Starting phenix.real_space_refine
on Tue Feb 11 15:01:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d9l_27265/02_2025/8d9l_27265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9l_27265/02_2025/8d9l_27265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d9l_27265/02_2025/8d9l_27265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9l_27265/02_2025/8d9l_27265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9l_27265/02_2025/8d9l_27265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9l_27265/02_2025/8d9l_27265.cif"
  }
  resolution = 4.04
  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=   0.003 sd=   0.023
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    3418      2.51       5
     N    1000      2.21       5
     O    1251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5757
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2557
          Classifications: {'peptide': 332}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 321}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1783
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 204}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 1390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1390
          Classifications: {'RNA': 65}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 28, 'rna3p_pyr': 27}
          Link IDs: {'rna2p': 10, 'rna3p': 54}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Residues with excluded nonbonded symmetry interactions: 40
    residue:
      pdb=" N   GLN B  12 " occ=0.85
      ... (7 atoms not shown)
      pdb=" NE2 GLN B  12 " occ=0.85
    residue:
      pdb=" N   ARG B  21 " occ=0.88
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  21 " occ=0.88
    residue:
      pdb=" N   CYS B  40 " occ=0.68
      ... (4 atoms not shown)
      pdb=" SG  CYS B  40 " occ=0.68
    residue:
      pdb=" N   SER B  61 " occ=0.82
      ... (4 atoms not shown)
      pdb=" OG  SER B  61 " occ=0.82
    residue:
      pdb=" N   ASP B  80 " occ=0.85
      ... (6 atoms not shown)
      pdb=" OD2 ASP B  80 " occ=0.85
    residue:
      pdb=" N   ASP B  81 " occ=0.80
      ... (6 atoms not shown)
      pdb=" OD2 ASP B  81 " occ=0.80
    residue:
      pdb=" N   ARG B  84 " occ=0.91
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  84 " occ=0.91
    residue:
      pdb=" N   ARG B  89 " occ=0.99
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  89 " occ=0.99
    residue:
      pdb=" N   CYS B 105 " occ=0.82
      ... (4 atoms not shown)
      pdb=" SG  CYS B 105 " occ=0.82
    residue:
      pdb=" N   LYS B 122 " occ=0.88
      ... (7 atoms not shown)
      pdb=" NZ  LYS B 122 " occ=0.88
    residue:
      pdb=" N   GLU B 133 " occ=0.89
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 133 " occ=0.89
    residue:
      pdb=" N   CYS B 137 " occ=0.86
      ... (4 atoms not shown)
      pdb=" SG  CYS B 137 " occ=0.86
    ... (remaining 28 not shown)
  Time building chain proxies: 3.91, per 1000 atoms: 0.68
  Number of scatterers: 5757
  At special positions: 0
  Unit cell: (65.52, 98.28, 112.14, 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    1251      8.00
     N    1000      7.00
     C    3418      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: 1.41
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1032

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 8 sheets defined
      19.0% alpha, 32.2% beta
      27 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 2.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.516A  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 353 through 359
      removed outlier: 3.817A  pdb=" N   SER B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 362
      No H-bonds generated for 'chain 'B' and resid 360 through 362'
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 109 through 126
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.830A  pdb=" N   GLU A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 214
      removed outlier: 3.513A  pdb=" N   ASP A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 3.907A  pdb=" N   SER A 226 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 235
      removed outlier: 4.256A  pdb=" N   GLY A 232 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLY A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
    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: 7.107A  pdb=" N   THR B  79 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   ALA B  77 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   PHE B  69 " --> pdb=" O   TYR B  75 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   TYR B  75 " --> pdb=" O   PHE B  69 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ARG B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   ARG B  89 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   CYS B  95 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 110
      removed outlier: 3.549A  pdb=" N   ALA B 107 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 126 " --> pdb=" O   GLU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 153
      removed outlier: 3.797A  pdb=" N   ASP B 150 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   ILE B 169 " --> pdb=" O   PHE B 183 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   PHE B 183 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL B 171 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.654A  pdb=" N   ARG B 193 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER B 208 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU B 213 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   CYS B 226 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU B 215 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG B 222 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 252
      removed outlier: 3.995A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU B 261 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   CYS B 262 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   VAL B 267 " --> pdb=" O   CYS B 262 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   GLN B 272 " --> pdb=" O   TYR B 282 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   TYR B 282 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ASP B 274 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 5.734A  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: 3.757A  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: 6.446A  pdb=" N   ILE A 103 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU A 137 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLY A 105 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   LEU A 104 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   LEU A 106 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLU A  79 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   MET A 157 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA A  81 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ILE A  83 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   THR A 155 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   TYR A 195 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   MET A 157 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   ILE A 197 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE A 159 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLY A 192 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)

    143 hydrogen bonds defined for protein.
    396 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      69 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.65 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: 1583
        1.34 -     1.45: 1447
        1.45 -     1.57: 2836
        1.57 -     1.69: 128
        1.69 -     1.81: 32
  Bond restraints: 6026
  Sorted by residual:
  bond pdb=" C2  SAM A 301 "
       pdb=" N3  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.322  1.381 -0.059 2.00e-02 2.50e+03 8.71e+00
  bond pdb=" C8  SAM A 301 "
       pdb=" N7  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.298  1.351 -0.053 2.00e-02 2.50e+03 7.13e+00
  bond pdb=" C2  SAM A 301 "
       pdb=" N1  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.329  1.380 -0.051 2.00e-02 2.50e+03 6.58e+00
  bond pdb=" C6  SAM A 301 "
       pdb=" N1  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.380 -0.043 2.00e-02 2.50e+03 4.57e+00
  bond pdb=" C   SAM A 301 "
       pdb=" OXT SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.256  1.230  0.026 2.00e-02 2.50e+03 1.64e+00
  ... (remaining 6021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 8400
        1.75 -     3.49: 71
        3.49 -     5.24: 10
        5.24 -     6.98: 3
        6.98 -     8.73: 3
  Bond angle restraints: 8487
  Sorted by residual:
  angle pdb=" O   SAM A 301 "
        pdb=" C   SAM A 301 "
        pdb=" OXT SAM A 301 "
      ideal   model   delta    sigma   weight residual
     126.77  118.04    8.73 3.00e+00 1.11e-01 8.47e+00
  angle pdb=" N1  SAM A 301 "
        pdb=" C2  SAM A 301 "
        pdb=" N3  SAM A 301 "
      ideal   model   delta    sigma   weight residual
     128.51  120.14    8.37 3.00e+00 1.11e-01 7.79e+00
  angle pdb=" C2  SAM A 301 "
        pdb=" N3  SAM A 301 "
        pdb=" C4  SAM A 301 "
      ideal   model   delta    sigma   weight residual
     112.25  120.28   -8.03 3.00e+00 1.11e-01 7.16e+00
  angle pdb=" C   SER B 113 "
        pdb=" N   GLU B 114 "
        pdb=" CA  GLU B 114 "
      ideal   model   delta    sigma   weight residual
     121.54  125.77   -4.23 1.91e+00 2.74e-01 4.90e+00
  angle pdb=" C2' SAM A 301 "
        pdb=" C3' SAM A 301 "
        pdb=" O3' SAM A 301 "
      ideal   model   delta    sigma   weight residual
     116.14  110.26    5.88 3.00e+00 1.11e-01 3.85e+00
  ... (remaining 8482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.87: 3304
       15.87 -    31.74: 180
       31.74 -    47.61: 86
       47.61 -    63.47: 75
       63.47 -    79.34: 44
  Dihedral angle restraints: 3689
    sinusoidal: 2094
      harmonic: 1595
  Sorted by residual:
  dihedral pdb=" CA  GLU B 114 "
           pdb=" CB  GLU B 114 "
           pdb=" CG  GLU B 114 "
           pdb=" CD  GLU B 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  110.71  -50.71     3      1.50e+01 4.44e-03 8.93e+00
  dihedral pdb=" O5'   U C  47 "
           pdb=" C5'   U C  47 "
           pdb=" C4'   U C  47 "
           pdb=" C3'   U C  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.00    9.35   45.65     3      1.50e+01 4.44e-03 8.21e+00
  dihedral pdb=" O5'   U C  20 "
           pdb=" C5'   U C  20 "
           pdb=" C4'   U C  20 "
           pdb=" C3'   U C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.00  130.27   44.73     3      1.50e+01 4.44e-03 8.05e+00
  ... (remaining 3686 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 794
       0.036 -    0.071: 132
       0.071 -    0.107: 61
       0.107 -    0.142: 14
       0.142 -    0.178: 1
  Chirality restraints: 1002
  Sorted by residual:
  chirality pdb=" C2' SAM A 301 "
            pdb=" C1' SAM A 301 "
            pdb=" C3' SAM A 301 "
            pdb=" O2' SAM A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.58   -0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" C1' SAM A 301 "
            pdb=" C2' SAM A 301 "
            pdb=" N9  SAM A 301 "
            pdb=" O4' SAM A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.30    2.43   -0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  ILE B  37 "
            pdb=" N   ILE B  37 "
            pdb=" C   ILE B  37 "
            pdb=" CB  ILE B  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  ... (remaining 999 not shown)

  Planarity restraints: 837
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  59 "   -0.019 2.00e-02 2.50e+03   8.07e-03 1.96e+00
        pdb=" N9    G C  59 "    0.019 2.00e-02 2.50e+03
        pdb=" C8    G C  59 "    0.002 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 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G C  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G C  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G C  59 "   -0.000 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 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 318 "   -0.013 5.00e-02 4.00e+02   1.96e-02 6.14e-01
        pdb=" N   PRO B 319 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO B 319 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 319 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 154 "    0.012 5.00e-02 4.00e+02   1.88e-02 5.67e-01
        pdb=" N   PRO B 155 "   -0.033 5.00e-02 4.00e+02
        pdb=" CA  PRO B 155 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 155 "    0.011 5.00e-02 4.00e+02
  ... (remaining 834 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1163
        2.78 -     3.31: 5195
        3.31 -     3.84: 10263
        3.84 -     4.37: 11749
        4.37 -     4.90: 18418
  Nonbonded interactions: 46788
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 154 "
            pdb=" OD1 ASP B 156 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR B 188 "
            pdb=" OE1 GLU B 189 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER B 130 "
            pdb=" OE1 GLU B 133 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O6    G C  10 "
            pdb=" N2    G C  45 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" OD2 ASP B 121 "
            pdb=" OG  SER B 123 "
     model   vdw
     2.307 3.040
  ... (remaining 46783 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=0.00 max=1.00 mean=0.99
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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     18.420
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
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   0.059   6026  Z= 0.131
  Angle     :  0.444   8.728   8487  Z= 0.201
  Chirality :  0.035   0.178   1002
  Planarity :  0.002   0.020    837
  Dihedral  : 16.630  79.343   2657
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.21 %
    Favored  : 93.36 %
  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:  1.09 (0.38), residues: 541
  helix:  1.26 (0.58), residues: 101
  sheet:  1.53 (0.39), residues: 183
  loop : -0.04 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 206 
 HIS   0.002   0.000   HIS A 210 
 PHE   0.010   0.001   PHE B  88 
 TYR   0.005   0.001   TYR A  37 
 ARG   0.001   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9286 (pttt) cc_final: 0.8970 (mtmm)
REVERT: B  157 ASP cc_start: 0.9118 (t0) cc_final: 0.8818 (t0)
REVERT: B  166 ASP cc_start: 0.8776 (m-30) cc_final: 0.8425 (m-30)
REVERT: B  195 SER cc_start: 0.9389 (t) cc_final: 0.8737 (m)
REVERT: B  206 SER cc_start: 0.8836 (m) cc_final: 0.8561 (p)
REVERT: A   44 MET cc_start: 0.5282 (tmm) cc_final: 0.3600 (tmm)
REVERT: A  115 TYR cc_start: 0.9514 (t80) cc_final: 0.8865 (t80)
REVERT: A  140 ASN cc_start: 0.9171 (t0) cc_final: 0.8937 (t0)
REVERT: A  157 MET cc_start: 0.9333 (ttm) cc_final: 0.8863 (ttm)
REVERT: A  176 ILE cc_start: 0.9329 (mm) cc_final: 0.9039 (tp)
REVERT: A  180 LEU cc_start: 0.9654 (mt) cc_final: 0.9402 (mm)
REVERT: A  183 GLU cc_start: 0.9262 (pt0) cc_final: 0.8846 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 65
  average time/residue: 0.2237
  time to fit residues: 18.2844
Evaluate side-chains
  43 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0010
   chunk 31 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   overall best weight:    3.9994

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.039706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.030285 restraints weight = 46185.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.031422 restraints weight = 23571.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.032243 restraints weight = 15176.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6026  Z= 0.236
  Angle     :  0.525   6.785   8487  Z= 0.268
  Chirality :  0.037   0.155   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 19.242  79.268   1658
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  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:  1.04 (0.37), residues: 541
  helix:  1.46 (0.59), residues: 97
  sheet:  1.30 (0.38), residues: 186
  loop : -0.02 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.011   0.002   PHE B 297 
 TYR   0.014   0.002   TYR B 127 
 ARG   0.004   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9373 (pttt) cc_final: 0.9113 (mtmm)
REVERT: B  157 ASP cc_start: 0.9105 (t0) cc_final: 0.8850 (t0)
REVERT: B  166 ASP cc_start: 0.8809 (m-30) cc_final: 0.8574 (m-30)
REVERT: A   27 SER cc_start: 0.9554 (m) cc_final: 0.9174 (t)
REVERT: A   44 MET cc_start: 0.6113 (tmm) cc_final: 0.4823 (tmm)
REVERT: A  115 TYR cc_start: 0.9578 (t80) cc_final: 0.9211 (t80)
REVERT: A  157 MET cc_start: 0.9326 (ttm) cc_final: 0.8788 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.2186
  time to fit residues: 12.8358
Evaluate side-chains
  35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    0.0670
   chunk 33 optimal weight:   20.0000
   chunk 41 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 52 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   overall best weight:    3.2922

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.038062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.028693 restraints weight = 46422.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.029826 restraints weight = 23702.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.030607 restraints weight = 15248.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6026  Z= 0.203
  Angle     :  0.480   4.949   8487  Z= 0.247
  Chirality :  0.037   0.157   1002
  Planarity :  0.003   0.019    837
  Dihedral  : 19.261  80.244   1658
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  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:  0.91 (0.37), residues: 541
  helix:  1.82 (0.61), residues: 91
  sheet:  1.13 (0.38), residues: 187
  loop : -0.18 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.020   0.002   PHE B  69 
 TYR   0.007   0.001   TYR A 186 
 ARG   0.002   0.000   ARG B 158 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9414 (pttt) cc_final: 0.9146 (mtmm)
REVERT: B  157 ASP cc_start: 0.9094 (t0) cc_final: 0.8829 (t0)
REVERT: B  166 ASP cc_start: 0.9022 (m-30) cc_final: 0.8807 (m-30)
REVERT: B  168 LYS cc_start: 0.9161 (mttt) cc_final: 0.8951 (mmtt)
REVERT: A   27 SER cc_start: 0.9613 (m) cc_final: 0.9290 (t)
REVERT: A   44 MET cc_start: 0.6260 (tmm) cc_final: 0.4922 (tmm)
REVERT: A  115 TYR cc_start: 0.9597 (t80) cc_final: 0.9160 (t80)
REVERT: A  157 MET cc_start: 0.9241 (ttm) cc_final: 0.8954 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1872
  time to fit residues: 10.9045
Evaluate side-chains
  34 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 35 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 272 GLN
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.035087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.026124 restraints weight = 51040.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.027151 restraints weight = 26082.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.027886 restraints weight = 17047.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2564 r_free = 0.2564    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6026  Z= 0.357
  Angle     :  0.635   6.430   8487  Z= 0.327
  Chirality :  0.041   0.160   1002
  Planarity :  0.003   0.021    837
  Dihedral  : 19.611  80.761   1658
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 16.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  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:  0.35 (0.35), residues: 541
  helix:  0.99 (0.55), residues: 91
  sheet:  0.76 (0.39), residues: 168
  loop : -0.30 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  93 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.017   0.002   PHE B  88 
 TYR   0.013   0.002   TYR B 127 
 ARG   0.005   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8917 (mtm) cc_final: 0.8443 (mtm)
REVERT: B  148 LEU cc_start: 0.9608 (mt) cc_final: 0.9312 (mt)
REVERT: B  168 LYS cc_start: 0.9183 (mttt) cc_final: 0.8781 (mmmm)
REVERT: B  361 TYR cc_start: 0.8611 (m-80) cc_final: 0.8394 (m-80)
REVERT: A   27 SER cc_start: 0.9705 (m) cc_final: 0.9413 (t)
REVERT: A   44 MET cc_start: 0.6972 (tmm) cc_final: 0.5970 (tmm)
REVERT: A  115 TYR cc_start: 0.9597 (t80) cc_final: 0.9080 (t80)
REVERT: A  157 MET cc_start: 0.9302 (ttm) cc_final: 0.8926 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.2064
  time to fit residues: 10.5350
Evaluate side-chains
  28 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 20 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.037466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.028139 restraints weight = 46783.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.029252 restraints weight = 23772.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.030003 restraints weight = 15341.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2638
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2638 r_free = 0.2638    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2637 r_free = 0.2637    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6026  Z= 0.135
  Angle     :  0.482   6.262   8487  Z= 0.240
  Chirality :  0.037   0.133   1002
  Planarity :  0.002   0.021    837
  Dihedral  : 19.336  81.729   1658
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  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:  0.72 (0.36), residues: 541
  helix:  1.53 (0.57), residues: 91
  sheet:  1.13 (0.38), residues: 181
  loop : -0.32 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 206 
 HIS   0.009   0.001   HIS A 233 
 PHE   0.013   0.001   PHE B  88 
 TYR   0.013   0.001   TYR B 361 
 ARG   0.002   0.000   ARG B 158 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8906 (mtm) cc_final: 0.8409 (mtm)
REVERT: B  148 LEU cc_start: 0.9549 (mt) cc_final: 0.9328 (mt)
REVERT: B  157 ASP cc_start: 0.9049 (t0) cc_final: 0.8758 (t0)
REVERT: B  166 ASP cc_start: 0.9331 (m-30) cc_final: 0.9086 (m-30)
REVERT: B  168 LYS cc_start: 0.9182 (mttt) cc_final: 0.8687 (mmmm)
REVERT: A   27 SER cc_start: 0.9644 (m) cc_final: 0.9335 (t)
REVERT: A   44 MET cc_start: 0.6728 (tmm) cc_final: 0.5745 (tmm)
REVERT: A  115 TYR cc_start: 0.9586 (t80) cc_final: 0.9030 (t80)
REVERT: A  157 MET cc_start: 0.9256 (ttm) cc_final: 0.8925 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1776
  time to fit residues: 10.9052
Evaluate side-chains
  34 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 47 optimal weight:    0.1980
   chunk 17 optimal weight:    8.9990
   overall best weight:    4.2388

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.035964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2549 r_free = 0.2549 target = 0.026955 restraints weight = 49078.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.028024 restraints weight = 25039.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.028763 restraints weight = 16213.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2594 r_free = 0.2594    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2595 r_free = 0.2595    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6026  Z= 0.241
  Angle     :  0.529   5.733   8487  Z= 0.271
  Chirality :  0.038   0.152   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 19.443  80.877   1658
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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:  0.53 (0.36), residues: 541
  helix:  1.46 (0.58), residues: 91
  sheet:  0.89 (0.38), residues: 183
  loop : -0.39 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 206 
 HIS   0.008   0.001   HIS A 233 
 PHE   0.017   0.002   PHE B 297 
 TYR   0.008   0.001   TYR A  50 
 ARG   0.003   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.577 
Fit side-chains
REVERT: B  148 LEU cc_start: 0.9610 (mt) cc_final: 0.9339 (mt)
REVERT: B  166 ASP cc_start: 0.9388 (m-30) cc_final: 0.9102 (m-30)
REVERT: A   27 SER cc_start: 0.9702 (m) cc_final: 0.9420 (t)
REVERT: A   44 MET cc_start: 0.6977 (tmm) cc_final: 0.6028 (tmm)
REVERT: A  115 TYR cc_start: 0.9595 (t80) cc_final: 0.9042 (t80)
REVERT: A  142 MET cc_start: 0.9547 (mmm) cc_final: 0.9274 (mmm)
REVERT: A  157 MET cc_start: 0.9284 (ttm) cc_final: 0.8861 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1832
  time to fit residues: 9.8014
Evaluate side-chains
  29 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.035255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2524 r_free = 0.2524 target = 0.026465 restraints weight = 50160.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2559 r_free = 0.2559 target = 0.027497 restraints weight = 25704.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.028220 restraints weight = 16765.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2564
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2564 r_free = 0.2564    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2564 r_free = 0.2564    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6026  Z= 0.287
  Angle     :  0.581   7.534   8487  Z= 0.297
  Chirality :  0.039   0.130   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 19.605  82.467   1658
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  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:  0.43 (0.37), residues: 541
  helix:  1.54 (0.56), residues: 91
  sheet:  0.68 (0.38), residues: 184
  loop : -0.40 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 252 
 HIS   0.007   0.002   HIS A 233 
 PHE   0.016   0.002   PHE B  88 
 TYR   0.020   0.002   TYR B 361 
 ARG   0.005   0.000   ARG A 168 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.670 
Fit side-chains
REVERT: B  148 LEU cc_start: 0.9478 (mt) cc_final: 0.9270 (mt)
REVERT: B  166 ASP cc_start: 0.9509 (m-30) cc_final: 0.9263 (m-30)
REVERT: B  168 LYS cc_start: 0.9122 (mttt) cc_final: 0.8826 (mmtt)
REVERT: A   27 SER cc_start: 0.9718 (m) cc_final: 0.9474 (t)
REVERT: A   44 MET cc_start: 0.7210 (tmm) cc_final: 0.6249 (tmm)
REVERT: A  115 TYR cc_start: 0.9597 (t80) cc_final: 0.9019 (t80)
REVERT: A  142 MET cc_start: 0.9481 (mmm) cc_final: 0.9263 (mmm)
REVERT: A  157 MET cc_start: 0.9288 (ttm) cc_final: 0.9033 (ttm)
REVERT: A  175 ILE cc_start: 0.9628 (tp) cc_final: 0.9401 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1565
  time to fit residues: 8.1257
Evaluate side-chains
  31 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.035407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2526 r_free = 0.2526 target = 0.026700 restraints weight = 49912.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.027700 restraints weight = 25531.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.028356 restraints weight = 16728.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6026  Z= 0.277
  Angle     :  0.559   5.412   8487  Z= 0.288
  Chirality :  0.039   0.139   1002
  Planarity :  0.003   0.031    837
  Dihedral  : 19.682  84.330   1658
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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:  0.26 (0.37), residues: 541
  helix:  1.37 (0.55), residues: 91
  sheet:  0.57 (0.39), residues: 176
  loop : -0.45 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 206 
 HIS   0.010   0.001   HIS A 233 
 PHE   0.014   0.002   PHE B  88 
 TYR   0.017   0.002   TYR B 361 
 ARG   0.004   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: B  148 LEU cc_start: 0.9603 (mt) cc_final: 0.9299 (mt)
REVERT: B  168 LYS cc_start: 0.9112 (mttt) cc_final: 0.8823 (mmtt)
REVERT: A   27 SER cc_start: 0.9724 (m) cc_final: 0.9494 (t)
REVERT: A   44 MET cc_start: 0.7318 (tmm) cc_final: 0.6417 (tmm)
REVERT: A  115 TYR cc_start: 0.9596 (t80) cc_final: 0.9006 (t80)
REVERT: A  142 MET cc_start: 0.9461 (mmm) cc_final: 0.9259 (mmm)
REVERT: A  176 ILE cc_start: 0.9393 (mm) cc_final: 0.9182 (mm)
REVERT: A  184 TYR cc_start: 0.9105 (m-80) cc_final: 0.8846 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1435
  time to fit residues: 8.3854
Evaluate side-chains
  32 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.035003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2523 r_free = 0.2523 target = 0.026323 restraints weight = 50174.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.027321 restraints weight = 25532.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.028035 restraints weight = 16598.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6026  Z= 0.259
  Angle     :  0.559   5.900   8487  Z= 0.286
  Chirality :  0.039   0.131   1002
  Planarity :  0.003   0.023    837
  Dihedral  : 19.696  85.556   1658
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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:  0.22 (0.37), residues: 541
  helix:  1.46 (0.56), residues: 91
  sheet:  0.50 (0.40), residues: 170
  loop : -0.47 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 206 
 HIS   0.009   0.001   HIS A 233 
 PHE   0.018   0.002   PHE B  88 
 TYR   0.016   0.002   TYR B 361 
 ARG   0.003   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.558 
Fit side-chains
REVERT: B  147 MET cc_start: 0.9084 (mtm) cc_final: 0.8685 (mmm)
REVERT: B  148 LEU cc_start: 0.9599 (mt) cc_final: 0.9358 (mt)
REVERT: B  166 ASP cc_start: 0.9578 (m-30) cc_final: 0.9343 (m-30)
REVERT: B  168 LYS cc_start: 0.9104 (mttt) cc_final: 0.8803 (mmtt)
REVERT: A   27 SER cc_start: 0.9723 (m) cc_final: 0.9497 (t)
REVERT: A   44 MET cc_start: 0.7332 (tmm) cc_final: 0.6460 (tmm)
REVERT: A  115 TYR cc_start: 0.9570 (t80) cc_final: 0.8992 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1472
  time to fit residues: 8.1049
Evaluate side-chains
  32 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.034974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2519 r_free = 0.2519 target = 0.026266 restraints weight = 50571.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.027295 restraints weight = 25812.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.028024 restraints weight = 16684.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2563 r_free = 0.2563    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2563
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6026  Z= 0.259
  Angle     :  0.559   6.719   8487  Z= 0.286
  Chirality :  0.039   0.132   1002
  Planarity :  0.003   0.027    837
  Dihedral  : 19.750  87.063   1658
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  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:  0.25 (0.37), residues: 541
  helix:  1.48 (0.56), residues: 91
  sheet:  0.46 (0.40), residues: 172
  loop : -0.42 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 206 
 HIS   0.008   0.001   HIS A 233 
 PHE   0.018   0.002   PHE B  88 
 TYR   0.015   0.001   TYR B 361 
 ARG   0.004   0.000   ARG B 170 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.578 
Fit side-chains
REVERT: B  147 MET cc_start: 0.9189 (mtm) cc_final: 0.8963 (mtm)
REVERT: B  148 LEU cc_start: 0.9691 (mt) cc_final: 0.9364 (mt)
REVERT: B  168 LYS cc_start: 0.9184 (mttt) cc_final: 0.8894 (mmtt)
REVERT: A   44 MET cc_start: 0.7367 (tmm) cc_final: 0.6505 (tmm)
REVERT: A  115 TYR cc_start: 0.9574 (t80) cc_final: 0.9002 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1522
  time to fit residues: 8.2143
Evaluate side-chains
  31 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 53 optimal weight:   20.0000
   chunk 15 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.035080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2521 r_free = 0.2521 target = 0.026450 restraints weight = 51626.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.027456 restraints weight = 26548.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.028121 restraints weight = 17262.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.5121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6026  Z= 0.279
  Angle     :  0.579   6.486   8487  Z= 0.297
  Chirality :  0.039   0.133   1002
  Planarity :  0.003   0.027    837
  Dihedral  : 19.824  89.303   1658
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  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:  0.19 (0.37), residues: 541
  helix:  1.42 (0.56), residues: 91
  sheet:  0.45 (0.40), residues: 172
  loop : -0.47 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 252 
 HIS   0.008   0.001   HIS A 233 
 PHE   0.019   0.002   PHE B  88 
 TYR   0.016   0.002   TYR B 361 
 ARG   0.004   0.000   ARG B 170 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1628.35 seconds
wall clock time: 30 minutes 16.94 seconds (1816.94 seconds total)