Starting phenix.real_space_refine
on Tue Feb 11 16:49:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eg0_28108/02_2025/8eg0_28108.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eg0_28108/02_2025/8eg0_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/cci-nas-00/data/ceres_data/8eg0_28108/02_2025/8eg0_28108.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eg0_28108/02_2025/8eg0_28108.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eg0_28108/02_2025/8eg0_28108.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eg0_28108/02_2025/8eg0_28108.cif"
  }
  resolution = 3.53
  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=   0.005 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. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.74, per 1000 atoms: 0.79
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 1.4 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...
    Secondary structure from input PDB file:
      15 helices and 8 sheets defined
      25.2% alpha, 30.5% beta
      25 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 2.26
  Creating SS restraints...
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.856A  pdb=" N   GLN B 233 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 229 through 233'
    Processing helix  chain 'B' and resid 330 through 343
    Processing helix  chain 'B' and resid 344 through 347
    Processing helix  chain 'B' and resid 352 through 361
      removed outlier: 4.262A  pdb=" N   SER B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TYR B 361 " --> pdb=" O   PHE B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 384
      removed outlier: 3.569A  pdb=" N   SER B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 44
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 109 through 126
    Processing helix  chain 'A' and resid 144 through 149
      removed outlier: 3.604A  pdb=" N   PHE A 148 " --> pdb=" O   HIS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 174
      removed outlier: 4.503A  pdb=" N   LYS A 172 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 187
      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 200 through 214
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 3.754A  pdb=" N   SER A 226 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 234
      removed outlier: 4.253A  pdb=" N   GLY A 232 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   HIS A 233 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 248
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=AA2, 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: 6.759A  pdb=" N   LEU B  85 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   VAL B  98 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU B  87 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 110
      removed outlier: 3.521A  pdb=" N   ALA B 107 " --> pdb=" O   ALA B 120 " (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=AA4, 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=AA5, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.711A  pdb=" N   ARG B 193 " --> pdb=" O   SER B 207 " (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=AA6, first strand: chain 'B' and resid 246 through 252
      removed outlier: 3.530A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 261 " (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=AA7, first strand: chain 'B' and resid 292 through 298
      removed outlier: 3.855A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 138
      removed outlier: 5.042A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   LEU A 104 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   LEU A 106 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   GLU A  79 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   MET A 157 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ALA A  81 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   ILE A  83 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   LEU A 154 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   GLY A 191 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   LYS A 156 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LEU A 193 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   PHE A 158 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   TYR A 195 " --> pdb=" O   PHE A 158 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   LEU A 160 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ILE A 197 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   ARG A 258 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   LEU A 193 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   PHE A 256 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   TYR A 195 " --> pdb=" O   ALA A 254 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ALA A 254 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ILE A 197 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE A 252 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    452 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: 2.13

  Time building geometry restraints manager: 1.74 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:
        0.00 -     2.40: 8813
        2.40 -     4.79: 47
        4.79 -     7.19: 3
        7.19 -     9.59: 3
        9.59 -    11.98: 1
  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: 3637
       35.74 -    71.49: 181
       71.49 -   107.23: 23
      107.23 -   142.97: 0
      142.97 -   178.72: 1
  Dihedral angle restraints: 3842
    sinusoidal: 2143
      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 3839 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: 1421
        2.80 -     3.32: 5474
        3.32 -     3.85: 10987
        3.85 -     4.37: 12762
        4.37 -     4.90: 19964
  Nonbonded interactions: 50608
  Sorted by model distance:
  nonbonded pdb=" N2    G C  15 "
            pdb=" O2    C C  48 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OG1 THR B 199 "
            pdb=" OE1 GLN B 200 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" N1    A C  14 "
            pdb=" O2'   A C  21 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   PRO B 201 "
            pdb=" OH  TYR B 218 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OD1 ASP B 121 "
            pdb=" OG  SER B 123 "
     model   vdw
     2.305 3.040
  ... (remaining 50603 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.150
  Find NCS groups from input model:        0.050
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.690
-------------------------------------------------------------------------------
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= 0.137
  Angle     :  0.486  11.983   8867  Z= 0.228
  Chirality :  0.035   0.134   1039
  Planarity :  0.003   0.034    886
  Dihedral  : 17.470 178.716   2744
  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 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 216 
 HIS   0.002   0.000   HIS A 210 
 PHE   0.012   0.001   PHE B  88 
 TYR   0.006   0.001   TYR A 195 
 ARG   0.001   0.000   ARG B 104 

*********************** 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 to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8893 (ttt) cc_final: 0.8501 (ttp)
REVERT: A  140 ASN cc_start: 0.9602 (t0) cc_final: 0.9248 (t0)
REVERT: A  142 MET cc_start: 0.9605 (ttm) cc_final: 0.9374 (ttm)
REVERT: A  147 ASN cc_start: 0.9579 (m110) cc_final: 0.9361 (m110)
REVERT: A  234 LEU cc_start: 0.9436 (mt) cc_final: 0.8850 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1670
  time to fit residues: 12.3057
Evaluate side-chains
  36 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    5.9990

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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.043929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.031328 restraints weight = 53644.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.032642 restraints weight = 21390.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.033561 restraints weight = 12643.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   6308  Z= 0.387
  Angle     :  0.645   6.678   8867  Z= 0.319
  Chirality :  0.041   0.177   1039
  Planarity :  0.003   0.022    886
  Dihedral  : 20.954 175.815   1671
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.30 %
    Favored  : 90.69 %
  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:  1.70 (0.36), residues: 573
  helix:  3.52 (0.53), residues: 107
  sheet:  0.98 (0.38), residues: 188
  loop :  0.34 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 216 
 HIS   0.005   0.001   HIS A 204 
 PHE   0.013   0.002   PHE B 288 
 TYR   0.008   0.001   TYR A  87 
 ARG   0.005   0.001   ARG A 138 

*********************** 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
  33 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.614 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8913 (ttt) cc_final: 0.8649 (ttp)
REVERT: B  170 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8084 (ttp80)
REVERT: A  140 ASN cc_start: 0.9515 (t0) cc_final: 0.9192 (t0)
REVERT: A  142 MET cc_start: 0.9509 (ttm) cc_final: 0.9304 (ttm)
REVERT: A  147 ASN cc_start: 0.9648 (m110) cc_final: 0.9349 (m110)
REVERT: A  234 LEU cc_start: 0.9529 (mt) cc_final: 0.9309 (tp)
  outliers start: 5
  outliers final: 1
  residues processed: 32
  average time/residue: 0.1506
  time to fit residues: 7.2650
Evaluate side-chains
  28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 59 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 21 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.1784

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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.045710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.032476 restraints weight = 72652.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.033972 restraints weight = 24036.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.035027 restraints weight = 13293.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2080

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= 0.123
  Angle     :  0.478   5.636   8867  Z= 0.235
  Chirality :  0.037   0.147   1039
  Planarity :  0.003   0.026    886
  Dihedral  : 20.561 179.873   1671
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.50 %
    Favored  : 90.89 %
  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:  3.43 (0.52), residues: 107
  sheet:  1.15 (0.39), residues: 177
  loop :  0.35 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 216 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.007   0.001   PHE B  22 
 TYR   0.013   0.001   TYR B 371 
 ARG   0.002   0.000   ARG A 138 

*********************** 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
  36 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.673 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.8848 (t80) cc_final: 0.8600 (t80)
REVERT: B  147 MET cc_start: 0.8840 (ttt) cc_final: 0.8523 (ttp)
REVERT: B  170 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8175 (ttp-170)
REVERT: A   77 GLN cc_start: 0.9087 (pm20) cc_final: 0.8810 (mp10)
REVERT: A  140 ASN cc_start: 0.9591 (t0) cc_final: 0.9201 (t0)
REVERT: A  142 MET cc_start: 0.9536 (ttm) cc_final: 0.9289 (ttm)
REVERT: A  147 ASN cc_start: 0.9630 (m110) cc_final: 0.9397 (m110)
REVERT: A  234 LEU cc_start: 0.9491 (mt) cc_final: 0.9271 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1506
  time to fit residues: 7.8695
Evaluate side-chains
  27 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 60 optimal weight:   20.0000
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   overall best weight:    4.7988

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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.043560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.030799 restraints weight = 46680.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.032086 restraints weight = 20051.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.032944 restraints weight = 12295.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6308  Z= 0.331
  Angle     :  0.595   5.865   8867  Z= 0.292
  Chirality :  0.039   0.138   1039
  Planarity :  0.003   0.023    886
  Dihedral  : 20.845 176.183   1671
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  7.69 %
    Favored  : 90.89 %
  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:  1.41 (0.36), residues: 573
  helix:  3.25 (0.53), residues: 108
  sheet:  0.73 (0.38), residues: 181
  loop :  0.24 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.004   0.001   HIS B 178 
 PHE   0.013   0.001   PHE B 288 
 TYR   0.010   0.001   TYR B 371 
 ARG   0.005   0.001   ARG A 138 

*********************** 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
  33 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.579 
Fit side-chains
REVERT: B  170 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8130 (ttp-170)
REVERT: A  117 GLN cc_start: 0.9716 (mt0) cc_final: 0.9324 (mt0)
REVERT: A  140 ASN cc_start: 0.9503 (t0) cc_final: 0.9208 (t0)
REVERT: A  142 MET cc_start: 0.9459 (ttm) cc_final: 0.9194 (ttm)
REVERT: A  147 ASN cc_start: 0.9642 (m110) cc_final: 0.9382 (m110)
  outliers start: 7
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1480
  time to fit residues: 7.2056
Evaluate side-chains
  25 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:   20.0000
   chunk 9 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3086 r_free = 0.3086 target = 0.044161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.031108 restraints weight = 77176.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.032569 restraints weight = 25198.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.033595 restraints weight = 13864.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6308  Z= 0.168
  Angle     :  0.506   7.163   8867  Z= 0.247
  Chirality :  0.038   0.155   1039
  Planarity :  0.003   0.024    886
  Dihedral  : 20.618 179.874   1671
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.91 %
    Favored  : 90.28 %
  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:  1.54 (0.36), residues: 573
  helix:  3.17 (0.52), residues: 108
  sheet:  0.93 (0.39), residues: 180
  loop :  0.32 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.009   0.001   PHE B  22 
 TYR   0.029   0.001   TYR B  38 
 ARG   0.003   0.000   ARG A 138 

*********************** 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
  31 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 ASP cc_start: 0.8550 (t0) cc_final: 0.8128 (t0)
REVERT: B  170 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8083 (ttp-170)
REVERT: A   77 GLN cc_start: 0.9154 (pm20) cc_final: 0.8850 (mm-40)
REVERT: A  117 GLN cc_start: 0.9702 (mt0) cc_final: 0.9283 (mt0)
REVERT: A  140 ASN cc_start: 0.9576 (t0) cc_final: 0.9209 (t0)
REVERT: A  142 MET cc_start: 0.9499 (ttm) cc_final: 0.9184 (ttm)
REVERT: A  147 ASN cc_start: 0.9641 (m110) cc_final: 0.9412 (m110)
  outliers start: 4
  outliers final: 2
  residues processed: 30
  average time/residue: 0.1413
  time to fit residues: 6.4410
Evaluate side-chains
  28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain A residue  197 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0870
   chunk 9 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   overall best weight:    1.8166

-------------------------------------------------------------------------------
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 = 0.3118 r_free = 0.3118 target = 0.045061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.031929 restraints weight = 62097.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.033354 restraints weight = 22454.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.034346 restraints weight = 12737.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6308  Z= 0.156
  Angle     :  0.491   7.731   8867  Z= 0.238
  Chirality :  0.037   0.145   1039
  Planarity :  0.003   0.022    886
  Dihedral  : 20.432 178.970   1671
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  9.72 %
    Favored  : 89.88 %
  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:  1.65 (0.36), residues: 573
  helix:  3.28 (0.52), residues: 107
  sheet:  1.11 (0.39), residues: 175
  loop :  0.32 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.011   0.001   PHE B  22 
 TYR   0.007   0.001   TYR B  38 
 ARG   0.003   0.000   ARG A 138 

*********************** 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
  30 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.572 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8548 (ttm) cc_final: 0.8108 (mtt)
REVERT: B  150 ASP cc_start: 0.8571 (t0) cc_final: 0.8171 (t0)
REVERT: B  170 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8075 (ttp-170)
REVERT: A   77 GLN cc_start: 0.9158 (pm20) cc_final: 0.8673 (mp10)
REVERT: A  117 GLN cc_start: 0.9695 (mt0) cc_final: 0.9225 (mt0)
REVERT: A  140 ASN cc_start: 0.9545 (t0) cc_final: 0.9151 (t0)
REVERT: A  142 MET cc_start: 0.9518 (ttm) cc_final: 0.9193 (ttm)
REVERT: A  147 ASN cc_start: 0.9636 (m110) cc_final: 0.9415 (m110)
  outliers start: 2
  outliers final: 1
  residues processed: 30
  average time/residue: 0.1557
  time to fit residues: 7.0533
Evaluate side-chains
  29 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 59 optimal weight:   20.0000
   overall best weight:    3.6988

-------------------------------------------------------------------------------
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 = 0.3078 r_free = 0.3078 target = 0.043888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.030739 restraints weight = 61286.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.032128 restraints weight = 23056.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.033081 restraints weight = 13421.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6308  Z= 0.253
  Angle     :  0.529   9.463   8867  Z= 0.257
  Chirality :  0.038   0.141   1039
  Planarity :  0.003   0.022    886
  Dihedral  : 20.583 178.027   1671
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.72 %
    Favored  : 89.68 %
  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:  1.57 (0.36), residues: 573
  helix:  3.26 (0.52), residues: 107
  sheet:  0.83 (0.39), residues: 181
  loop :  0.41 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 216 
 HIS   0.002   0.001   HIS A 204 
 PHE   0.011   0.001   PHE B  22 
 TYR   0.010   0.001   TYR B  38 
 ARG   0.004   0.000   ARG A 138 

*********************** 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
  30 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 ASP cc_start: 0.8575 (t0) cc_final: 0.8275 (t0)
REVERT: B  170 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8127 (ttp-170)
REVERT: A  117 GLN cc_start: 0.9711 (mt0) cc_final: 0.9325 (mt0)
REVERT: A  140 ASN cc_start: 0.9542 (t0) cc_final: 0.9209 (t0)
REVERT: A  142 MET cc_start: 0.9475 (ttm) cc_final: 0.9201 (ttm)
REVERT: A  147 ASN cc_start: 0.9622 (m110) cc_final: 0.9405 (m110)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 0.1588
  time to fit residues: 7.3505
Evaluate side-chains
  29 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0270
   overall best weight:    1.9844

-------------------------------------------------------------------------------
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 = 0.3104 r_free = 0.3104 target = 0.044640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.031454 restraints weight = 67102.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.032899 restraints weight = 23908.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.033909 restraints weight = 13468.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.3373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6308  Z= 0.160
  Angle     :  0.498   9.869   8867  Z= 0.240
  Chirality :  0.037   0.144   1039
  Planarity :  0.002   0.022    886
  Dihedral  : 20.500 179.004   1671
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 10.32 %
    Favored  : 89.07 %
  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:  1.61 (0.36), residues: 573
  helix:  3.23 (0.51), residues: 107
  sheet:  1.07 (0.39), residues: 175
  loop :  0.31 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.009   0.001   PHE B  22 
 TYR   0.005   0.001   TYR B  38 
 ARG   0.003   0.000   ARG A 138 

*********************** 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
  33 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.539 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8515 (ttm) cc_final: 0.8163 (mtt)
REVERT: B  150 ASP cc_start: 0.8586 (t0) cc_final: 0.8195 (t0)
REVERT: B  170 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8103 (ttp-170)
REVERT: A  117 GLN cc_start: 0.9702 (mt0) cc_final: 0.9260 (mt0)
REVERT: A  140 ASN cc_start: 0.9556 (t0) cc_final: 0.9204 (t0)
REVERT: A  142 MET cc_start: 0.9492 (ttm) cc_final: 0.9190 (ttm)
REVERT: A  147 ASN cc_start: 0.9616 (m110) cc_final: 0.9399 (m110)
  outliers start: 3
  outliers final: 1
  residues processed: 33
  average time/residue: 0.1492
  time to fit residues: 7.3882
Evaluate side-chains
  29 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.7184

-------------------------------------------------------------------------------
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 = 0.3152 r_free = 0.3152 target = 0.047188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.034490 restraints weight = 61242.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.035943 restraints weight = 23760.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.036943 restraints weight = 13876.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6308  Z= 0.150
  Angle     :  0.496   9.928   8867  Z= 0.239
  Chirality :  0.037   0.144   1039
  Planarity :  0.003   0.021    886
  Dihedral  : 20.445 178.027   1671
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 10.93 %
    Favored  : 88.87 %
  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:  1.66 (0.36), residues: 573
  helix:  3.22 (0.51), residues: 107
  sheet:  1.27 (0.39), residues: 181
  loop :  0.20 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.002   0.001   HIS A  26 
 PHE   0.009   0.001   PHE B  22 
 TYR   0.007   0.001   TYR B  38 
 ARG   0.003   0.000   ARG A 138 

*********************** 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
  29 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.630 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8526 (ttm) cc_final: 0.8223 (mtt)
REVERT: B  150 ASP cc_start: 0.8581 (t0) cc_final: 0.8220 (t0)
REVERT: B  170 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8164 (ttp-170)
REVERT: A  117 GLN cc_start: 0.9699 (mt0) cc_final: 0.9254 (mt0)
REVERT: A  140 ASN cc_start: 0.9565 (t0) cc_final: 0.9208 (t0)
REVERT: A  142 MET cc_start: 0.9459 (ttm) cc_final: 0.9162 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1559
  time to fit residues: 6.8899
Evaluate side-chains
  28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 61 optimal weight:   20.0000
   chunk 31 optimal weight:    8.9990
   overall best weight:    5.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.043074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.030598 restraints weight = 46879.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.031795 restraints weight = 20347.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.032609 restraints weight = 12567.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6308  Z= 0.343
  Angle     :  0.595   8.915   8867  Z= 0.290
  Chirality :  0.039   0.141   1039
  Planarity :  0.003   0.022    886
  Dihedral  : 20.781 175.109   1671
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 10.73 %
    Favored  : 88.87 %
  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:  1.43 (0.36), residues: 573
  helix:  3.23 (0.52), residues: 108
  sheet:  0.87 (0.38), residues: 186
  loop :  0.14 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.007   0.001   HIS A 144 
 PHE   0.012   0.001   PHE B 288 
 TYR   0.009   0.001   TYR A 195 
 ARG   0.004   0.001   ARG A 138 

********************** 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
  27 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 ASP cc_start: 0.8626 (t0) cc_final: 0.8199 (t0)
REVERT: B  170 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.7925 (ttp80)
REVERT: A  117 GLN cc_start: 0.9719 (mt0) cc_final: 0.9355 (mt0)
REVERT: A  140 ASN cc_start: 0.9501 (t0) cc_final: 0.9179 (t0)
REVERT: A  142 MET cc_start: 0.9443 (ttm) cc_final: 0.9089 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 27
  average time/residue: 0.1609
  time to fit residues: 6.6353
Evaluate side-chains
  27 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 46 optimal weight:    0.7980
   chunk 60 optimal weight:   20.0000
   chunk 63 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0870
   chunk 26 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3421 r_free = 0.3421 target = 0.060429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.048859 restraints weight = 97846.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.050252 restraints weight = 29445.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.051190 restraints weight = 14344.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2810
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2810
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6308  Z= 0.129
  Angle     :  0.507  10.367   8867  Z= 0.245
  Chirality :  0.037   0.142   1039
  Planarity :  0.003   0.022    886
  Dihedral  : 20.500 178.045   1671
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 11.13 %
    Favored  : 88.66 %
  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:  1.57 (0.36), residues: 573
  helix:  3.20 (0.51), residues: 107
  sheet:  1.06 (0.40), residues: 175
  loop :  0.26 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.008   0.001   PHE B  22 
 TYR   0.007   0.001   TYR B  38 
 ARG   0.002   0.000   ARG A 138 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1916.39 seconds
wall clock time: 35 minutes 14.17 seconds (2114.17 seconds total)