Starting phenix.real_space_refine
on Fri Apr  5 22:28:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2024/8eg0_28108_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2024/8eg0_28108.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2024/8eg0_28108.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2024/8eg0_28108.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2024/8eg0_28108_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg0_28108/04_2024/8eg0_28108_updated.pdb"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      65      5.49       5
     S      23      5.16       5
     C    3592      2.51       5
     N    1056      2.21       5
     O    1295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 6031
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2733
          Classifications: {'peptide': 353}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 342}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "A"
      Number of atoms: 1882
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 230, 1865
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 213}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 16
      Conformer: "B"
        Number of residues, atoms: 230, 1865
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 213}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 16
          bond proxies already assigned to first conformer: 1900
    Chain: "C"
      Number of atoms: 1390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1390
          Classifications: {'RNA': 65}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 26, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 13, 'rna3p': 51}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Time building chain proxies: 4.87, per 1000 atoms: 0.81
  Number of scatterers: 6031
  At special positions: 0
  Unit cell: (69.72, 95.865, 112.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P      65     15.00
     O    1295      8.00
     N    1056      7.00
     C    3592      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

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

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      14 helices and 8 sheets defined
      20.2% alpha, 29.3% beta
      25 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 3.43
  Creating SS restraints...
    Processing helix  chain 'B' and resid 229 through 232
      No H-bonds generated for 'chain 'B' and resid 229 through 232'
    Processing helix  chain 'B' and resid 331 through 343
    Processing helix  chain 'B' and resid 353 through 360
      removed outlier: 3.606A  pdb=" N   SER B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'A' and resid 41 through 43
      No H-bonds generated for 'chain 'A' and resid 41 through 43'
    Processing helix  chain 'A' and resid 89 through 95
    Processing helix  chain 'A' and resid 110 through 125
    Processing helix  chain 'A' and resid 145 through 148
      No H-bonds generated for 'chain 'A' and resid 145 through 148'
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 4.503A  pdb=" N   LYS A 172 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 4.107A  pdb=" N   ALA A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLU A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 213
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.665A  pdb=" N   HIS A 233 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 233'
    Processing helix  chain 'A' and resid 239 through 247
    Processing sheet with id=  A, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=  B, first strand: chain 'B' and resid 64 through 69
      removed outlier: 6.966A  pdb=" N   THR B  79 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   ALA B  77 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   PHE B  69 " --> pdb=" O   TYR B  75 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR B  75 " --> pdb=" O   PHE B  69 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ARG B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ARG B  89 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   CYS B  95 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 105 through 110
      removed outlier: 7.154A  pdb=" N   ALA B 120 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   LEU B 108 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   LEU B 118 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   PHE B 110 " --> pdb=" O   LYS B 116 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   LYS B 116 " --> pdb=" O   PHE B 110 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B 142 " --> pdb=" O   VAL B 126 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   SER B 128 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 150 through 153
      removed outlier: 3.708A  pdb=" N   ASP B 150 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE B 169 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   TRP B 173 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ILE B 180 " --> pdb=" O   TRP B 173 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 191 through 196
      removed outlier: 6.986A  pdb=" N   SER B 207 " --> pdb=" O   SER B 192 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ILE B 194 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   SER B 208 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   THR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   GLU B 217 " --> pdb=" O   GLN B 223 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   GLN B 223 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 246 through 252
      removed outlier: 7.088A  pdb=" N   LEU B 261 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ILE B 249 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA B 259 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   PHE B 251 " --> pdb=" O   CYS B 257 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   CYS B 257 " --> pdb=" O   PHE B 251 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   CYS B 262 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   VAL B 267 " --> pdb=" O   CYS B 262 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   GLN B 272 " --> pdb=" O   TYR B 282 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   TYR B 282 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ASP B 274 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   LEU B 280 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 323 through 326
      removed outlier: 3.855A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'A' and resid 217 through 220
      removed outlier: 4.514A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   LEU A 160 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   LEU A 102 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ALA A  81 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   LEU A 104 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ILE A  83 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU A 106 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)

    155 hydrogen bonds defined for protein.
    431 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      65 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      25 basepair parallelities
      29 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 2.88 seconds

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

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

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

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 3637
       35.74 -    71.49: 181
       71.49 -   107.23: 23
      107.23 -   142.97: 0
      142.97 -   178.72: 1
  Dihedral angle restraints: 3842
    sinusoidal: 2143
      harmonic: 1699
  Sorted by residual:
  dihedral pdb=" O4'   U C  20 "
           pdb=" C1'   U C  20 "
           pdb=" N1    U C  20 "
           pdb=" C2    U C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.72 -178.72     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  TRP B 216 "
           pdb=" C   TRP B 216 "
           pdb=" N   GLU B 217 "
           pdb=" CA  GLU B 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.39   18.61     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" O4'   G C  44 "
           pdb=" C1'   G C  44 "
           pdb=" N9    G C  44 "
           pdb=" C4    G C  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -158.27   52.27     1      1.70e+01 3.46e-03 1.29e+01
  ... (remaining 3839 not shown)

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

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

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1427
        2.80 -     3.32: 5479
        3.32 -     3.85: 11006
        3.85 -     4.37: 12779
        4.37 -     4.90: 19969
  Nonbonded interactions: 50660
  Sorted by model distance:
  nonbonded pdb=" N2    G C  15 "
            pdb=" O2    C C  48 "
     model   vdw
     2.269 2.520
  nonbonded pdb=" OG1 THR B 199 "
            pdb=" OE1 GLN B 200 "
     model   vdw
     2.270 2.440
  nonbonded pdb=" N1    A C  14 "
            pdb=" O2'   A C  21 "
     model   vdw
     2.278 2.520
  nonbonded pdb=" O   PRO B 201 "
            pdb=" OH  TYR B 218 "
     model   vdw
     2.281 2.440
  nonbonded pdb=" OD1 ASP B 121 "
            pdb=" OG  SER B 123 "
     model   vdw
     2.305 2.440
  ... (remaining 50655 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  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:          0.980
  Check model and map are aligned:         0.090
  Set scattering table:                    0.050
  Process input model:                     24.650
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.057   6308  Z= 0.138
  Angle     :  0.486  11.983   8867  Z= 0.228
  Chirality :  0.035   0.134   1039
  Planarity :  0.003   0.034    886
  Dihedral  : 17.470 178.716   2744
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.36), residues: 573
  helix:  3.40 (0.52), residues: 106
  sheet:  1.24 (0.40), residues: 180
  loop :  0.41 (0.37), residues: 287

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

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8893 (ttt) cc_final: 0.8501 (ttp)
REVERT: A  140 ASN cc_start: 0.9602 (t0) cc_final: 0.9248 (t0)
REVERT: A  142 MET cc_start: 0.9605 (ttm) cc_final: 0.9374 (ttm)
REVERT: A  147 ASN cc_start: 0.9579 (m110) cc_final: 0.9361 (m110)
REVERT: A  234 LEU cc_start: 0.9436 (mt) cc_final: 0.8850 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1752
  time to fit residues: 12.7365
Evaluate side-chains
  36 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    3.6588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6308  Z= 0.247
  Angle     :  0.520   5.777   8867  Z= 0.256
  Chirality :  0.038   0.170   1039
  Planarity :  0.003   0.027    886
  Dihedral  : 20.669 177.161   1671
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  7.49 %
    Favored  : 91.09 %
  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:  1.77 (0.36), residues: 573
  helix:  3.42 (0.53), residues: 107
  sheet:  1.02 (0.40), residues: 180
  loop :  0.49 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.015   0.001   PHE B  88 
 TYR   0.008   0.001   TYR B 371 
 ARG   0.003   0.000   ARG A 138 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.630 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8915 (ttt) cc_final: 0.8550 (ttp)
REVERT: B  170 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7987 (ttp80)
REVERT: A   77 GLN cc_start: 0.8927 (pm20) cc_final: 0.8699 (mp-120)
REVERT: A  140 ASN cc_start: 0.9538 (t0) cc_final: 0.9188 (t0)
REVERT: A  147 ASN cc_start: 0.9624 (m110) cc_final: 0.9321 (m110)
REVERT: A  234 LEU cc_start: 0.9501 (mt) cc_final: 0.9033 (tp)
  outliers start: 7
  outliers final: 2
  residues processed: 37
  average time/residue: 0.1538
  time to fit residues: 8.5168
Evaluate side-chains
  33 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 ASP
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain B residue  256 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:   10.0000
   chunk 48 optimal weight:    0.3980
   chunk 39 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 57 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6308  Z= 0.143
  Angle     :  0.464   6.097   8867  Z= 0.228
  Chirality :  0.036   0.141   1039
  Planarity :  0.003   0.031    886
  Dihedral  : 20.477 179.407   1671
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.11 %
    Favored  : 90.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.36), residues: 573
  helix:  3.31 (0.52), residues: 107
  sheet:  1.06 (0.39), residues: 179
  loop :  0.44 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 216 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.013   0.001   PHE B  88 
 TYR   0.007   0.001   TYR B 371 
 ARG   0.002   0.000   ARG A 138 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.540 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.8774 (t80) cc_final: 0.8532 (t80)
REVERT: B  147 MET cc_start: 0.8826 (ttt) cc_final: 0.8509 (ttp)
REVERT: B  170 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7978 (ttp80)
REVERT: A  140 ASN cc_start: 0.9592 (t0) cc_final: 0.9194 (t0)
REVERT: A  147 ASN cc_start: 0.9623 (m110) cc_final: 0.9359 (m110)
REVERT: A  234 LEU cc_start: 0.9471 (mt) cc_final: 0.9075 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1566
  time to fit residues: 7.8030
Evaluate side-chains
  29 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 55 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    7.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.046   6308  Z= 0.497
  Angle     :  0.737   8.911   8867  Z= 0.361
  Chirality :  0.042   0.132   1039
  Planarity :  0.004   0.034    886
  Dihedral  : 21.171 173.298   1671
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.70 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.35), residues: 573
  helix:  2.65 (0.51), residues: 106
  sheet:  0.55 (0.39), residues: 180
  loop :  0.22 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 216 
 HIS   0.007   0.002   HIS B 178 
 PHE   0.019   0.002   PHE B 288 
 TYR   0.011   0.002   TYR A  21 
 ARG   0.005   0.001   ARG A 138 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 24
  time to evaluate  : 0.589 
Fit side-chains
REVERT: B  147 MET cc_start: 0.8850 (ttt) cc_final: 0.8629 (ttm)
REVERT: B  150 ASP cc_start: 0.8288 (t0) cc_final: 0.8022 (t0)
REVERT: B  170 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7705 (ttp80)
REVERT: A  140 ASN cc_start: 0.9429 (t0) cc_final: 0.9193 (t0)
REVERT: A  147 ASN cc_start: 0.9686 (m110) cc_final: 0.9396 (m110)
REVERT: A  255 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9347 (mm)
  outliers start: 10
  outliers final: 5
  residues processed: 32
  average time/residue: 0.1558
  time to fit residues: 7.6894
Evaluate side-chains
  28 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 ASP
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  263 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0040
   chunk 20 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    0.9594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6308  Z= 0.122
  Angle     :  0.488   7.049   8867  Z= 0.239
  Chirality :  0.037   0.140   1039
  Planarity :  0.003   0.029    886
  Dihedral  : 20.492 179.376   1671
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.51 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.36), residues: 573
  helix:  3.09 (0.51), residues: 107
  sheet:  0.96 (0.39), residues: 179
  loop :  0.30 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 216 
 HIS   0.004   0.001   HIS B 144 
 PHE   0.008   0.001   PHE B  88 
 TYR   0.007   0.001   TYR A 195 
 ARG   0.003   0.000   ARG A  24 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.619 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.8544 (t80) cc_final: 0.8255 (t80)
REVERT: B  147 MET cc_start: 0.8797 (ttt) cc_final: 0.8536 (ttm)
REVERT: B  170 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.7844 (ttp80)
REVERT: A   77 GLN cc_start: 0.9118 (pm20) cc_final: 0.8890 (mm-40)
REVERT: A  117 GLN cc_start: 0.9697 (mt0) cc_final: 0.9229 (mt0)
REVERT: A  140 ASN cc_start: 0.9564 (t0) cc_final: 0.9256 (t0)
REVERT: A  147 ASN cc_start: 0.9644 (m110) cc_final: 0.9350 (m110)
  outliers start: 6
  outliers final: 3
  residues processed: 32
  average time/residue: 0.1486
  time to fit residues: 7.2824
Evaluate side-chains
  27 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 51 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 59 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    5.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6308  Z= 0.363
  Angle     :  0.595   5.420   8867  Z= 0.292
  Chirality :  0.039   0.133   1039
  Planarity :  0.003   0.026    886
  Dihedral  : 20.836 176.108   1671
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.92 %
    Favored  : 88.46 %
  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:  1.29 (0.36), residues: 573
  helix:  3.00 (0.52), residues: 106
  sheet:  0.65 (0.39), residues: 180
  loop :  0.26 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 216 
 HIS   0.005   0.001   HIS A 204 
 PHE   0.016   0.002   PHE B  88 
 TYR   0.011   0.002   TYR B  38 
 ARG   0.004   0.000   ARG A 138 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.622 
Fit side-chains
REVERT: B  150 ASP cc_start: 0.8390 (t0) cc_final: 0.7927 (t0)
REVERT: B  170 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7785 (ttp80)
REVERT: A  117 GLN cc_start: 0.9727 (mt0) cc_final: 0.9298 (mt0)
REVERT: A  140 ASN cc_start: 0.9429 (t0) cc_final: 0.9150 (t0)
REVERT: A  147 ASN cc_start: 0.9670 (m110) cc_final: 0.9383 (m110)
  outliers start: 8
  outliers final: 4
  residues processed: 29
  average time/residue: 0.1482
  time to fit residues: 6.6146
Evaluate side-chains
  28 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0370
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 61 optimal weight:   20.0000
   chunk 38 optimal weight:    0.0370
   chunk 37 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 36 optimal weight:   20.0000
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.0142

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6308  Z= 0.158
  Angle     :  0.485   6.365   8867  Z= 0.235
  Chirality :  0.037   0.137   1039
  Planarity :  0.003   0.029    886
  Dihedral  : 20.614 179.327   1671
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.12 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.36), residues: 573
  helix:  3.10 (0.51), residues: 107
  sheet:  0.76 (0.39), residues: 179
  loop :  0.32 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.012   0.001   PHE B  88 
 TYR   0.010   0.001   TYR B 371 
 ARG   0.002   0.000   ARG A 138 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 26
  time to evaluate  : 0.657 
Fit side-chains
REVERT: B  150 ASP cc_start: 0.8171 (t0) cc_final: 0.7749 (t0)
REVERT: B  170 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.7946 (ttp80)
REVERT: A  117 GLN cc_start: 0.9698 (mt0) cc_final: 0.9241 (mt0)
REVERT: A  140 ASN cc_start: 0.9434 (t0) cc_final: 0.9167 (t0)
REVERT: A  147 ASN cc_start: 0.9654 (m110) cc_final: 0.9342 (m110)
REVERT: A  255 ILE cc_start: 0.9667 (OUTLIER) cc_final: 0.9400 (mm)
  outliers start: 9
  outliers final: 4
  residues processed: 33
  average time/residue: 0.1470
  time to fit residues: 7.3577
Evaluate side-chains
  32 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  255 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 59 optimal weight:   20.0000
   chunk 53 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   overall best weight:    2.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6308  Z= 0.208
  Angle     :  0.504   5.386   8867  Z= 0.245
  Chirality :  0.038   0.173   1039
  Planarity :  0.003   0.029    886
  Dihedral  : 20.640 177.416   1671
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 10.12 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.36), residues: 573
  helix:  3.11 (0.51), residues: 107
  sheet:  0.77 (0.39), residues: 181
  loop :  0.39 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 216 
 HIS   0.002   0.001   HIS A 204 
 PHE   0.014   0.001   PHE B  88 
 TYR   0.009   0.001   TYR B 371 
 ARG   0.003   0.000   ARG A 138 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.589 
Fit side-chains
REVERT: B  150 ASP cc_start: 0.8275 (t0) cc_final: 0.8035 (t0)
REVERT: B  170 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7943 (ttp80)
REVERT: A  140 ASN cc_start: 0.9398 (t0) cc_final: 0.9147 (t0)
REVERT: A  147 ASN cc_start: 0.9642 (m110) cc_final: 0.9360 (m110)
REVERT: A  255 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9396 (mm)
  outliers start: 8
  outliers final: 4
  residues processed: 32
  average time/residue: 0.1453
  time to fit residues: 6.9969
Evaluate side-chains
  30 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  255 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 45 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 60 optimal weight:   20.0000
   chunk 28 optimal weight:    4.9990
   overall best weight:    3.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6308  Z= 0.245
  Angle     :  0.522   5.152   8867  Z= 0.254
  Chirality :  0.038   0.175   1039
  Planarity :  0.003   0.028    886
  Dihedral  : 20.681 176.491   1671
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.73 %
    Favored  : 87.85 %
  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:  1.40 (0.36), residues: 573
  helix:  3.03 (0.51), residues: 107
  sheet:  0.71 (0.39), residues: 181
  loop :  0.36 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 216 
 HIS   0.002   0.001   HIS A 204 
 PHE   0.014   0.001   PHE B  88 
 TYR   0.008   0.001   TYR B 371 
 ARG   0.003   0.000   ARG A 138 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.750 
Fit side-chains
REVERT: B  150 ASP cc_start: 0.8202 (t0) cc_final: 0.7976 (t0)
REVERT: B  170 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7890 (ttp80)
REVERT: A  140 ASN cc_start: 0.9369 (t0) cc_final: 0.9147 (t0)
REVERT: A  147 ASN cc_start: 0.9649 (m110) cc_final: 0.9362 (m110)
REVERT: A  255 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9396 (mm)
  outliers start: 7
  outliers final: 3
  residues processed: 31
  average time/residue: 0.1545
  time to fit residues: 7.2838
Evaluate side-chains
  30 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  255 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 50 optimal weight:    0.0770
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.1742

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6308  Z= 0.124
  Angle     :  0.474   6.035   8867  Z= 0.230
  Chirality :  0.037   0.139   1039
  Planarity :  0.003   0.031    886
  Dihedral  : 20.455 178.530   1671
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.73 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.36), residues: 573
  helix:  3.00 (0.50), residues: 107
  sheet:  0.84 (0.39), residues: 181
  loop :  0.37 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.012   0.001   PHE B  88 
 TYR   0.014   0.001   TYR B 371 
 ARG   0.002   0.000   ARG A  24 

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

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

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

  1146 Ramachandran restraints generated.
    573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.576 
Fit side-chains
REVERT: B  147 MET cc_start: 0.7705 (tpp) cc_final: 0.7342 (tpp)
REVERT: B  150 ASP cc_start: 0.8062 (t0) cc_final: 0.7849 (t0)
REVERT: B  170 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7980 (ttp80)
REVERT: A  140 ASN cc_start: 0.9460 (t0) cc_final: 0.9126 (t0)
REVERT: A  142 MET cc_start: 0.9506 (mmt) cc_final: 0.9133 (mmm)
REVERT: A  147 ASN cc_start: 0.9625 (m110) cc_final: 0.9351 (m110)
  outliers start: 6
  outliers final: 3
  residues processed: 28
  average time/residue: 0.1699
  time to fit residues: 7.1755
Evaluate side-chains
  28 residues out of total 501 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ARG
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue  196 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 44 optimal weight:    0.1980
   chunk 2 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    4.6388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.043523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.030781 restraints weight = 61991.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.032132 restraints weight = 23851.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.033037 restraints weight = 13917.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   6308  Z= 0.312
  Angle     :  0.559   6.979   8867  Z= 0.271
  Chirality :  0.039   0.144   1039
  Planarity :  0.003   0.027    886
  Dihedral  : 20.643 175.408   1671
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.34 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.36), residues: 573
  helix:  3.12 (0.52), residues: 107
  sheet:  0.69 (0.39), residues: 181
  loop :  0.31 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 216 
 HIS   0.004   0.001   HIS A 204 
 PHE   0.016   0.001   PHE B  88 
 TYR   0.011   0.001   TYR B 371 
 ARG   0.003   0.000   ARG A 138 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1177.54 seconds
wall clock time: 22 minutes 50.57 seconds (1370.57 seconds total)