Starting phenix.real_space_refine
on Fri Dec  8 03:09:32 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/12_2023/6ybv_10774.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/12_2023/6ybv_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_10774/12_2023/6ybv_10774.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/12_2023/6ybv_10774.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/12_2023/6ybv_10774.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/12_2023/6ybv_10774.pdb"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic.
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      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.
Process input model

  Symmetric amino acids flipped
    Residue "s TYR  176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "s ARG  188": "NH1" <-> "NH2"
    Residue "s ARG  200": "NH1" <-> "NH2"
    Residue "s ARG  211": "NH1" <-> "NH2"
    Residue "s PHE  219": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "s GLU  243": "OE1" <-> "OE2"
    Residue "s ARG  261": "NH1" <-> "NH2"
    Residue "s PHE  262": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "s GLU  268": "OE1" <-> "OE2"
    Residue "s GLU  277": "OE1" <-> "OE2"
    Residue "s ARG  285": "NH1" <-> "NH2"
    Residue "s ASP  288": "OD1" <-> "OD2"
    Residue "s ASP  294": "OD1" <-> "OD2"
    Residue "s ARG  296": "NH1" <-> "NH2"
    Residue "s PHE  299": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "s ARG  308": "NH1" <-> "NH2"
    Residue "r ARG    7": "NH1" <-> "NH2"
    Residue "r ARG   25": "NH1" <-> "NH2"
    Residue "r ARG   57": "NH1" <-> "NH2"
    Residue "r ARG   75": "NH1" <-> "NH2"
    Residue "r ASP   77": "OD1" <-> "OD2"
    Residue "r GLU   79": "OE1" <-> "OE2"
    Residue "r ARG   88": "NH1" <-> "NH2"
    Residue "r ARG   89": "NH1" <-> "NH2"
    Residue "r ARG  113": "NH1" <-> "NH2"
    Residue "r GLU  128": "OE1" <-> "OE2"
    Residue "r PHE  131": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "r ARG  133": "NH1" <-> "NH2"
    Residue "r ARG  144": "NH1" <-> "NH2"
    Residue "r ARG  173": "NH1" <-> "NH2"
    Residue "r ARG  182": "NH1" <-> "NH2"
    Residue "r ARG  183": "NH1" <-> "NH2"
    Residue "r ASP  194": "OD1" <-> "OD2"
    Residue "r GLU  221": "OE1" <-> "OE2"
    Residue "r ARG  234": "NH1" <-> "NH2"
    Residue "r ARG  244": "NH1" <-> "NH2"
    Residue "r ARG  266": "NH1" <-> "NH2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 12, 'rna3p': 62}
    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: 36
          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: 4.85, 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: 3.91
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 2.62
  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: 2.09

  Time building geometry restraints manager: 4.16 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: 3750
       24.56 -    49.11: 374
       49.11 -    73.67: 124
       73.67 -    98.23: 18
       98.23 -   122.78: 2
  Dihedral angle restraints: 4268
    sinusoidal: 2046
      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 4265 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
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:             22.690
  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:             0.000
  Extract box with map and model:          26.600
  Check model and map are aligned:         0.080
  Set scattering table:                    0.050
  Process input model:                     25.010
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   77.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5583
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  : 21.018 122.782   2824
  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 %
    Allowed  : 22.67 %
    Favored  : 70.67 %
  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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.004   TRP r 136 
   HIS   0.007   0.003   HIS r 155 
   PHE   0.032   0.005   PHE r 131 
   TYR   0.030   0.004   TYR s 176 
   ARG   0.016   0.002   ARG s 285 

*********************** 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  : 0.651 
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: 0.2694
  time to fit residues: 39.6930
Evaluate side-chains
  59 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.631 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0601
  time to fit residues: 1.4798
-------------------------------------------------------------------------------
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:    0.6980
   chunk 47 optimal weight:   20.0000
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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: 0.5651
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6970  Z= 0.226
  Angle     :  0.697   6.915   9840  Z= 0.376
  Chirality :  0.045   0.214   1235
  Planarity :  0.005   0.057   1011
  Dihedral  : 20.351 113.340   1963
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 18.99
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.43 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 31.47 %
    Favored  : 65.07 %
  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: -1.85 (0.27), residues: 755
  helix: -0.12 (0.32), residues: 217
  sheet: -0.67 (0.43), residues: 136
  loop : -2.12 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP r 136 
   HIS   0.015   0.002   HIS s 306 
   PHE   0.008   0.002   PHE s 239 
   TYR   0.017   0.002   TYR r 150 
   ARG   0.005   0.001   ARG r 234 

*********************** 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
  71 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.544 
Fit side-chains
  outliers start: 13
  outliers final: 1
  residues processed: 69
  average time/residue: 0.2248
  time to fit residues: 20.2176
Evaluate side-chains
  44 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.619 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0605
  time to fit residues: 0.9007
-------------------------------------------------------------------------------
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:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   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:    0.8980
   chunk 59 optimal weight:    7.9990
   overall best weight:    2.5784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5773
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6970  Z= 0.264
  Angle     :  0.736  14.327   9840  Z= 0.385
  Chirality :  0.045   0.181   1235
  Planarity :  0.005   0.056   1011
  Dihedral  : 20.455 115.485   1963
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 19.92
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.62 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 31.47 %
    Favored  : 64.00 %
  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: -1.95 (0.28), residues: 755
  helix: -0.10 (0.32), residues: 222
  sheet: -0.92 (0.43), residues: 133
  loop : -2.20 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.002   TRP r 136 
   HIS   0.005   0.001   HIS s 235 
   PHE   0.027   0.002   PHE s 239 
   TYR   0.018   0.002   TYR r 109 
   ARG   0.006   0.001   ARG s 231 

*********************** 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
  65 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.635 
Fit side-chains
  outliers start: 17
  outliers final: 5
  residues processed: 62
  average time/residue: 0.1826
  time to fit residues: 15.4860
Evaluate side-chains
  48 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.578 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0613
  time to fit residues: 1.3411
-------------------------------------------------------------------------------
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:   20.0000
   chunk 56 optimal weight:    0.0050
   chunk 38 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 50 optimal weight:    0.3980
   chunk 74 optimal weight:    8.9990
   chunk 79 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9980
   chunk 70 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7396

-------------------------------------------------------------------------------
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: 0.5625
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6970  Z= 0.151
  Angle     :  0.569   9.236   9840  Z= 0.302
  Chirality :  0.042   0.193   1235
  Planarity :  0.003   0.038   1011
  Dihedral  : 20.192 118.741   1963
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.37 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 32.53 %
    Favored  : 64.00 %
  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: -1.35 (0.29), residues: 755
  helix:  0.63 (0.34), residues: 224
  sheet: -0.68 (0.46), residues: 113
  loop : -1.90 (0.27), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.003   0.001   TRP r 136 
   HIS   0.003   0.001   HIS s 230 
   PHE   0.014   0.001   PHE s 239 
   TYR   0.012   0.001   TYR r  82 
   ARG   0.003   0.000   ARG s 211 

*********************** 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
  70 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.694 
Fit side-chains
  outliers start: 13
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1728
  time to fit residues: 15.8489
Evaluate side-chains
  49 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.658 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0638
  time to fit residues: 1.1919
-------------------------------------------------------------------------------
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:    0.7980
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 67 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   chunk 71 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    4.4986

-------------------------------------------------------------------------------
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  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5935
moved from start:          0.4775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.098   6970  Z= 0.412
  Angle     :  0.912  16.547   9840  Z= 0.470
  Chirality :  0.050   0.259   1235
  Planarity :  0.006   0.055   1011
  Dihedral  : 20.964 132.429   1963
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 25.94
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.87 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 33.33 %
    Favored  : 61.87 %
  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: -2.45 (0.28), residues: 755
  helix: -0.61 (0.31), residues: 224
  sheet: -2.03 (0.49), residues: 96
  loop : -2.14 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.002   TRP r 136 
   HIS   0.006   0.002   HIS s 306 
   PHE   0.020   0.003   PHE s 299 
   TYR   0.022   0.003   TYR s 274 
   ARG   0.009   0.001   ARG s 211 

*********************** 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
  66 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.648 
Fit side-chains
  outliers start: 18
  outliers final: 5
  residues processed: 63
  average time/residue: 0.1740
  time to fit residues: 15.1729
Evaluate side-chains
  46 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.677 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0656
  time to fit residues: 1.5149
-------------------------------------------------------------------------------
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:    7.9990
   chunk 71 optimal weight:   40.0000
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5874
moved from start:          0.4990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6970  Z= 0.274
  Angle     :  0.743  12.884   9840  Z= 0.387
  Chirality :  0.046   0.196   1235
  Planarity :  0.005   0.043   1011
  Dihedral  : 20.789 122.229   1963
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 21.87
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.34 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 34.93 %
    Favored  : 63.20 %
  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: -2.37 (0.28), residues: 755
  helix: -0.35 (0.31), residues: 223
  sheet: -2.56 (0.49), residues: 86
  loop : -2.09 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP r 136 
   HIS   0.004   0.001   HIS s 306 
   PHE   0.012   0.002   PHE s 239 
   TYR   0.013   0.002   TYR s 278 
   ARG   0.006   0.001   ARG s 211 

*********************** 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
  54 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.679 
Fit side-chains
  outliers start: 7
  outliers final: 1
  residues processed: 52
  average time/residue: 0.1918
  time to fit residues: 13.8914
Evaluate side-chains
  46 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.699 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0660
  time to fit residues: 0.9506
-------------------------------------------------------------------------------
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:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 57 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 66 optimal weight:   30.0000
   chunk 79 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 47 optimal weight:   20.0000
   overall best weight:    4.3388

-------------------------------------------------------------------------------
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  10 GLN ** 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: 0.5999
moved from start:          0.5785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087   6970  Z= 0.398
  Angle     :  0.928  19.207   9840  Z= 0.476
  Chirality :  0.050   0.203   1235
  Planarity :  0.006   0.067   1011
  Dihedral  : 21.296 115.193   1963
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 27.72
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 12.32 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 33.33 %
    Favored  : 62.67 %
  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: -2.99 (0.27), residues: 755
  helix: -1.06 (0.30), residues: 226
  sheet: -2.19 (0.62), residues: 63
  loop : -2.56 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.002   TRP r 136 
   HIS   0.006   0.002   HIS s 306 
   PHE   0.014   0.002   PHE s 239 
   TYR   0.016   0.002   TYR r 147 
   ARG   0.008   0.001   ARG s 211 

*********************** 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
  61 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.649 
Fit side-chains
  outliers start: 15
  outliers final: 2
  residues processed: 60
  average time/residue: 0.2028
  time to fit residues: 16.3742
Evaluate side-chains
  46 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.657 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0632
  time to fit residues: 1.0659
-------------------------------------------------------------------------------
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:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0000
   chunk 39 optimal weight:    0.0050
   chunk 7 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0980
   chunk 75 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   chunk 73 optimal weight:   40.0000
   overall best weight:    1.2202

-------------------------------------------------------------------------------
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 132 GLN ** 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: 0.5823
moved from start:          0.5694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6970  Z= 0.182
  Angle     :  0.684  12.164   9840  Z= 0.354
  Chirality :  0.045   0.231   1235
  Planarity :  0.004   0.038   1011
  Dihedral  : 20.745 104.954   1963
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 17.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.68 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 34.67 %
    Favored  : 64.00 %
  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: -2.49 (0.28), residues: 755
  helix: -0.28 (0.33), residues: 225
  sheet: -2.63 (0.45), residues: 104
  loop : -2.23 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.002   TRP r 136 
   HIS   0.002   0.001   HIS s 230 
   PHE   0.012   0.002   PHE s 239 
   TYR   0.011   0.001   TYR r  82 
   ARG   0.004   0.000   ARG s 188 

*********************** 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
  58 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.707 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 57
  average time/residue: 0.1672
  time to fit residues: 13.7499
Evaluate side-chains
  52 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.518 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0653
  time to fit residues: 1.0364
-------------------------------------------------------------------------------
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:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   chunk 69 optimal weight:    4.9990
   chunk 73 optimal weight:   20.0000
   chunk 48 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6046
moved from start:          0.6316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.112   6970  Z= 0.465
  Angle     :  1.006  19.632   9840  Z= 0.512
  Chirality :  0.053   0.243   1235
  Planarity :  0.007   0.069   1011
  Dihedral  : 21.386 115.398   1963
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 29.84
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 13.77 %
    Favored  : 85.96 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 35.73 %
    Favored  : 62.40 %
  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: -3.23 (0.27), residues: 755
  helix: -1.29 (0.30), residues: 224
  sheet: -2.45 (0.59), residues: 72
  loop : -2.66 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.003   TRP r 136 
   HIS   0.006   0.002   HIS s 235 
   PHE   0.021   0.003   PHE s 239 
   TYR   0.029   0.003   TYR s 274 
   ARG   0.006   0.001   ARG s 211 

*********************** 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
  54 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.688 
Fit side-chains
  outliers start: 7
  outliers final: 1
  residues processed: 51
  average time/residue: 0.1798
  time to fit residues: 13.0574
Evaluate side-chains
  48 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.676 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0651
  time to fit residues: 0.9724
-------------------------------------------------------------------------------
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:    7.9990
   chunk 81 optimal weight:    9.9990
   chunk 75 optimal weight:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 6 optimal weight:    0.4980
   chunk 50 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 69 optimal weight:   30.0000
   chunk 19 optimal weight:    0.9980
   overall best weight:    2.6986

-------------------------------------------------------------------------------
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 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
moved from start:          0.6278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6970  Z= 0.281
  Angle     :  0.801  16.453   9840  Z= 0.409
  Chirality :  0.048   0.233   1235
  Planarity :  0.005   0.058   1011
  Dihedral  : 21.021 108.207   1963
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 22.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.33 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 36.53 %
    Favored  : 62.67 %
  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: -2.88 (0.28), residues: 755
  helix: -0.86 (0.31), residues: 225
  sheet: -2.65 (0.51), residues: 88
  loop : -2.41 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP r 136 
   HIS   0.003   0.001   HIS s 235 
   PHE   0.015   0.002   PHE s 239 
   TYR   0.017   0.002   TYR s 274 
   ARG   0.005   0.001   ARG s 188 

********************** 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
  52 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.651 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 52
  average time/residue: 0.1643
  time to fit residues: 12.3827
Evaluate side-chains
  50 residues out of total 673 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.657 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0766
  time to fit residues: 1.1042
-------------------------------------------------------------------------------
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:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:   20.0000
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.114425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.107850 restraints weight = 40404.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.108020 restraints weight = 37481.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.108325 restraints weight = 31885.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4169 r_free = 0.4169    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.4169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5916
moved from start:          0.6315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6970  Z= 0.219
  Angle     :  0.725  15.456   9840  Z= 0.370
  Chirality :  0.045   0.235   1235
  Planarity :  0.005   0.057   1011
  Dihedral  : 20.723 105.759   1963
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 18.73
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.80 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 36.53 %
    Favored  : 62.67 %
  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: -2.55 (0.29), residues: 755
  helix: -0.48 (0.33), residues: 226
  sheet: -2.23 (0.48), residues: 103
  loop : -2.30 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP r 136 
   HIS   0.002   0.001   HIS r 114 
   PHE   0.013   0.002   PHE s 239 
   TYR   0.018   0.002   TYR s 274 
   ARG   0.004   0.000   ARG s 211 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1519.41 seconds
wall clock time: 32 minutes 2.08 seconds (1922.08 seconds total)