Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 06:13:10 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2023/8eg0_28108_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2023/8eg0_28108.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2023/8eg0_28108.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2023/8eg0_28108.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2023/8eg0_28108_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2023/8eg0_28108_updated.pdb"
  }
  resolution = 3.53
  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=   0.005 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      65      5.49       5
     S      23      5.16       5
     C    3592      2.51       5
     N    1056      2.21       5
     O    1295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  150": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 6031
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2733
          Classifications: {'peptide': 353}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 342}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "A"
      Number of atoms: 1882
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 230, 1865
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 213}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 16
      Conformer: "B"
        Number of residues, atoms: 230, 1865
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 213}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 16
          bond proxies already assigned to first conformer: 1900
    Chain: "C"
      Number of atoms: 1390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1390
          Classifications: {'RNA': 65}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 26, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 13, 'rna3p': 51}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Time building chain proxies: 4.89, per 1000 atoms: 0.81
  Number of scatterers: 6031
  At special positions: 0
  Unit cell: (69.72, 95.865, 112.05, 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      23     16.00
     P      65     15.00
     O    1295      8.00
     N    1056      7.00
     C    3592      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: 2.77
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1098

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      14 helices and 8 sheets defined
      20.2% alpha, 29.3% beta
      25 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 2.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 229 through 232
      No H-bonds generated for 'chain 'B' and resid 229 through 232'
    Processing helix  chain 'B' and resid 331 through 343
    Processing helix  chain 'B' and resid 353 through 360
      removed outlier: 3.606A  pdb=" N   SER B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'A' and resid 41 through 43
      No H-bonds generated for 'chain 'A' and resid 41 through 43'
    Processing helix  chain 'A' and resid 89 through 95
    Processing helix  chain 'A' and resid 110 through 125
    Processing helix  chain 'A' and resid 145 through 148
      No H-bonds generated for 'chain 'A' and resid 145 through 148'
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 4.503A  pdb=" N   LYS A 172 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 4.107A  pdb=" N   ALA A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLU A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 213
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.665A  pdb=" N   HIS A 233 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 233'
    Processing helix  chain 'A' and resid 239 through 247
    Processing sheet with id=  A, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=  B, first strand: chain 'B' and resid 64 through 69
      removed outlier: 6.966A  pdb=" N   THR B  79 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   ALA B  77 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   PHE B  69 " --> pdb=" O   TYR B  75 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR B  75 " --> pdb=" O   PHE B  69 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ARG B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ARG B  89 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   CYS B  95 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 105 through 110
      removed outlier: 7.154A  pdb=" N   ALA B 120 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   LEU B 108 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   LEU B 118 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   PHE B 110 " --> pdb=" O   LYS B 116 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   LYS B 116 " --> pdb=" O   PHE B 110 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B 142 " --> pdb=" O   VAL B 126 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   SER B 128 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 150 through 153
      removed outlier: 3.708A  pdb=" N   ASP B 150 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE B 169 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   TRP B 173 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ILE B 180 " --> pdb=" O   TRP B 173 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 191 through 196
      removed outlier: 6.986A  pdb=" N   SER B 207 " --> pdb=" O   SER B 192 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ILE B 194 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   SER B 208 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   THR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   GLU B 217 " --> pdb=" O   GLN B 223 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   GLN B 223 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 246 through 252
      removed outlier: 7.088A  pdb=" N   LEU B 261 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ILE B 249 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA B 259 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   PHE B 251 " --> pdb=" O   CYS B 257 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   CYS B 257 " --> pdb=" O   PHE B 251 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   CYS B 262 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   VAL B 267 " --> pdb=" O   CYS B 262 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   GLN B 272 " --> pdb=" O   TYR B 282 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   TYR B 282 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ASP B 274 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   LEU B 280 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 323 through 326
      removed outlier: 3.855A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'A' and resid 217 through 220
      removed outlier: 4.514A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   LEU A 160 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   LEU A 102 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ALA A  81 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   LEU A 104 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ILE A  83 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU A 106 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)

    155 hydrogen bonds defined for protein.
    431 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      65 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      25 basepair parallelities
      29 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1621
        1.34 -     1.45: 1492
        1.45 -     1.57: 3036
        1.57 -     1.69: 128
        1.69 -     1.81: 31
  Bond restraints: 6308
  Sorted by residual:
  bond pdb=" C2  SAH A 301 "
       pdb=" N3  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.322  1.379 -0.057 2.00e-02 2.50e+03 8.26e+00
  bond pdb=" C8  SAH A 301 "
       pdb=" N7  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.299  1.352 -0.053 2.00e-02 2.50e+03 6.98e+00
  bond pdb=" C2  SAH A 301 "
       pdb=" N1  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.330  1.379 -0.049 2.00e-02 2.50e+03 5.99e+00
  bond pdb=" C6  SAH A 301 "
       pdb=" N1  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.338  1.378 -0.040 2.00e-02 2.50e+03 4.06e+00
  bond pdb=" C1' SAH A 301 "
       pdb=" N9  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.440  1.474 -0.034 2.00e-02 2.50e+03 2.85e+00
  ... (remaining 6303 not shown)

  Histogram of bond angle deviations from ideal:
       89.79 -    98.62: 1
       98.62 -   107.45: 576
      107.45 -   116.28: 4142
      116.28 -   125.11: 3826
      125.11 -   133.95: 322
  Bond angle restraints: 8867
  Sorted by residual:
  angle pdb=" CG  SAH A 301 "
        pdb=" SD  SAH A 301 "
        pdb=" C5' SAH A 301 "
      ideal   model   delta    sigma   weight residual
     101.77   89.79   11.98 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" O   SAH A 301 "
        pdb=" C   SAH A 301 "
        pdb=" OXT SAH A 301 "
      ideal   model   delta    sigma   weight residual
     126.79  118.03    8.76 3.00e+00 1.11e-01 8.53e+00
  angle pdb=" C2  SAH A 301 "
        pdb=" N3  SAH A 301 "
        pdb=" C4  SAH A 301 "
      ideal   model   delta    sigma   weight residual
     111.67  120.08   -8.41 3.00e+00 1.11e-01 7.86e+00
  angle pdb=" N1  SAH A 301 "
        pdb=" C2  SAH A 301 "
        pdb=" N3  SAH A 301 "
      ideal   model   delta    sigma   weight residual
     128.45  120.38    8.07 3.00e+00 1.11e-01 7.23e+00
  angle pdb=" C5  SAH A 301 "
        pdb=" C4  SAH A 301 "
        pdb=" N3  SAH A 301 "
      ideal   model   delta    sigma   weight residual
     126.55  120.38    6.17 3.00e+00 1.11e-01 4.23e+00
  ... (remaining 8862 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 3521
       35.74 -    71.49: 58
       71.49 -   107.23: 6
      107.23 -   142.97: 0
      142.97 -   178.72: 1
  Dihedral angle restraints: 3586
    sinusoidal: 1887
      harmonic: 1699
  Sorted by residual:
  dihedral pdb=" O4'   U C  20 "
           pdb=" C1'   U C  20 "
           pdb=" N1    U C  20 "
           pdb=" C2    U C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.72 -178.72     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  TRP B 216 "
           pdb=" C   TRP B 216 "
           pdb=" N   GLU B 217 "
           pdb=" CA  GLU B 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.39   18.61     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" O4'   G C  44 "
           pdb=" C1'   G C  44 "
           pdb=" N9    G C  44 "
           pdb=" C4    G C  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -158.27   52.27     1      1.70e+01 3.46e-03 1.29e+01
  ... (remaining 3583 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 728
       0.027 -    0.054: 194
       0.054 -    0.080: 51
       0.080 -    0.107: 49
       0.107 -    0.134: 17
  Chirality restraints: 1039
  Sorted by residual:
  chirality pdb=" CA  VAL B  98 "
            pdb=" N   VAL B  98 "
            pdb=" C   VAL B  98 "
            pdb=" CB  VAL B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.50e-01
  chirality pdb=" CA  ILE B 160 "
            pdb=" N   ILE B 160 "
            pdb=" C   ILE B 160 "
            pdb=" CB  ILE B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.96e-01
  chirality pdb=" C3' SAH A 301 "
            pdb=" C2' SAH A 301 "
            pdb=" C4' SAH A 301 "
            pdb=" O3' SAH A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.58   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1036 not shown)

  Planarity restraints: 886
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  59 "    0.029 2.00e-02 2.50e+03   1.27e-02 4.80e+00
        pdb=" N9    G C  59 "   -0.030 2.00e-02 2.50e+03
        pdb=" C8    G C  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G C  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G C  59 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  59 "    0.005 2.00e-02 2.50e+03
        pdb=" O6    G C  59 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    G C  59 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G C  59 "   -0.005 2.00e-02 2.50e+03
        pdb=" N2    G C  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    G C  59 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 252 "   -0.022 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A 253 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 253 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 253 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  43 "    0.017 2.00e-02 2.50e+03   7.65e-03 1.61e+00
        pdb=" N9    A C  43 "   -0.015 2.00e-02 2.50e+03
        pdb=" C8    A C  43 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A C  43 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A C  43 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    A C  43 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A C  43 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    A C  43 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A C  43 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A C  43 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A C  43 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 883 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1427
        2.80 -     3.32: 5479
        3.32 -     3.85: 11006
        3.85 -     4.37: 12779
        4.37 -     4.90: 19969
  Nonbonded interactions: 50660
  Sorted by model distance:
  nonbonded pdb=" N2    G C  15 "
            pdb=" O2    C C  48 "
     model   vdw
     2.269 2.520
  nonbonded pdb=" OG1 THR B 199 "
            pdb=" OE1 GLN B 200 "
     model   vdw
     2.270 2.440
  nonbonded pdb=" N1    A C  14 "
            pdb=" O2'   A C  21 "
     model   vdw
     2.278 2.520
  nonbonded pdb=" O   PRO B 201 "
            pdb=" OH  TYR B 218 "
     model   vdw
     2.281 2.440
  nonbonded pdb=" OD1 ASP B 121 "
            pdb=" OG  SER B 123 "
     model   vdw
     2.305 2.440
  ... (remaining 50655 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=0.50 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:             0.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          1.190
  Check model and map are aligned:         0.090
  Set scattering table:                    0.050
  Process input model:                     23.030
  Find NCS groups from input model:        0.140
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
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      :  0.002   0.057   6308  Z= 0.138
  Angle     :  0.486  11.983   8867  Z= 0.228
  Chirality :  0.035   0.134   1039
  Planarity :  0.003   0.034    886
  Dihedral  : 11.732 178.716   2488
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.82 (0.36), residues: 573
  helix:  3.40 (0.52), residues: 106
  sheet:  1.24 (0.40), residues: 180
  loop :  0.41 (0.37), residues: 287

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1722
  time to fit residues: 12.5659
Evaluate side-chains
  33 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.650 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8098
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6308  Z= 0.300
  Angle     :  0.562   5.774   8867  Z= 0.278
  Chirality :  0.039   0.168   1039
  Planarity :  0.003   0.026    886
  Dihedral  : 13.294 176.953   1415
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer Outliers :  1.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.74 (0.36), residues: 573
  helix:  3.63 (0.53), residues: 101
  sheet:  1.02 (0.40), residues: 180
  loop :  0.43 (0.36), residues: 292

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 35
  average time/residue: 0.1535
  time to fit residues: 8.0052
Evaluate side-chains
  29 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.650 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0619
  time to fit residues: 1.0172
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0980
   chunk 39 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 58 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0980
   chunk 19 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.5582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6308  Z= 0.136
  Angle     :  0.476   6.345   8867  Z= 0.232
  Chirality :  0.037   0.145   1039
  Planarity :  0.003   0.031    886
  Dihedral  : 13.066 179.410   1415
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer Outliers :  0.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.73 (0.35), residues: 573
  helix:  3.53 (0.51), residues: 101
  sheet:  1.17 (0.39), residues: 178
  loop :  0.34 (0.35), residues: 294

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.721 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1602
  time to fit residues: 7.1940
Evaluate side-chains
  26 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.652 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8603
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   overall best weight:    6.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.037   6308  Z= 0.435
  Angle     :  0.669   8.005   8867  Z= 0.326
  Chirality :  0.041   0.143   1039
  Planarity :  0.004   0.029    886
  Dihedral  : 13.777 175.039   1415
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer Outliers :  1.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.39 (0.35), residues: 573
  helix:  3.15 (0.51), residues: 100
  sheet:  0.86 (0.39), residues: 179
  loop :  0.25 (0.35), residues: 294

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.618 
Fit side-chains
  outliers start: 6
  outliers final: 1
  residues processed: 31
  average time/residue: 0.1523
  time to fit residues: 7.2179
Evaluate side-chains
  22 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.615 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0605
  time to fit residues: 0.8875
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   overall best weight:    4.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6308  Z= 0.286
  Angle     :  0.560   7.434   8867  Z= 0.274
  Chirality :  0.039   0.141   1039
  Planarity :  0.003   0.029    886
  Dihedral  : 13.633 177.181   1415
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer Outliers :  1.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.45 (0.35), residues: 573
  helix:  3.25 (0.51), residues: 100
  sheet:  0.82 (0.39), residues: 179
  loop :  0.33 (0.36), residues: 294

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.615 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 30
  average time/residue: 0.1496
  time to fit residues: 6.9029
Evaluate side-chains
  24 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.768 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0649
  time to fit residues: 1.1193
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 51 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 59 optimal weight:   20.0000
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    3.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6308  Z= 0.280
  Angle     :  0.551   6.887   8867  Z= 0.271
  Chirality :  0.039   0.167   1039
  Planarity :  0.003   0.027    886
  Dihedral  : 13.653 178.217   1415
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer Outliers :  0.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.39 (0.35), residues: 573
  helix:  3.23 (0.51), residues: 100
  sheet:  0.74 (0.39), residues: 179
  loop :  0.31 (0.36), residues: 294

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.580 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 25
  average time/residue: 0.1680
  time to fit residues: 6.4040
Evaluate side-chains
  24 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.617 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0574
  time to fit residues: 0.8917
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 61 optimal weight:   20.0000
   chunk 38 optimal weight:    0.0470
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0030
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.5892

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6308  Z= 0.147
  Angle     :  0.483   7.596   8867  Z= 0.236
  Chirality :  0.037   0.144   1039
  Planarity :  0.003   0.027    886
  Dihedral  : 13.383 179.015   1415
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer Outliers :  0.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.58 (0.36), residues: 573
  helix:  3.33 (0.50), residues: 101
  sheet:  0.94 (0.39), residues: 179
  loop :  0.38 (0.37), residues: 293

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.608 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1569
  time to fit residues: 6.0595
Evaluate side-chains
  23 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.563 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7459
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 53 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    5.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6308  Z= 0.349
  Angle     :  0.584   5.800   8867  Z= 0.286
  Chirality :  0.039   0.141   1039
  Planarity :  0.003   0.024    886
  Dihedral  : 13.622 177.147   1415
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer Outliers :  0.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.37 (0.35), residues: 573
  helix:  3.18 (0.51), residues: 100
  sheet:  0.71 (0.38), residues: 179
  loop :  0.32 (0.37), residues: 294

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.615 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 24
  average time/residue: 0.1584
  time to fit residues: 5.9104
Evaluate side-chains
  22 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.612 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0577
  time to fit residues: 0.8766
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   overall best weight:    2.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6308  Z= 0.196
  Angle     :  0.516   9.826   8867  Z= 0.249
  Chirality :  0.038   0.149   1039
  Planarity :  0.003   0.026    886
  Dihedral  : 13.235 179.103   1415
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer Outliers :  0.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.47 (0.36), residues: 573
  helix:  3.21 (0.50), residues: 101
  sheet:  0.73 (0.38), residues: 181
  loop :  0.42 (0.38), residues: 291

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.609 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1324
  time to fit residues: 5.6562
Evaluate side-chains
  23 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.606 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7862
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 50 optimal weight:    0.0570
   chunk 5 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.9700

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6308  Z= 0.122
  Angle     :  0.497  12.435   8867  Z= 0.236
  Chirality :  0.037   0.145   1039
  Planarity :  0.003   0.029    886
  Dihedral  : 12.944 179.723   1415
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.59 (0.36), residues: 573
  helix:  3.24 (0.50), residues: 101
  sheet:  0.91 (0.39), residues: 181
  loop :  0.46 (0.38), residues: 291

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.644 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1317
  time to fit residues: 5.6593
Evaluate side-chains
  24 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.571 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7541
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0570
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    3.2106

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.044079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.031119 restraints weight = 66188.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.032529 restraints weight = 24233.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.033502 restraints weight = 13882.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6308  Z= 0.239
  Angle     :  0.525   6.237   8867  Z= 0.254
  Chirality :  0.037   0.145   1039
  Planarity :  0.003   0.027    886
  Dihedral  : 13.111 178.220   1415
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.60 (0.36), residues: 573
  helix:  3.36 (0.50), residues: 101
  sheet:  0.86 (0.39), residues: 181
  loop :  0.46 (0.38), residues: 291

===============================================================================
Job complete
usr+sys time: 1077.39 seconds
wall clock time: 20 minutes 33.04 seconds (1233.04 seconds total)