Starting phenix.real_space_refine (version: dev)
on Mon Apr  4 14:57:08 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/04_2022/6ybv_10774.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/04_2022/6ybv_10774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/04_2022/6ybv_10774.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/04_2022/6ybv_10774.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/04_2022/6ybv_10774.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/04_2022/6ybv_10774.pdb"
  }
  resolution = 3.8
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 6731
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "s"
      Number of atoms: 1123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1123
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "r"
      Number of atoms: 2215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2215
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 9, 'TRANS': 265}
    Chain: "w"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1604
          Classifications: {'RNA': 75}
          Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna3p_pur': 34, 'rna2p_pyr': 4, 'rna3p_pyr': 29}
          Link IDs: {'rna3p': 62, 'rna2p': 12}
    Chain: "k"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Classifications: {'RNA': 3}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2}
          Link IDs: {'rna3p': 2}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'  A%rna2p_pur:plan': 1, '  A%rna2p_pur:plan2': 1, '  A%rna3p_pur:plan2': 2, '  A%rna3p_pur:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "t"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 356, 1750
          Classifications: {'peptide': 356}
          Incomplete info: {'truncation_to_alanine': 298}
          Link IDs: {'PTRANS': 15, 'TRANS': 340}
          Chain breaks: 4
          Unresolved chain link angles: 15
          Unresolved non-hydrogen bonds: 1009
          Unresolved non-hydrogen angles: 1285
          Unresolved non-hydrogen dihedrals: 814
          Unresolved non-hydrogen chiralities: 125
          Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 23, 'ARG:plan': 17}
          Unresolved non-hydrogen planarities: 445
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   ALA t  51 " occ=0.32
      ... (3 atoms not shown)
      pdb=" CB  ALA t  51 " occ=0.32
    residue:
      pdb=" N   GLN t 206 " occ=0.55
      ... (3 atoms not shown)
      pdb=" CB  GLN t 206 " occ=0.55
    residue:
      pdb=" N   LEU t 208 " occ=0.35
      ... (3 atoms not shown)
      pdb=" CB  LEU t 208 " occ=0.35
    residue:
      pdb=" N   ASN t 431 " occ=0.42
      ... (3 atoms not shown)
      pdb=" CB  ASN t 431 " occ=0.42
  Time building chain proxies: 4.82, per 1000 atoms: 0.72
  Number of scatterers: 6731
  At special positions: 0
  Unit cell: (111.696, 117.066, 106.326, 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      21     16.00
     P      77     15.00
     O    1506      8.00
     N    1250      7.00
     C    3877      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  - 3.50
        Amino acid           : False - 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: 3.61
  Conformation dependent library (CDL) restraints added in 882.1 milliseconds
  

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 9 sheets defined
      33.7% alpha, 16.4% beta
      14 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 2.15
  Creating SS restraints...
    Processing helix  chain 's' and resid 176 through 186
    Processing helix  chain 's' and resid 221 through 229
    Processing helix  chain 's' and resid 234 through 243
      removed outlier: 4.012A  pdb=" N   ALA s 238 " --> pdb=" O   LYS s 234 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   PHE s 239 " --> pdb=" O   HIS s 235 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 244 through 246
      No H-bonds generated for 'chain 's' and resid 244 through 246'
    Processing helix  chain 's' and resid 263 through 278
    Processing helix  chain 'r' and resid 58 through 63
      removed outlier: 3.609A  pdb=" N   LEU r  62 " --> pdb=" O   SER r  58 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 91 through 119
    Processing helix  chain 'r' and resid 123 through 134
    Processing helix  chain 'r' and resid 134 through 142
    Processing helix  chain 'r' and resid 146 through 157
    Processing helix  chain 'r' and resid 161 through 166
      removed outlier: 3.694A  pdb=" N   LEU r 166 " --> pdb=" O   LEU r 163 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 169 through 181
      removed outlier: 3.697A  pdb=" N   ARG r 173 " --> pdb=" O   ASN r 169 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU r 174 " --> pdb=" O   GLU r 170 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 203 through 218
    Processing helix  chain 'r' and resid 243 through 262
      removed outlier: 3.720A  pdb=" N   GLY r 247 " --> pdb=" O   GLU r 243 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER r 249 " --> pdb=" O   THR r 245 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 53 through 63
    Processing helix  chain 't' and resid 69 through 76
    Processing helix  chain 't' and resid 141 through 152
      removed outlier: 3.949A  pdb=" N   MET t 145 " --> pdb=" O   LEU t 141 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL t 151 " --> pdb=" O   ASN t 147 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 168 through 181
    Processing helix  chain 't' and resid 196 through 212
    Processing helix  chain 't' and resid 214 through 219
      removed outlier: 4.131A  pdb=" N   GLY t 218 " --> pdb=" O   VAL t 215 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 231 through 243
    Processing helix  chain 't' and resid 344 through 349
    Processing sheet with id=AA1, first strand: chain 's' and resid 218 through 219
      removed outlier: 4.107A  pdb=" N   VAL s 257 " --> pdb=" O   SER s 249 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER s 249 " --> pdb=" O   VAL s 257 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 's' and resid 291 through 293
      removed outlier: 3.693A  pdb=" N   GLN s 292 " --> pdb=" O   PHE s 299 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE s 299 " --> pdb=" O   GLN s 292 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'r' and resid 19 through 24
      removed outlier: 8.870A  pdb=" N   LEU r  85 " --> pdb=" O   GLU r  43 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   MET r  45 " --> pdb=" O   LEU r  85 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ASP r  84 " --> pdb=" O   ILE r  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'r' and resid 226 through 229
      removed outlier: 3.751A  pdb=" N   ASN r 228 " --> pdb=" O   VAL r 236 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU r 196 " --> pdb=" O   ASN r 270 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN r 270 " --> pdb=" O   GLU r 196 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 't' and resid 84 through 86
      removed outlier: 3.615A  pdb=" N   ALA t  84 " --> pdb=" O   PHE t 132 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ILE t  44 " --> pdb=" O   VAL t 133 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   GLY t  45 " --> pdb=" O   LEU t 156 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU t 158 " --> pdb=" O   GLY t  45 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   ILE t  47 " --> pdb=" O   LEU t 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ALA t 155 " --> pdb=" O   LEU t 186 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   LEU t 188 " --> pdb=" O   ALA t 155 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LEU t 157 " --> pdb=" O   LEU t 188 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE t 222 " --> pdb=" O   ILE t 187 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 't' and resid 283 through 285
      removed outlier: 6.429A  pdb=" N   ARG t 255 " --> pdb=" O   LEU t 284 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 't' and resid 279 through 281
      removed outlier: 3.777A  pdb=" N   ALA t 279 " --> pdb=" O   VAL t 339 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 't' and resid 367 through 368
      removed outlier: 3.908A  pdb=" N   VAL t 433 " --> pdb=" O   PHE t 368 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 't' and resid 411 through 413
      removed outlier: 3.756A  pdb=" N   ASN t 407 " --> pdb=" O   ALA t 442 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   ALA t 442 " --> pdb=" O   ASN t 407 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ILE t 441 " --> pdb=" O   TRP t 456 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   TRP t 456 " --> pdb=" O   ILE t 441 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LEU t 443 " --> pdb=" O   ILE t 454 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TRP t 456 " --> pdb=" O   PHE t 376 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE t 373 " --> pdb=" O   GLY t 425 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLY t 425 " --> pdb=" O   ILE t 373 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LEU t 424 " --> pdb=" O   VAL t 420 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   VAL t 420 " --> pdb=" O   LEU t 424 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   LYS t 426 " --> pdb=" O   SER t 418 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER t 418 " --> pdb=" O   LYS t 426 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL t 428 " --> pdb=" O   ARG t 416 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    624 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 2.37

  Time building geometry restraints manager: 3.30 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: 1471
        1.33 -     1.45: 1866
        1.45 -     1.57: 3452
        1.57 -     1.70: 150
        1.70 -     1.82: 31
  Bond restraints: 6970
  Sorted by residual:
  bond pdb=" C   VAL r  90 "
       pdb=" N   SER r  91 "
    ideal  model  delta    sigma   weight residual
    1.339  1.213  0.126 5.57e-02 3.22e+02 5.13e+00
  bond pdb=" C   CYS t 311 "
       pdb=" N   LYS t 312 "
    ideal  model  delta    sigma   weight residual
    1.335  1.256  0.079 3.59e-02 7.76e+02 4.81e+00
  bond pdb=" N   GLU t 324 "
       pdb=" CA  GLU t 324 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.64e+00
  bond pdb=" C5'   G w  10 "
       pdb=" C4'   G w  10 "
    ideal  model  delta    sigma   weight residual
    1.508  1.480  0.028 1.50e-02 4.44e+03 3.59e+00
  bond pdb=" CB  VAL r  71 "
       pdb=" CG2 VAL r  71 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.58e+00
  ... (remaining 6965 not shown)

  Histogram of bond angle deviations from ideal:
       97.09 -   105.55: 504
      105.55 -   114.02: 4059
      114.02 -   122.48: 4044
      122.48 -   130.94: 1201
      130.94 -   139.40: 32
  Bond angle restraints: 9840
  Sorted by residual:
  angle pdb=" N   PRO t 168 "
        pdb=" CA  PRO t 168 "
        pdb=" C   PRO t 168 "
      ideal   model   delta    sigma   weight residual
     112.47  124.78  -12.31 2.06e+00 2.36e-01 3.57e+01
  angle pdb=" N   VAL s 203 "
        pdb=" CA  VAL s 203 "
        pdb=" C   VAL s 203 "
      ideal   model   delta    sigma   weight residual
     109.34   97.09   12.25 2.08e+00 2.31e-01 3.47e+01
  angle pdb=" N   GLY s 252 "
        pdb=" CA  GLY s 252 "
        pdb=" C   GLY s 252 "
      ideal   model   delta    sigma   weight residual
     112.18  105.50    6.68 1.34e+00 5.57e-01 2.48e+01
  angle pdb=" CA  ARG s 272 "
        pdb=" CB  ARG s 272 "
        pdb=" CG  ARG s 272 "
      ideal   model   delta    sigma   weight residual
     114.10  124.02   -9.92 2.00e+00 2.50e-01 2.46e+01
  angle pdb=" C4'   G w  52 "
        pdb=" C3'   G w  52 "
        pdb=" O3'   G w  52 "
      ideal   model   delta    sigma   weight residual
     113.00  120.35   -7.35 1.50e+00 4.44e-01 2.40e+01
  ... (remaining 9835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.56: 3655
       24.56 -    49.11: 332
       49.11 -    73.67: 45
       73.67 -    98.23: 8
       98.23 -   122.78: 2
  Dihedral angle restraints: 4042
    sinusoidal: 1820
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" O4'   C w  73 "
           pdb=" C1'   C w  73 "
           pdb=" N1    C w  73 "
           pdb=" C2    C w  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -44.83  -83.17     1      1.70e+01 3.46e-03 2.93e+01
  dihedral pdb=" O4'   A k  17 "
           pdb=" C2'   A k  17 "
           pdb=" C1'   A k  17 "
           pdb=" C3'   A k  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -9.51   34.51     1      8.00e+00 1.56e-02 2.64e+01
  dihedral pdb=" O4'   A k  16 "
           pdb=" C2'   A k  16 "
           pdb=" C1'   A k  16 "
           pdb=" C3'   A k  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -9.08   34.08     1      8.00e+00 1.56e-02 2.58e+01
  ... (remaining 4039 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 883
       0.068 -    0.136: 271
       0.136 -    0.204: 68
       0.204 -    0.272: 9
       0.272 -    0.340: 4
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" C1'   C w  73 "
            pdb=" O4'   C w  73 "
            pdb=" C2'   C w  73 "
            pdb=" N1    C w  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.11    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CB  VAL r  34 "
            pdb=" CA  VAL r  34 "
            pdb=" CG1 VAL r  34 "
            pdb=" CG2 VAL r  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  PRO t 168 "
            pdb=" N   PRO t 168 "
            pdb=" C   PRO t 168 "
            pdb=" CB  PRO t 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.34e+00
  ... (remaining 1232 not shown)

  Planarity restraints: 1011
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN s 292 "   -0.018 2.00e-02 2.50e+03   3.63e-02 1.32e+01
        pdb=" CD  GLN s 292 "    0.063 2.00e-02 2.50e+03
        pdb=" OE1 GLN s 292 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE2 GLN s 292 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G w  12 "   -0.008 2.00e-02 2.50e+03   2.03e-02 1.24e+01
        pdb=" N9    G w  12 "    0.037 2.00e-02 2.50e+03
        pdb=" C8    G w  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G w  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    G w  12 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G w  12 "    0.009 2.00e-02 2.50e+03
        pdb=" O6    G w  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    G w  12 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G w  12 "    0.033 2.00e-02 2.50e+03
        pdb=" N2    G w  12 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3    G w  12 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G w  12 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA t 323 "    0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   ALA t 323 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ALA t 323 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU t 324 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1008 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 888
        2.74 -     3.28: 6205
        3.28 -     3.82: 11334
        3.82 -     4.36: 12440
        4.36 -     4.90: 19659
  Nonbonded interactions: 50526
  Sorted by model distance:
  nonbonded pdb=" O6    G w   9 "
            pdb=" O2'   A w  19 "
     model   vdw
     2.202 2.440
  nonbonded pdb=" O   ALA s 196 "
            pdb=" NH2 ARG s 285 "
     model   vdw
     2.245 2.520
  nonbonded pdb=" OG1 THR s 246 "
            pdb=" O   LYS s 259 "
     model   vdw
     2.251 2.440
  nonbonded pdb=" OG1 THR r 220 "
            pdb=" O   MET r 223 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" O   LYS r 104 "
            pdb=" OG1 THR r 107 "
     model   vdw
     2.277 2.440
  ... (remaining 50521 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      77      5.49       5
     S      21      5.16       5
     C    3877      2.51       5
     N    1250      2.21       5
     O    1506      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.32 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:             4.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          24.230
  Check model and map are aligned:         0.110
  Convert atoms to be neutral:             0.060
  Process input model:                     26.960
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5584
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      :  0.008   0.126   6970  Z= 0.532
  Angle     :  1.466  15.017   9840  Z= 0.842
  Chirality :  0.071   0.340   1235
  Planarity :  0.009   0.069   1011
  Dihedral  : 17.695 122.782   2598
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.09 %
    Favored  : 93.38 %
  Rotamer Outliers :  6.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.26 (0.26), residues: 755
  helix: -0.78 (0.32), residues: 214
  sheet:  0.05 (0.50), residues: 109
  loop : -2.41 (0.24), residues: 432

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 6
  residues processed: 120
  average time/residue: 0.2555
  time to fit residues: 38.1607
Evaluate side-chains
  59 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.689 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0720
  time to fit residues: 1.8001
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:   20.0000
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** s 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 306 HIS
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5657
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6970  Z= 0.232
  Angle     :  0.702   7.118   9840  Z= 0.378
  Chirality :  0.045   0.219   1235
  Planarity :  0.005   0.059   1011
  Dihedral  : 15.080 113.327   1737
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.43 %
    Favored  : 94.17 %
  Rotamer Outliers :  3.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.27), residues: 755
  helix: -0.13 (0.32), residues: 216
  sheet: -0.66 (0.43), residues: 136
  loop : -2.14 (0.27), residues: 403

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 1
  residues processed: 67
  average time/residue: 0.2017
  time to fit residues: 17.9157
Evaluate side-chains
  44 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.662 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0600
  time to fit residues: 1.0109
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   chunk 73 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   chunk 59 optimal weight:    7.9990
   overall best weight:    2.4142

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

Flipped N/Q/H residues before XYZ refinement:
** s 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5768
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6970  Z= 0.252
  Angle     :  0.724  14.372   9840  Z= 0.378
  Chirality :  0.045   0.188   1235
  Planarity :  0.005   0.059   1011
  Dihedral  : 15.248 116.970   1737
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 20.43
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.75 %
    Favored  : 93.11 %
  Rotamer Outliers :  4.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.28), residues: 755
  helix: -0.02 (0.33), residues: 222
  sheet: -0.56 (0.46), residues: 121
  loop : -2.18 (0.27), residues: 412

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.730 
Fit side-chains
  outliers start: 15
  outliers final: 4
  residues processed: 64
  average time/residue: 0.1806
  time to fit residues: 15.9787
Evaluate side-chains
  49 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.709 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0548
  time to fit residues: 1.2175
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0570
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:   20.0000
   chunk 74 optimal weight:    8.9990
   chunk 79 optimal weight:   20.0000
   chunk 39 optimal weight:    0.5980
   chunk 70 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.0902

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

Flipped N/Q/H residues before XYZ refinement:
s 181 ASN
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5662
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6970  Z= 0.158
  Angle     :  0.588   9.477   9840  Z= 0.309
  Chirality :  0.043   0.194   1235
  Planarity :  0.004   0.039   1011
  Dihedral  : 14.713 121.314   1737
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.77 %
    Favored  : 94.97 %
  Rotamer Outliers :  4.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.29), residues: 755
  helix:  0.42 (0.33), residues: 226
  sheet: -0.65 (0.46), residues: 113
  loop : -1.90 (0.28), residues: 416

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.701 
Fit side-chains
  outliers start: 16
  outliers final: 3
  residues processed: 66
  average time/residue: 0.2005
  time to fit residues: 19.6920
Evaluate side-chains
  49 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.977 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0753
  time to fit residues: 1.4606
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:   30.0000
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 54 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 71 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
r 179 ASN
** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5933
moved from start:          0.4829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.074   6970  Z= 0.402
  Angle     :  0.893  16.416   9840  Z= 0.460
  Chirality :  0.050   0.276   1235
  Planarity :  0.006   0.057   1011
  Dihedral  : 15.985 130.509   1737
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 25.60
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.27 %
    Favored  : 90.46 %
  Rotamer Outliers :  4.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.40 (0.28), residues: 755
  helix: -0.60 (0.30), residues: 224
  sheet: -1.55 (0.53), residues: 87
  loop : -2.22 (0.27), residues: 444

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.707 
Fit side-chains
  outliers start: 17
  outliers final: 5
  residues processed: 61
  average time/residue: 0.1805
  time to fit residues: 15.3285
Evaluate side-chains
  48 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.703 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0616
  time to fit residues: 1.4779
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 71 optimal weight:   50.0000
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 79 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
s 221 ASN
** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5861
moved from start:          0.5032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6970  Z= 0.252
  Angle     :  0.715  12.456   9840  Z= 0.375
  Chirality :  0.046   0.190   1235
  Planarity :  0.004   0.042   1011
  Dihedral  : 15.590 120.129   1737
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 19.58
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.55 %
    Favored  : 92.19 %
  Rotamer Outliers :  3.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.27 (0.28), residues: 755
  helix: -0.26 (0.32), residues: 223
  sheet: -1.99 (0.55), residues: 77
  loop : -2.16 (0.27), residues: 455

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.727 
Fit side-chains
  outliers start: 12
  outliers final: 3
  residues processed: 60
  average time/residue: 0.1720
  time to fit residues: 14.5798
Evaluate side-chains
  49 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.712 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0635
  time to fit residues: 1.2014
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 66 optimal weight:   30.0000
   chunk 79 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:   20.0000
   overall best weight:    5.5788

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

Flipped N/Q/H residues before XYZ refinement:
r 179 ASN
** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6056
moved from start:          0.5979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.008   0.106   6970  Z= 0.485
  Angle     :  1.037  21.329   9840  Z= 0.530
  Chirality :  0.054   0.227   1235
  Planarity :  0.007   0.065   1011
  Dihedral  : 16.878 117.143   1737
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 31.62
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 12.45 %
    Favored  : 87.28 %
  Rotamer Outliers :  2.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.27 (0.27), residues: 755
  helix: -1.30 (0.30), residues: 225
  sheet: -2.30 (0.63), residues: 63
  loop : -2.75 (0.25), residues: 467

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.718 
Fit side-chains
  outliers start: 11
  outliers final: 3
  residues processed: 60
  average time/residue: 0.2261
  time to fit residues: 17.8268
Evaluate side-chains
  48 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.676 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0621
  time to fit residues: 1.1546
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 50 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0570
   chunk 39 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0970
   chunk 75 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 73 optimal weight:   40.0000
   overall best weight:    1.3900

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

Flipped N/Q/H residues before XYZ refinement:
** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5857
moved from start:          0.5868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6970  Z= 0.198
  Angle     :  0.707  12.764   9840  Z= 0.367
  Chirality :  0.046   0.252   1235
  Planarity :  0.004   0.041   1011
  Dihedral  : 15.744 104.893   1737
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.95 %
    Favored  : 91.79 %
  Rotamer Outliers :  1.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.65 (0.28), residues: 755
  helix: -0.44 (0.33), residues: 223
  sheet: -2.61 (0.47), residues: 102
  loop : -2.34 (0.27), residues: 430

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 0.1504
  time to fit residues: 11.9253
Evaluate side-chains
  51 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.653 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0714
  time to fit residues: 1.5975
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 57 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 69 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 48 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 47 optimal weight:   20.0000
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6000
moved from start:          0.6190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.081   6970  Z= 0.363
  Angle     :  0.873  17.892   9840  Z= 0.450
  Chirality :  0.049   0.250   1235
  Planarity :  0.006   0.055   1011
  Dihedral  : 16.254 113.704   1737
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 24.41
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 12.58 %
    Favored  : 87.15 %
  Rotamer Outliers :  0.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.94 (0.28), residues: 755
  helix: -0.95 (0.32), residues: 224
  sheet: -2.37 (0.55), residues: 82
  loop : -2.50 (0.27), residues: 449

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.735 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1643
  time to fit residues: 12.0489
Evaluate side-chains
  46 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.726 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9100
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   chunk 81 optimal weight:    7.9990
   chunk 75 optimal weight:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0570
   chunk 50 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.6106

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

Flipped N/Q/H residues before XYZ refinement:
** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5865
moved from start:          0.6172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6970  Z= 0.202
  Angle     :  0.698  14.020   9840  Z= 0.363
  Chirality :  0.045   0.226   1235
  Planarity :  0.004   0.037   1011
  Dihedral  : 15.644 105.349   1737
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.48 %
    Favored  : 91.39 %
  Rotamer Outliers :  0.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.55 (0.29), residues: 755
  helix: -0.46 (0.33), residues: 224
  sheet: -2.38 (0.45), residues: 115
  loop : -2.24 (0.29), residues: 416

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.769 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1759
  time to fit residues: 12.1986
Evaluate side-chains
  45 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.720 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0639
  time to fit residues: 1.0172
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0980
   chunk 47 optimal weight:   20.0000
   overall best weight:    2.5584

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

Flipped N/Q/H residues before XYZ refinement:
** r 187 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 = 0.4265 r_free = 0.4265 target = 0.113175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.106648 restraints weight = 40668.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.106841 restraints weight = 37536.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.107124 restraints weight = 33387.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4265 r_free = 0.4265    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4261 r_free = 0.4261    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.4261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5960
moved from start:          0.6333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6970  Z= 0.262
  Angle     :  0.756  16.834   9840  Z= 0.390
  Chirality :  0.046   0.235   1235
  Planarity :  0.005   0.044   1011
  Dihedral  : 15.841 109.838   1737
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 20.34
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.92 %
    Favored  : 87.95 %
  Rotamer Outliers :  0.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.61 (0.29), residues: 755
  helix: -0.58 (0.33), residues: 224
  sheet: -2.32 (0.47), residues: 109
  loop : -2.27 (0.29), residues: 422

===============================================================================
Job complete
usr+sys time: 1424.46 seconds
wall clock time: 26 minutes 47.74 seconds (1607.74 seconds total)