Starting phenix.real_space_refine
on Sun Mar 10 22:47:43 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/03_2024/8d9l_27265_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/03_2024/8d9l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/03_2024/8d9l_27265.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/03_2024/8d9l_27265.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/03_2024/8d9l_27265_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/03_2024/8d9l_27265_updated.pdb"
  }
  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

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.94, 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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.71
  Conformation dependent library (CDL) restraints added in 951.3 milliseconds
  

  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...
  running ksdssp...
    Secondary structure from input PDB file:
      10 helices and 8 sheets defined
      16.3% alpha, 30.9% beta
      27 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 2.63
  Creating SS restraints...
    Processing helix  chain 'B' and resid 229 through 232
      No H-bonds generated for 'chain 'B' and resid 229 through 232'
    Processing helix  chain 'B' and resid 331 through 343
    Processing helix  chain 'B' and resid 354 through 361
      removed outlier: 3.817A  pdb=" N   SER B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU B 360 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR B 361 " --> pdb=" O   PHE B 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 95
    Processing helix  chain 'A' and resid 110 through 125
    Processing helix  chain 'A' and resid 178 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 201 through 213
      removed outlier: 3.513A  pdb=" N   ASP A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 229 through 235
      removed outlier: 4.120A  pdb=" N   GLY A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 246
    Processing sheet with id=  A, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=  B, first strand: chain 'B' and resid 64 through 69
      removed outlier: 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=  C, first strand: chain 'B' and resid 105 through 110
      removed outlier: 7.022A  pdb=" N   ALA B 120 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   LEU B 108 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   LEU B 118 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   PHE B 110 " --> pdb=" O   LYS B 116 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   LYS B 116 " --> pdb=" O   PHE B 110 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU B 142 " --> pdb=" O   VAL B 126 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   SER B 128 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 148 through 153
      removed outlier: 7.087A  pdb=" N   ALA B 163 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   VAL B 151 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU B 161 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   VAL B 153 " --> pdb=" O   PHE B 159 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   PHE B 159 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B 182 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   TRP B 173 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   ILE B 180 " --> pdb=" O   TRP B 173 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 191 through 196
      removed outlier: 7.241A  pdb=" N   SER B 207 " --> pdb=" O   SER B 192 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ILE B 194 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 194 " (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: 3.693A  pdb=" N   HIS B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   GLU B 217 " --> pdb=" O   GLN B 223 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   GLN B 223 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 246 through 252
      removed outlier: 7.215A  pdb=" N   LEU B 261 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ILE B 249 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ALA B 259 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   PHE B 251 " --> pdb=" O   CYS B 257 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   CYS B 257 " --> pdb=" O   PHE B 251 " (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=  G, first strand: chain 'B' and resid 323 through 326
      removed outlier: 3.757A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'A' and resid 217 through 220
      removed outlier: 4.339A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LEU A 160 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   LEU A 102 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ALA A  81 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   LEU A 104 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ILE A  83 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU A 106 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)

    135 hydrogen bonds defined for protein.
    375 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: 1.94

  Time building geometry restraints manager: 2.90 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:
      100.69 -   107.34: 549
      107.34 -   114.00: 3497
      114.00 -   120.66: 2278
      120.66 -   127.31: 1987
      127.31 -   133.97: 176
  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: 1172
        2.78 -     3.31: 5189
        3.31 -     3.84: 10279
        3.84 -     4.37: 11756
        4.37 -     4.90: 18424
  Nonbonded interactions: 46820
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 154 "
            pdb=" OD1 ASP B 156 "
     model   vdw
     2.250 2.440
  nonbonded pdb=" OG1 THR B 188 "
            pdb=" OE1 GLU B 189 "
     model   vdw
     2.261 2.440
  nonbonded pdb=" OG  SER B 130 "
            pdb=" OE1 GLU B 133 "
     model   vdw
     2.277 2.440
  nonbonded pdb=" O6    G C  10 "
            pdb=" N2    G C  45 "
     model   vdw
     2.301 2.520
  nonbonded pdb=" OD2 ASP B 121 "
            pdb=" OG  SER B 123 "
     model   vdw
     2.307 2.440
  ... (remaining 46815 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.350
  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:          0.960
  Check model and map are aligned:         0.080
  Set scattering table:                    0.060
  Process input model:                     22.430
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.660
-------------------------------------------------------------------------------
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= 0.124
  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 fitting.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.589 
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: 0.2336
  time to fit residues: 19.0082
Evaluate side-chains
  43 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 46 optimal weight:    0.0570
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    3.6106

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6026  Z= 0.227
  Angle     :  0.512   5.442   8487  Z= 0.261
  Chirality :  0.036   0.163   1002
  Planarity :  0.003   0.018    837
  Dihedral  : 19.057  77.758   1658
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 13.94
  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:  1.02 (0.37), residues: 541
  helix:  1.23 (0.58), residues: 100
  sheet:  1.34 (0.39), residues: 179
  loop :  0.05 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 206 
 HIS   0.002   0.001   HIS B 187 
 PHE   0.013   0.002   PHE B 110 
 TYR   0.010   0.001   TYR A  50 
 ARG   0.003   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
  46 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9306 (pttt) cc_final: 0.8908 (mtmm)
REVERT: B  157 ASP cc_start: 0.9157 (t0) cc_final: 0.8900 (t0)
REVERT: B  166 ASP cc_start: 0.8769 (m-30) cc_final: 0.8568 (m-30)
REVERT: A   27 SER cc_start: 0.9598 (m) cc_final: 0.9219 (t)
REVERT: A   44 MET cc_start: 0.6145 (tmm) cc_final: 0.4821 (tmm)
REVERT: A   50 TYR cc_start: 0.8334 (m-80) cc_final: 0.7611 (m-10)
REVERT: A  115 TYR cc_start: 0.9560 (t80) cc_final: 0.9198 (t80)
REVERT: A  157 MET cc_start: 0.9360 (ttm) cc_final: 0.8912 (ttm)
REVERT: A  176 ILE cc_start: 0.9191 (mm) cc_final: 0.8777 (tp)
REVERT: A  183 GLU cc_start: 0.9495 (pt0) cc_final: 0.9171 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.2051
  time to fit residues: 12.2857
Evaluate side-chains
  35 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 37 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   chunk 59 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 44 optimal weight:    8.9990
   chunk 54 optimal weight:    9.9990
   overall best weight:    4.7988

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2895

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= 0.274
  Angle     :  0.539   4.591   8487  Z= 0.278
  Chirality :  0.037   0.166   1002
  Planarity :  0.003   0.055    837
  Dihedral  : 19.319  77.346   1658
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  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:  0.55 (0.36), residues: 541
  helix:  1.10 (0.56), residues: 96
  sheet:  1.10 (0.38), residues: 179
  loop : -0.40 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  93 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.021   0.002   PHE B  69 
 TYR   0.009   0.001   TYR B 127 
 ARG   0.003   0.000   ARG B  99 

*********************** 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
  40 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9319 (pttt) cc_final: 0.8889 (mtmm)
REVERT: B  148 LEU cc_start: 0.9377 (mt) cc_final: 0.9169 (mm)
REVERT: A   27 SER cc_start: 0.9692 (m) cc_final: 0.9348 (t)
REVERT: A   44 MET cc_start: 0.6597 (tmm) cc_final: 0.5648 (tmm)
REVERT: A  115 TYR cc_start: 0.9616 (t80) cc_final: 0.9176 (t80)
REVERT: A  157 MET cc_start: 0.9303 (ttm) cc_final: 0.9068 (ttm)
REVERT: A  183 GLU cc_start: 0.9610 (pt0) cc_final: 0.9120 (pm20)
REVERT: A  184 TYR cc_start: 0.9640 (m-80) cc_final: 0.9358 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1769
  time to fit residues: 9.7908
Evaluate side-chains
  31 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 58 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 15 optimal weight:    0.3980
   chunk 49 optimal weight:    4.9990
   overall best weight:    4.8788

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6026  Z= 0.276
  Angle     :  0.547   5.005   8487  Z= 0.281
  Chirality :  0.038   0.156   1002
  Planarity :  0.003   0.029    837
  Dihedral  : 19.434  79.458   1658
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  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 (0.36), residues: 541
  helix:  0.87 (0.54), residues: 97
  sheet:  0.95 (0.39), residues: 169
  loop : -0.61 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  93 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.011   0.002   PHE B 110 
 TYR   0.007   0.001   TYR B 127 
 ARG   0.003   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
  40 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: B  157 ASP cc_start: 0.9205 (t0) cc_final: 0.8860 (t0)
REVERT: B  166 ASP cc_start: 0.9280 (m-30) cc_final: 0.8972 (m-30)
REVERT: A   27 SER cc_start: 0.9741 (m) cc_final: 0.9469 (t)
REVERT: A   44 MET cc_start: 0.6978 (tmm) cc_final: 0.6009 (tmm)
REVERT: A  115 TYR cc_start: 0.9583 (t80) cc_final: 0.9039 (t80)
REVERT: A  157 MET cc_start: 0.9355 (ttm) cc_final: 0.8984 (ttm)
REVERT: A  183 GLU cc_start: 0.9610 (pt0) cc_final: 0.9005 (pm20)
REVERT: A  184 TYR cc_start: 0.9640 (m-80) cc_final: 0.9397 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1654
  time to fit residues: 9.3840
Evaluate side-chains
  29 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 43 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3498

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= 0.129
  Angle     :  0.468   4.970   8487  Z= 0.233
  Chirality :  0.036   0.155   1002
  Planarity :  0.002   0.017    837
  Dihedral  : 19.249  78.801   1658
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  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:  0.60 (0.37), residues: 541
  helix:  1.58 (0.58), residues: 95
  sheet:  1.10 (0.40), residues: 168
  loop : -0.46 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 206 
 HIS   0.004   0.001   HIS A 144 
 PHE   0.016   0.001   PHE B  88 
 TYR   0.008   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
  40 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.585 
Fit side-chains
REVERT: B  148 LEU cc_start: 0.9422 (mt) cc_final: 0.9183 (mt)
REVERT: B  157 ASP cc_start: 0.9184 (t0) cc_final: 0.8832 (t0)
REVERT: B  166 ASP cc_start: 0.9317 (m-30) cc_final: 0.9054 (m-30)
REVERT: A   27 SER cc_start: 0.9715 (m) cc_final: 0.9442 (t)
REVERT: A   44 MET cc_start: 0.6795 (tmm) cc_final: 0.5677 (tmm)
REVERT: A  115 TYR cc_start: 0.9551 (t80) cc_final: 0.8983 (t80)
REVERT: A  157 MET cc_start: 0.9352 (ttm) cc_final: 0.8994 (ttm)
REVERT: A  175 ILE cc_start: 0.9498 (tp) cc_final: 0.9194 (tp)
REVERT: A  180 LEU cc_start: 0.9837 (mm) cc_final: 0.9632 (mt)
REVERT: A  183 GLU cc_start: 0.9617 (pt0) cc_final: 0.9047 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1671
  time to fit residues: 9.4005
Evaluate side-chains
  35 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 59 optimal weight:   20.0000
   chunk 48 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    0.0670
   chunk 56 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   overall best weight:    5.8126

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   6026  Z= 0.314
  Angle     :  0.588   5.508   8487  Z= 0.303
  Chirality :  0.038   0.136   1002
  Planarity :  0.003   0.023    837
  Dihedral  : 19.555  80.418   1658
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 21.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  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:  0.16 (0.36), residues: 541
  helix:  0.99 (0.53), residues: 94
  sheet:  0.78 (0.39), residues: 175
  loop : -0.64 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 252 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.016   0.002   PHE B  88 
 TYR   0.013   0.002   TYR A 186 
 ARG   0.004   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
  33 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
REVERT: B  148 LEU cc_start: 0.9487 (mt) cc_final: 0.9193 (mt)
REVERT: B  168 LYS cc_start: 0.9277 (mtmt) cc_final: 0.9066 (mttt)
REVERT: A   27 SER cc_start: 0.9771 (m) cc_final: 0.9504 (t)
REVERT: A   44 MET cc_start: 0.7191 (tmm) cc_final: 0.6121 (tmm)
REVERT: A  115 TYR cc_start: 0.9587 (t80) cc_final: 0.9012 (t80)
REVERT: A  142 MET cc_start: 0.9624 (mmm) cc_final: 0.9344 (mmp)
REVERT: A  157 MET cc_start: 0.9401 (ttm) cc_final: 0.8996 (ttm)
REVERT: A  183 GLU cc_start: 0.9664 (pt0) cc_final: 0.9038 (pm20)
REVERT: A  184 TYR cc_start: 0.9650 (m-80) cc_final: 0.9435 (m-80)
REVERT: A  207 MET cc_start: 0.9585 (mpp) cc_final: 0.9236 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1742
  time to fit residues: 8.0678
Evaluate side-chains
  28 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 58 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6026  Z= 0.223
  Angle     :  0.534  11.248   8487  Z= 0.268
  Chirality :  0.037   0.144   1002
  Planarity :  0.003   0.019    837
  Dihedral  : 19.506  80.712   1658
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 17.01
  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:  0.17 (0.36), residues: 541
  helix:  1.05 (0.54), residues: 95
  sheet:  0.77 (0.40), residues: 169
  loop : -0.61 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 206 
 HIS   0.011   0.001   HIS A 204 
 PHE   0.012   0.001   PHE B  88 
 TYR   0.009   0.001   TYR A 186 
 ARG   0.003   0.000   ARG B  99 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: B  148 LEU cc_start: 0.9371 (mt) cc_final: 0.9104 (mt)
REVERT: A   27 SER cc_start: 0.9752 (m) cc_final: 0.9509 (t)
REVERT: A   44 MET cc_start: 0.7225 (tmm) cc_final: 0.6237 (tmm)
REVERT: A  115 TYR cc_start: 0.9518 (t80) cc_final: 0.8940 (t80)
REVERT: A  140 ASN cc_start: 0.9353 (t0) cc_final: 0.9135 (t0)
REVERT: A  142 MET cc_start: 0.9614 (mmm) cc_final: 0.9356 (mmp)
REVERT: A  157 MET cc_start: 0.9411 (ttm) cc_final: 0.9004 (ttm)
REVERT: A  175 ILE cc_start: 0.9550 (tp) cc_final: 0.9293 (tp)
REVERT: A  183 GLU cc_start: 0.9637 (pt0) cc_final: 0.9043 (pm20)
REVERT: A  207 MET cc_start: 0.9588 (mpp) cc_final: 0.9226 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1765
  time to fit residues: 8.6624
Evaluate side-chains
  32 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 29 optimal weight:    0.1980
   chunk 5 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 56 optimal weight:   20.0000
   chunk 51 optimal weight:    0.9980
   chunk 54 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   overall best weight:    2.8386

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4277

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= 0.175
  Angle     :  0.492   5.965   8487  Z= 0.246
  Chirality :  0.036   0.130   1002
  Planarity :  0.003   0.021    837
  Dihedral  : 19.420  79.485   1658
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  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:  0.31 (0.37), residues: 541
  helix:  1.24 (0.56), residues: 95
  sheet:  0.82 (0.40), residues: 168
  loop : -0.52 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 206 
 HIS   0.007   0.001   HIS A 204 
 PHE   0.014   0.001   PHE B  88 
 TYR   0.008   0.001   TYR A 186 
 ARG   0.003   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
  36 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
REVERT: B  148 LEU cc_start: 0.9337 (mt) cc_final: 0.9070 (mt)
REVERT: B  166 ASP cc_start: 0.9503 (m-30) cc_final: 0.9219 (m-30)
REVERT: A   27 SER cc_start: 0.9738 (m) cc_final: 0.9500 (t)
REVERT: A   44 MET cc_start: 0.7081 (tmm) cc_final: 0.6260 (tmm)
REVERT: A  115 TYR cc_start: 0.9535 (t80) cc_final: 0.8937 (t80)
REVERT: A  140 ASN cc_start: 0.9341 (t0) cc_final: 0.9095 (t0)
REVERT: A  142 MET cc_start: 0.9544 (mmm) cc_final: 0.9272 (mmm)
REVERT: A  157 MET cc_start: 0.9413 (ttm) cc_final: 0.9077 (ttm)
REVERT: A  175 ILE cc_start: 0.9459 (tp) cc_final: 0.9241 (tp)
REVERT: A  183 GLU cc_start: 0.9592 (pt0) cc_final: 0.9012 (pm20)
REVERT: A  184 TYR cc_start: 0.9624 (m-80) cc_final: 0.9257 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1827
  time to fit residues: 9.2808
Evaluate side-chains
  34 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 35 optimal weight:    0.4980
   chunk 57 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
A 204 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6026  Z= 0.208
  Angle     :  0.511   8.099   8487  Z= 0.257
  Chirality :  0.036   0.129   1002
  Planarity :  0.003   0.024    837
  Dihedral  : 19.471  80.037   1658
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  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:  0.29 (0.37), residues: 541
  helix:  1.10 (0.55), residues: 95
  sheet:  0.73 (0.39), residues: 175
  loop : -0.46 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 252 
 HIS   0.006   0.001   HIS A 204 
 PHE   0.012   0.001   PHE B  88 
 TYR   0.007   0.001   TYR A 186 
 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
  36 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
REVERT: B  148 LEU cc_start: 0.9315 (mt) cc_final: 0.9078 (mt)
REVERT: B  166 ASP cc_start: 0.9514 (m-30) cc_final: 0.9248 (m-30)
REVERT: A   44 MET cc_start: 0.7288 (tmm) cc_final: 0.6544 (tmm)
REVERT: A  115 TYR cc_start: 0.9518 (t80) cc_final: 0.8933 (t80)
REVERT: A  140 ASN cc_start: 0.9358 (t0) cc_final: 0.9108 (t0)
REVERT: A  142 MET cc_start: 0.9492 (mmm) cc_final: 0.9273 (mmm)
REVERT: A  157 MET cc_start: 0.9421 (ttm) cc_final: 0.9009 (ttm)
REVERT: A  183 GLU cc_start: 0.9589 (pt0) cc_final: 0.9015 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1752
  time to fit residues: 8.9679
Evaluate side-chains
  29 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 55 optimal weight:   20.0000
   chunk 48 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0970
   chunk 29 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0070
   chunk 14 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.4327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6026  Z= 0.127
  Angle     :  0.489   6.660   8487  Z= 0.237
  Chirality :  0.036   0.133   1002
  Planarity :  0.003   0.021    837
  Dihedral  : 19.195  78.835   1658
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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:  0.50 (0.37), residues: 541
  helix:  1.47 (0.58), residues: 95
  sheet:  0.83 (0.39), residues: 175
  loop : -0.37 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 206 
 HIS   0.005   0.001   HIS A 233 
 PHE   0.013   0.001   PHE B  88 
 TYR   0.007   0.001   TYR A 186 
 ARG   0.001   0.000   ARG B 165 

********************** 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
  42 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 ASP cc_start: 0.9493 (m-30) cc_final: 0.9213 (m-30)
REVERT: A   44 MET cc_start: 0.6946 (tmm) cc_final: 0.6198 (tmm)
REVERT: A  115 TYR cc_start: 0.9529 (t80) cc_final: 0.8922 (t80)
REVERT: A  140 ASN cc_start: 0.9363 (t0) cc_final: 0.9103 (t0)
REVERT: A  142 MET cc_start: 0.9436 (mmm) cc_final: 0.9180 (mmm)
REVERT: A  157 MET cc_start: 0.9412 (ttm) cc_final: 0.9016 (ttm)
REVERT: A  183 GLU cc_start: 0.9556 (pt0) cc_final: 0.9022 (pm20)
REVERT: A  184 TYR cc_start: 0.9617 (m-80) cc_final: 0.9405 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1667
  time to fit residues: 9.8253
Evaluate side-chains
  35 residues out of total 472 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 49 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0970
   overall best weight:    5.4186

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.036329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.027785 restraints weight = 51557.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.028804 restraints weight = 26724.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.029510 restraints weight = 17557.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2603
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2603 r_free = 0.2603    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 = 0.2597 r_free = 0.2597    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.4745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6026  Z= 0.302
  Angle     :  0.572   5.813   8487  Z= 0.291
  Chirality :  0.038   0.180   1002
  Planarity :  0.003   0.020    837
  Dihedral  : 19.533  81.273   1658
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 20.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  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:  0.17 (0.36), residues: 541
  helix:  1.03 (0.55), residues: 94
  sheet:  0.65 (0.39), residues: 175
  loop : -0.53 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 252 
 HIS   0.005   0.001   HIS A 233 
 PHE   0.017   0.002   PHE B  88 
 TYR   0.009   0.001   TYR A  50 
 ARG   0.004   0.000   ARG B  99 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1138.20 seconds
wall clock time: 21 minutes 36.71 seconds (1296.71 seconds total)