraints: 5357
    sinusoidal: 2570
      harmonic: 2787
  Sorted by residual:
  dihedral pdb=" CA  ASN B 418 "
           pdb=" C   ASN B 418 "
           pdb=" N   THR B 419 "
           pdb=" CA  THR B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.74  -27.26     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  GLU A 194 "
           pdb=" C   GLU A 194 "
           pdb=" N   ILE A 195 "
           pdb=" CA  ILE A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.17  -25.83     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  GLY A 490 "
           pdb=" C   GLY A 490 "
           pdb=" N   LEU A 491 "
           pdb=" CA  LEU A 491 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.52  -23.48     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 5354 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1257
       0.077 -    0.153: 143
       0.153 -    0.230: 17
       0.230 -    0.307: 16
       0.307 -    0.383: 4
  Chirality restraints: 1437
  Sorted by residual:
  chirality pdb=" CG  LEU A 491 "
            pdb=" CB  LEU A 491 "
            pdb=" CD1 LEU A 491 "
            pdb=" CD2 LEU A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.21   -0.38 2.00e-01 2.50e+01 3.67e+00
  chirality pdb=" CB  VAL B 261 "
            pdb=" CA  VAL B 261 "
            pdb=" CG1 VAL B 261 "
            pdb=" CG2 VAL B 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.26   -0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CB  VAL A 423 "
            pdb=" CA  VAL A 423 "
            pdb=" CG1 VAL A 423 "
            pdb=" CG2 VAL A 423 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.06e+00
  ... (remaining 1434 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 194 "    0.014 2.00e-02 2.50e+03   2.92e-02 8.52e+00
        pdb=" CD  GLU A 194 "   -0.050 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 194 "    0.018 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 194 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 300 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.64e+00
        pdb=" C   GLU A 300 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLU A 300 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 301 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 370 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.43e+00
        pdb=" CD  GLU A 370 "    0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 370 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 370 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 51
        2.52 -     3.12: 6402
        3.12 -     3.71: 13680
        3.71 -     4.31: 17409
        4.31 -     4.90: 27770
  Nonbonded interactions: 65312
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 177 "
            pdb=" OD1 ASP B 177 "
     model   vdw
     1.931 3.040
  nonbonded pdb=" O   THR A 215 "
            pdb=" OG1 THR A 216 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" O   PHE A  61 "
            pdb=" CD2 LEU A  74 "
     model   vdw
     2.207 3.460
  nonbonded pdb=" OG  SER B 379 "
            pdb=" O   LYS B 385 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OE2 GLU A 492 "
            pdb=" OE2 GLU A 529 "
     model   vdw
     2.237 3.040
  ... (remaining 65307 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:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.570
  Find NCS groups from input model:        0.030
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
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   0.070   8873  Z= 0.183
  Angle     :  0.788   8.330  12367  Z= 0.423
  Chirality :  0.058   0.383   1437
  Planarity :  0.005   0.050   1358
  Dihedral  : 17.883  87.163   3559
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.08 %
    Favored  : 94.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.73 (0.22), residues: 945
  helix: -2.19 (0.23), residues: 310
  sheet: -3.76 (0.43), residues: 93
  loop : -3.78 (0.22), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 206 
 TYR   0.013   0.001   TYR B 339 
 PHE   0.017   0.002   PHE B 416 
 TRP   0.019   0.001   TRP A 402 
 HIS   0.005   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 8873)
  covalent geometry    : angle       0.78808 (12367)
  hydrogen bonds       : bond        0.13300 (  329)
  hydrogen bonds       : angle       6.47094 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 PHE cc_start: 0.7908 (t80) cc_final: 0.7656 (t80)
REVERT: A  181 TYR cc_start: 0.7804 (m-10) cc_final: 0.6386 (m-10)
REVERT: A  246 LEU cc_start: 0.8617 (tp) cc_final: 0.8357 (tp)
REVERT: A  373 GLN cc_start: 0.8584 (pp30) cc_final: 0.8256 (tm-30)
REVERT: A  524 GLN cc_start: 0.8040 (tt0) cc_final: 0.7661 (tt0)
REVERT: A  552 VAL cc_start: 0.9119 (m) cc_final: 0.8883 (t)
REVERT: B   75 VAL cc_start: 0.8919 (t) cc_final: 0.8694 (t)
REVERT: B  254 VAL cc_start: 0.8808 (t) cc_final: 0.7895 (t)
REVERT: B  258 GLN cc_start: 0.8897 (mt0) cc_final: 0.8690 (mp10)
REVERT: B  318 TYR cc_start: 0.7723 (m-80) cc_final: 0.7132 (m-80)
REVERT: B  395 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8176 (ttpt)
REVERT: B  405 TYR cc_start: 0.7679 (m-80) cc_final: 0.7172 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1279
  time to fit residues: 29.3975
Evaluate side-chains
  95 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 208 HIS
A 315 HIS
A 394 GLN
A 475 GLN
A 507 GLN
A 524 GLN
A 547 GLN
B 145 GLN
** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 363 ASN
B 373 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.096225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.079451 restraints weight = 25393.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.081169 restraints weight = 14253.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.082349 restraints weight = 9415.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.083142 restraints weight = 6960.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.083622 restraints weight = 5613.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8873  Z= 0.162
  Angle     :  0.634   6.706  12367  Z= 0.316
  Chirality :  0.043   0.160   1437
  Planarity :  0.005   0.051   1358
  Dihedral  : 16.822  74.367   1845
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.81 %
    Favored  : 95.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.25), residues: 945
  helix: -0.51 (0.28), residues: 312
  sheet: -3.47 (0.41), residues: 110
  loop : -3.14 (0.24), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 277 
 TYR   0.013   0.002   TYR A 183 
 PHE   0.019   0.001   PHE A 171 
 TRP   0.021   0.001   TRP A 402 
 HIS   0.004   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8873)
  covalent geometry    : angle       0.63367 (12367)
  hydrogen bonds       : bond        0.03565 (  329)
  hydrogen bonds       : angle       4.51226 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 TYR cc_start: 0.7978 (m-10) cc_final: 0.6505 (m-10)
REVERT: A  246 LEU cc_start: 0.8389 (tp) cc_final: 0.8096 (tt)
REVERT: A  351 THR cc_start: 0.9372 (t) cc_final: 0.9017 (p)
REVERT: A  367 GLN cc_start: 0.7778 (mt0) cc_final: 0.7572 (mt0)
REVERT: A  524 GLN cc_start: 0.8109 (tt0) cc_final: 0.7701 (tt0)
REVERT: A  552 VAL cc_start: 0.9056 (m) cc_final: 0.8786 (p)
REVERT: B   75 VAL cc_start: 0.9043 (t) cc_final: 0.8732 (t)
REVERT: B  254 VAL cc_start: 0.8801 (t) cc_final: 0.7861 (t)
REVERT: B  318 TYR cc_start: 0.7785 (m-80) cc_final: 0.7202 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1040
  time to fit residues: 19.2002
Evaluate side-chains
  89 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 47 optimal weight:    0.6980
   chunk 75 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0570
   overall best weight:    1.3504

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
B 151 GLN
B 332 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.094579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.077799 restraints weight = 25072.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.079524 restraints weight = 14023.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.080690 restraints weight = 9224.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.081469 restraints weight = 6808.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.081959 restraints weight = 5496.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8873  Z= 0.149
  Angle     :  0.592   6.309  12367  Z= 0.292
  Chirality :  0.041   0.140   1437
  Planarity :  0.004   0.052   1358
  Dihedral  : 16.829  74.185   1845
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.95 %
    Favored  : 94.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.92 (0.26), residues: 945
  helix: -0.13 (0.29), residues: 325
  sheet: -3.37 (0.39), residues: 128
  loop : -2.89 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 284 
 TYR   0.012   0.001   TYR B 181 
 PHE   0.019   0.002   PHE A 171 
 TRP   0.025   0.001   TRP B 426 
 HIS   0.004   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8873)
  covalent geometry    : angle       0.59202 (12367)
  hydrogen bonds       : bond        0.03393 (  329)
  hydrogen bonds       : angle       4.25736 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.8291 (mmp) cc_final: 0.8043 (mmm)
REVERT: A  246 LEU cc_start: 0.8533 (tp) cc_final: 0.8066 (tt)
REVERT: A  370 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8351 (mm-30)
REVERT: A  524 GLN cc_start: 0.8202 (tt0) cc_final: 0.7730 (tt0)
REVERT: A  552 VAL cc_start: 0.9110 (m) cc_final: 0.8870 (p)
REVERT: B   75 VAL cc_start: 0.9150 (t) cc_final: 0.8876 (t)
REVERT: B  254 VAL cc_start: 0.8707 (t) cc_final: 0.8049 (t)
REVERT: B  258 GLN cc_start: 0.8964 (mt0) cc_final: 0.8739 (mp10)
REVERT: B  318 TYR cc_start: 0.7848 (m-80) cc_final: 0.7227 (m-80)
REVERT: B  378 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8002 (tt0)
REVERT: B  395 LYS cc_start: 0.9126 (tptt) cc_final: 0.8744 (ttpt)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1043
  time to fit residues: 17.2544
Evaluate side-chains
  83 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 68 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0050
   chunk 12 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
B 373 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.095922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.078321 restraints weight = 25479.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.080194 restraints weight = 14006.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.081465 restraints weight = 9108.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.082236 restraints weight = 6652.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.082834 restraints weight = 5379.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8873  Z= 0.111
  Angle     :  0.560   7.012  12367  Z= 0.274
  Chirality :  0.040   0.131   1437
  Planarity :  0.004   0.055   1358
  Dihedral  : 16.675  74.134   1845
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.31 (0.27), residues: 945
  helix:  0.47 (0.30), residues: 322
  sheet: -2.94 (0.43), residues: 127
  loop : -2.61 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 358 
 TYR   0.021   0.001   TYR A 405 
 PHE   0.014   0.001   PHE A 171 
 TRP   0.025   0.001   TRP A 402 
 HIS   0.003   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8873)
  covalent geometry    : angle       0.56003 (12367)
  hydrogen bonds       : bond        0.03069 (  329)
  hydrogen bonds       : angle       4.07007 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.8369 (mmp) cc_final: 0.8093 (mmm)
REVERT: A  210 LEU cc_start: 0.8591 (tp) cc_final: 0.8119 (pp)
REVERT: A  246 LEU cc_start: 0.8340 (tp) cc_final: 0.7959 (tt)
REVERT: A  370 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8267 (mm-30)
REVERT: A  524 GLN cc_start: 0.8335 (tt0) cc_final: 0.7869 (tt0)
REVERT: A  552 VAL cc_start: 0.9095 (m) cc_final: 0.8867 (p)
REVERT: B  279 LEU cc_start: 0.8951 (mp) cc_final: 0.8677 (mt)
REVERT: B  318 TYR cc_start: 0.7892 (m-80) cc_final: 0.7244 (m-80)
REVERT: B  378 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7987 (tt0)
REVERT: B  395 LYS cc_start: 0.9048 (tptt) cc_final: 0.8806 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0912
  time to fit residues: 17.0384
Evaluate side-chains
  79 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0980
   chunk 29 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 40 optimal weight:    0.3980
   chunk 81 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
B 373 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.091778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.074533 restraints weight = 25360.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.076219 restraints weight = 14381.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.077366 restraints weight = 9573.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.078044 restraints weight = 7127.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.078609 restraints weight = 5866.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8873  Z= 0.177
  Angle     :  0.611   6.915  12367  Z= 0.302
  Chirality :  0.041   0.142   1437
  Planarity :  0.004   0.054   1358
  Dihedral  : 16.720  74.193   1845
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.27), residues: 945
  helix:  0.43 (0.30), residues: 326
  sheet: -2.62 (0.44), residues: 117
  loop : -2.48 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 211 
 TYR   0.018   0.002   TYR A 405 
 PHE   0.018   0.002   PHE A 171 
 TRP   0.030   0.002   TRP B 414 
 HIS   0.006   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 8873)
  covalent geometry    : angle       0.61115 (12367)
  hydrogen bonds       : bond        0.03386 (  329)
  hydrogen bonds       : angle       4.07407 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 LEU cc_start: 0.8251 (tp) cc_final: 0.7940 (tt)
REVERT: A  370 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8139 (tp30)
REVERT: A  524 GLN cc_start: 0.8156 (tt0) cc_final: 0.7878 (tt0)
REVERT: A  552 VAL cc_start: 0.9162 (m) cc_final: 0.8941 (p)
REVERT: B  178 ILE cc_start: 0.9332 (mt) cc_final: 0.9032 (tt)
REVERT: B  279 LEU cc_start: 0.8864 (mp) cc_final: 0.8619 (mt)
REVERT: B  378 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8002 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0975
  time to fit residues: 15.7347
Evaluate side-chains
  82 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 306 ASN
A 475 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.093539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.076069 restraints weight = 25376.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.078008 restraints weight = 13421.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.079282 restraints weight = 8514.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080129 restraints weight = 6159.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.080593 restraints weight = 4913.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8873  Z= 0.122
  Angle     :  0.565   6.317  12367  Z= 0.277
  Chirality :  0.040   0.153   1437
  Planarity :  0.004   0.057   1358
  Dihedral  : 16.638  74.180   1845
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.27), residues: 945
  helix:  0.64 (0.30), residues: 328
  sheet: -2.41 (0.45), residues: 121
  loop : -2.37 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 307 
 TYR   0.014   0.001   TYR A 405 
 PHE   0.020   0.002   PHE A 171 
 TRP   0.024   0.001   TRP B 414 
 HIS   0.003   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8873)
  covalent geometry    : angle       0.56470 (12367)
  hydrogen bonds       : bond        0.03125 (  329)
  hydrogen bonds       : angle       4.04203 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 TYR cc_start: 0.8180 (m-10) cc_final: 0.6921 (m-10)
REVERT: A  246 LEU cc_start: 0.8331 (tp) cc_final: 0.7895 (tt)
REVERT: A  370 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8385 (tp30)
REVERT: A  440 PHE cc_start: 0.9079 (m-80) cc_final: 0.8686 (m-80)
REVERT: A  464 GLN cc_start: 0.8265 (pp30) cc_final: 0.8025 (pp30)
REVERT: A  552 VAL cc_start: 0.9188 (m) cc_final: 0.8938 (p)
REVERT: B  279 LEU cc_start: 0.8982 (mp) cc_final: 0.8768 (mt)
REVERT: B  378 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8057 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0934
  time to fit residues: 15.0371
Evaluate side-chains
  77 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 87 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 221 HIS
B 147 ASN
B 373 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.093884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.076170 restraints weight = 26158.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.078062 restraints weight = 13999.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.079315 restraints weight = 9024.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080163 restraints weight = 6621.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.080756 restraints weight = 5319.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8873  Z= 0.111
  Angle     :  0.554   6.334  12367  Z= 0.272
  Chirality :  0.040   0.178   1437
  Planarity :  0.004   0.055   1358
  Dihedral  : 16.629  74.187   1845
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.28), residues: 945
  helix:  0.77 (0.30), residues: 325
  sheet: -2.38 (0.44), residues: 128
  loop : -2.19 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 277 
 TYR   0.012   0.001   TYR A 405 
 PHE   0.022   0.001   PHE A 171 
 TRP   0.022   0.001   TRP A 402 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8873)
  covalent geometry    : angle       0.55396 (12367)
  hydrogen bonds       : bond        0.03023 (  329)
  hydrogen bonds       : angle       3.95899 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.6903 (t0) cc_final: 0.6641 (t70)
REVERT: A  370 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8320 (tp30)
REVERT: A  552 VAL cc_start: 0.9170 (m) cc_final: 0.8941 (p)
REVERT: B  279 LEU cc_start: 0.8914 (mp) cc_final: 0.8694 (mt)
REVERT: B  378 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8073 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0925
  time to fit residues: 14.5017
Evaluate side-chains
  83 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 88 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0170
   chunk 62 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.3022

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
B 373 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.092385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.074840 restraints weight = 26051.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.076718 restraints weight = 13891.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.077981 restraints weight = 8915.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.078734 restraints weight = 6492.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.079305 restraints weight = 5262.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8873  Z= 0.142
  Angle     :  0.572   7.903  12367  Z= 0.282
  Chirality :  0.040   0.149   1437
  Planarity :  0.004   0.051   1358
  Dihedral  : 16.652  74.170   1845
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.57 (0.28), residues: 945
  helix:  0.84 (0.30), residues: 324
  sheet: -2.18 (0.46), residues: 120
  loop : -2.10 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 199 
 TYR   0.013   0.001   TYR A 405 
 PHE   0.024   0.002   PHE B 416 
 TRP   0.030   0.001   TRP B 414 
 HIS   0.003   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8873)
  covalent geometry    : angle       0.57181 (12367)
  hydrogen bonds       : bond        0.03182 (  329)
  hydrogen bonds       : angle       3.99409 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.6950 (t0) cc_final: 0.6708 (t0)
REVERT: A  370 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8335 (tp30)
REVERT: A  464 GLN cc_start: 0.8426 (pp30) cc_final: 0.8168 (pp30)
REVERT: A  552 VAL cc_start: 0.9172 (m) cc_final: 0.8946 (p)
REVERT: B  110 ASP cc_start: 0.8582 (m-30) cc_final: 0.7851 (p0)
REVERT: B  279 LEU cc_start: 0.8934 (mp) cc_final: 0.8706 (mt)
REVERT: B  307 ARG cc_start: 0.8378 (mpp80) cc_final: 0.7947 (mtm-85)
REVERT: B  378 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8107 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0953
  time to fit residues: 13.3294
Evaluate side-chains
  79 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0170
   chunk 17 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   chunk 44 optimal weight:    6.9990
   chunk 98 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0270
   overall best weight:    0.4078

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

Flipped N/Q/H residues before XYZ refinement:
A  96 HIS
** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.094745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.076976 restraints weight = 25681.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.078917 restraints weight = 13699.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.080220 restraints weight = 8789.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.081024 restraints weight = 6400.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.081637 restraints weight = 5168.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.4533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8873  Z= 0.097
  Angle     :  0.543   7.347  12367  Z= 0.265
  Chirality :  0.039   0.143   1437
  Planarity :  0.004   0.051   1358
  Dihedral  : 16.573  74.213   1845
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.28), residues: 945
  helix:  0.98 (0.31), residues: 334
  sheet: -2.24 (0.42), residues: 140
  loop : -1.97 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 125 
 TYR   0.009   0.001   TYR B 181 
 PHE   0.022   0.002   PHE A 171 
 TRP   0.025   0.001   TRP A 402 
 HIS   0.003   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8873)
  covalent geometry    : angle       0.54321 (12367)
  hydrogen bonds       : bond        0.02838 (  329)
  hydrogen bonds       : angle       3.88995 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.6946 (t0) cc_final: 0.6658 (t0)
REVERT: A  370 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8335 (tp30)
REVERT: B  279 LEU cc_start: 0.8911 (mp) cc_final: 0.8699 (mt)
REVERT: B  307 ARG cc_start: 0.8398 (mpp80) cc_final: 0.8004 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1015
  time to fit residues: 14.9117
Evaluate side-chains
  81 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 255 ASN
B 373 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.093744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.076067 restraints weight = 25763.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.077984 restraints weight = 13726.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.079274 restraints weight = 8845.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.080124 restraints weight = 6441.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.080692 restraints weight = 5170.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.4705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8873  Z= 0.111
  Angle     :  0.559   7.078  12367  Z= 0.273
  Chirality :  0.040   0.144   1437
  Planarity :  0.004   0.050   1358
  Dihedral  : 16.588  74.183   1845
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.28), residues: 945
  helix:  0.94 (0.30), residues: 334
  sheet: -2.13 (0.41), residues: 146
  loop : -1.88 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 358 
 TYR   0.010   0.001   TYR A 405 
 PHE   0.024   0.002   PHE A 171 
 TRP   0.023   0.001   TRP B 414 
 HIS   0.002   0.000   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8873)
  covalent geometry    : angle       0.55931 (12367)
  hydrogen bonds       : bond        0.02984 (  329)
  hydrogen bonds       : angle       3.93326 (  839)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  370 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8354 (tp30)
REVERT: A  552 VAL cc_start: 0.9184 (m) cc_final: 0.8965 (p)
REVERT: B  307 ARG cc_start: 0.8456 (mpp80) cc_final: 0.8051 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0940
  time to fit residues: 13.3481
Evaluate side-chains
  76 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 45 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 361 HIS
B 147 ASN
B 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.089854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.072313 restraints weight = 25211.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.074119 restraints weight = 13526.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.075333 restraints weight = 8673.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.075964 restraints weight = 6322.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.076511 restraints weight = 5204.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.4833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   8873  Z= 0.221
  Angle     :  0.655   7.759  12367  Z= 0.326
  Chirality :  0.042   0.164   1437
  Planarity :  0.005   0.047   1358
  Dihedral  : 16.742  74.249   1845
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.28), residues: 945
  helix:  0.70 (0.30), residues: 333
  sheet: -2.04 (0.42), residues: 143
  loop : -1.94 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 358 
 TYR   0.015   0.002   TYR A 405 
 PHE   0.025   0.002   PHE A 171 
 TRP   0.047   0.002   TRP B 414 
 HIS   0.004   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 8873)
  covalent geometry    : angle       0.65520 (12367)
  hydrogen bonds       : bond        0.03591 (  329)
  hydrogen bonds       : angle       4.18099 (  839)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1406.61 seconds
wall clock time: 25 minutes 11.97 seconds (1511.97 seconds total)