Starting phenix.real_space_refine
on Fri Dec 27 18:05:30 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eg0_28108/12_2024/8eg0_28108.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eg0_28108/12_2024/8eg0_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_28108/12_2024/8eg0_28108.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eg0_28108/12_2024/8eg0_28108.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eg0_28108/12_2024/8eg0_28108.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eg0_28108/12_2024/8eg0_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.95, per 1000 atoms: 0.82
  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: 1.89
  Conformation dependent library (CDL) restraints added in 899.8 milliseconds
  

  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: 2.12
  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: 2.29

  Time building geometry restraints manager: 1.75 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:             0.140
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.580
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.040
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.030
-------------------------------------------------------------------------------
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  : 0.573 
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: 0.1662
  time to fit residues: 12.1184
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  : 0.576 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
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  : 0.537 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8926 (ttt) cc_final: 0.8644 (ttp)
REVERT: B  170 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8048 (ttp80)
REVERT: A  140 ASN cc_start: 0.9497 (t0) cc_final: 0.9165 (t0)
REVERT: A  142 MET cc_start: 0.9517 (ttm) cc_final: 0.9310 (ttm)
REVERT: A  147 ASN cc_start: 0.9666 (m110) cc_final: 0.9351 (m110)
REVERT: A  234 LEU cc_start: 0.9522 (mt) cc_final: 0.9300 (tp)
  outliers start: 5
  outliers final: 1
  residues processed: 32
  average time/residue: 0.1502
  time to fit residues: 7.2957
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  : 0.585 
-------------------------------------------------------------------------------
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 32 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 58 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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: 0.8429
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6308  Z= 0.167
  Angle     :  0.489   5.392   8867  Z= 0.242
  Chirality :  0.037   0.144   1039
  Planarity :  0.003   0.024    886
  Dihedral  : 20.624 179.528   1671
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.30 %
    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:  1.69 (0.36), residues: 573
  helix:  3.45 (0.53), residues: 107
  sheet:  0.96 (0.39), residues: 182
  loop :  0.40 (0.37), residues: 284

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   0.008   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
  32 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.585 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.8853 (t80) cc_final: 0.8608 (t80)
REVERT: B  147 MET cc_start: 0.8846 (ttt) cc_final: 0.8545 (ttp)
REVERT: B  170 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8170 (ttp-170)
REVERT: A   77 GLN cc_start: 0.9092 (pm20) cc_final: 0.8765 (mp-120)
REVERT: A  140 ASN cc_start: 0.9571 (t0) cc_final: 0.9208 (t0)
REVERT: A  142 MET cc_start: 0.9542 (ttm) cc_final: 0.9263 (ttm)
REVERT: A  147 ASN cc_start: 0.9656 (m110) cc_final: 0.9399 (m110)
  outliers start: 4
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1521
  time to fit residues: 6.8631
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  : 0.595 
-------------------------------------------------------------------------------
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 57 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 55 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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: 0.8470
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6308  Z= 0.252
  Angle     :  0.535   5.564   8867  Z= 0.263
  Chirality :  0.038   0.141   1039
  Planarity :  0.003   0.023    886
  Dihedral  : 20.716 177.385   1671
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  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:  1.55 (0.36), residues: 573
  helix:  3.43 (0.53), residues: 108
  sheet:  0.84 (0.38), residues: 181
  loop :  0.28 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.003   0.001   HIS A 204 
 PHE   0.010   0.001   PHE B  22 
 TYR   0.011   0.001   TYR B 371 
 ARG   0.004   0.000   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
  29 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.582 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8855 (ttt) cc_final: 0.8563 (ttp)
REVERT: B  170 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8010 (ttp-170)
REVERT: A  140 ASN cc_start: 0.9518 (t0) cc_final: 0.9176 (t0)
REVERT: A  142 MET cc_start: 0.9489 (ttm) cc_final: 0.9219 (ttm)
REVERT: A  147 ASN cc_start: 0.9665 (m110) cc_final: 0.9395 (m110)
  outliers start: 4
  outliers final: 1
  residues processed: 29
  average time/residue: 0.1535
  time to fit residues: 6.7520
Evaluate side-chains
  24 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain A residue   34 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6308  Z= 0.127
  Angle     :  0.484   7.412   8867  Z= 0.235
  Chirality :  0.037   0.156   1039
  Planarity :  0.003   0.024    886
  Dihedral  : 20.500 179.857   1671
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.70 %
    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:  1.61 (0.36), residues: 573
  helix:  3.33 (0.52), residues: 108
  sheet:  0.99 (0.39), residues: 180
  loop :  0.29 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.010   0.001   PHE B  22 
 TYR   0.007   0.001   TYR B  38 
 ARG   0.002   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
  34 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.539 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8832 (ttt) cc_final: 0.8524 (ttp)
REVERT: B  170 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8081 (ttp-170)
REVERT: A   77 GLN cc_start: 0.9102 (pm20) cc_final: 0.8834 (mm-40)
REVERT: A  117 GLN cc_start: 0.9694 (mt0) cc_final: 0.9215 (mt0)
REVERT: A  140 ASN cc_start: 0.9598 (t0) cc_final: 0.9234 (t0)
REVERT: A  142 MET cc_start: 0.9521 (ttm) cc_final: 0.9167 (ttm)
REVERT: A  147 ASN cc_start: 0.9641 (m110) cc_final: 0.9409 (m110)
  outliers start: 5
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1427
  time to fit residues: 7.3455
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  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0030
   chunk 61 optimal weight:   20.0000
   chunk 51 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 59 optimal weight:   20.0000
   chunk 6 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0870
   overall best weight:    3.2172

-------------------------------------------------------------------------------
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: 0.8469
moved from start:          0.3070

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= 0.229
  Angle     :  0.524   9.533   8867  Z= 0.255
  Chirality :  0.038   0.143   1039
  Planarity :  0.003   0.021    886
  Dihedral  : 20.576 178.085   1671
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.51 %
    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:  1.62 (0.36), residues: 573
  helix:  3.37 (0.53), residues: 108
  sheet:  0.94 (0.39), residues: 181
  loop :  0.33 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.003   0.001   HIS A 204 
 PHE   0.011   0.001   PHE B  22 
 TYR   0.009   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
  31 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.600 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8891 (ttt) cc_final: 0.8595 (ttp)
REVERT: B  150 ASP cc_start: 0.8590 (t0) cc_final: 0.8139 (t0)
REVERT: B  170 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8061 (ttp-170)
REVERT: A   77 GLN cc_start: 0.9169 (pm20) cc_final: 0.8695 (mp10)
REVERT: A  117 GLN cc_start: 0.9702 (mt0) cc_final: 0.9294 (mt0)
REVERT: A  140 ASN cc_start: 0.9534 (t0) cc_final: 0.9148 (t0)
REVERT: A  142 MET cc_start: 0.9515 (ttm) cc_final: 0.9199 (ttm)
REVERT: A  147 ASN cc_start: 0.9658 (m110) cc_final: 0.9398 (m110)
  outliers start: 3
  outliers final: 1
  residues processed: 31
  average time/residue: 0.1467
  time to fit residues: 6.8724
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  : 0.600 
-------------------------------------------------------------------------------
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 45 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 52 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 61 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   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: 0.8489
moved from start:          0.3473

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= 0.271
  Angle     :  0.549   8.423   8867  Z= 0.268
  Chirality :  0.039   0.141   1039
  Planarity :  0.003   0.023    886
  Dihedral  : 20.704 178.650   1671
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  9.92 %
    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:  1.47 (0.36), residues: 573
  helix:  3.33 (0.52), residues: 108
  sheet:  0.82 (0.38), residues: 180
  loop :  0.22 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.003   0.001   HIS A 204 
 PHE   0.009   0.001   PHE B 288 
 TYR   0.008   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
  28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.7794 (ttp80)
REVERT: A  117 GLN cc_start: 0.9716 (mt0) cc_final: 0.9324 (mt0)
REVERT: A  140 ASN cc_start: 0.9495 (t0) cc_final: 0.9183 (t0)
REVERT: A  142 MET cc_start: 0.9514 (ttm) cc_final: 0.9226 (ttm)
REVERT: A  147 ASN cc_start: 0.9675 (m110) cc_final: 0.9401 (m110)
  outliers start: 2
  outliers final: 1
  residues processed: 28
  average time/residue: 0.1644
  time to fit residues: 6.9698
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  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 59 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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: 0.8495
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6308  Z= 0.271
  Angle     :  0.552   8.390   8867  Z= 0.270
  Chirality :  0.039   0.138   1039
  Planarity :  0.003   0.020    886
  Dihedral  : 20.788 177.447   1671
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 10.32 %
    Favored  : 89.27 %
  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:  3.40 (0.52), residues: 107
  sheet:  0.82 (0.38), residues: 186
  loop :  0.13 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 216 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B  22 
 TYR   0.008   0.001   TYR A 195 
 ARG   0.004   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
  28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.592 
Fit side-chains
REVERT: B  150 ASP cc_start: 0.8595 (t0) cc_final: 0.8140 (t0)
REVERT: B  170 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.7818 (ttp80)
REVERT: A  117 GLN cc_start: 0.9709 (mt0) cc_final: 0.9314 (mt0)
REVERT: A  140 ASN cc_start: 0.9513 (t0) cc_final: 0.9202 (t0)
REVERT: A  147 ASN cc_start: 0.9674 (m110) cc_final: 0.9412 (m110)
  outliers start: 2
  outliers final: 1
  residues processed: 28
  average time/residue: 0.1604
  time to fit residues: 6.8358
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  : 0.477 
-------------------------------------------------------------------------------
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 59 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0040
   chunk 57 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   overall best weight:    2.7396

-------------------------------------------------------------------------------
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: 0.8482
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6308  Z= 0.203
  Angle     :  0.519   8.738   8867  Z= 0.252
  Chirality :  0.038   0.142   1039
  Planarity :  0.003   0.022    886
  Dihedral  : 20.716 178.322   1671
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 10.12 %
    Favored  : 89.47 %
  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:  1.48 (0.36), residues: 573
  helix:  3.38 (0.51), residues: 107
  sheet:  0.93 (0.39), residues: 174
  loop :  0.16 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.009   0.001   PHE B  22 
 TYR   0.005   0.001   TYR A 195 
 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: 2
    poor density    : 27
  time to evaluate  : 0.597 
Fit side-chains
REVERT: B  150 ASP cc_start: 0.8613 (t0) cc_final: 0.8045 (t0)
REVERT: B  170 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.7840 (ttp80)
REVERT: A  117 GLN cc_start: 0.9680 (mt0) cc_final: 0.9269 (mt0)
REVERT: A  140 ASN cc_start: 0.9521 (t0) cc_final: 0.9237 (t0)
REVERT: A  147 ASN cc_start: 0.9662 (m110) cc_final: 0.9399 (m110)
  outliers start: 2
  outliers final: 1
  residues processed: 29
  average time/residue: 0.1544
  time to fit residues: 6.8105
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  : 0.597 
-------------------------------------------------------------------------------
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 42 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 50 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 31 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    2.8588

-------------------------------------------------------------------------------
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: 0.8485
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6308  Z= 0.212
  Angle     :  0.538   8.832   8867  Z= 0.262
  Chirality :  0.038   0.203   1039
  Planarity :  0.003   0.023    886
  Dihedral  : 20.703 177.495   1671
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  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:  1.57 (0.36), residues: 573
  helix:  3.41 (0.51), residues: 107
  sheet:  0.99 (0.38), residues: 185
  loop :  0.20 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.002   0.001   HIS A 144 
 PHE   0.010   0.001   PHE B  22 
 TYR   0.005   0.001   TYR A 195 
 ARG   0.003   0.000   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
  30 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.608 
Fit side-chains
REVERT: B  150 ASP cc_start: 0.8590 (t0) cc_final: 0.8034 (t0)
REVERT: B  170 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.7846 (ttp80)
REVERT: A  117 GLN cc_start: 0.9680 (mt0) cc_final: 0.9413 (mt0)
REVERT: A  140 ASN cc_start: 0.9490 (t0) cc_final: 0.9219 (t0)
REVERT: A  147 ASN cc_start: 0.9651 (m110) cc_final: 0.9380 (m110)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 0.1567
  time to fit residues: 7.1559
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  : 0.575 
-------------------------------------------------------------------------------
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  260 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 44 optimal weight:    0.5980
   chunk 2 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    4.3188

-------------------------------------------------------------------------------
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 = 0.3058 r_free = 0.3058 target = 0.043139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.030507 restraints weight = 57900.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.031839 restraints weight = 22734.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.032739 restraints weight = 13386.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6308  Z= 0.295
  Angle     :  0.581   8.394   8867  Z= 0.283
  Chirality :  0.039   0.177   1039
  Planarity :  0.003   0.025    886
  Dihedral  : 20.813 175.962   1671
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 10.53 %
    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:  1.51 (0.37), residues: 573
  helix:  3.44 (0.51), residues: 107
  sheet:  0.90 (0.38), residues: 186
  loop :  0.16 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.004   0.001   HIS A 144 
 PHE   0.010   0.001   PHE B  22 
 TYR   0.007   0.001   TYR A 195 
 ARG   0.004   0.000   ARG A 138 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1145.37 seconds
wall clock time: 23 minutes 33.64 seconds (1413.64 seconds total)