Starting phenix.real_space_refine
on Thu Nov 14 15:13:26 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbv_36147/11_2024/8jbv_36147.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbv_36147/11_2024/8jbv_36147.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbv_36147/11_2024/8jbv_36147.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbv_36147/11_2024/8jbv_36147.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbv_36147/11_2024/8jbv_36147.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbv_36147/11_2024/8jbv_36147.cif"
  }
  resolution = 3.02
  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=  -0.002 sd=   0.090
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: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    4244      2.51       5
     N    1114      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 6624
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "m"
      Number of atoms: 1576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1576
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 8, 'TRANS': 190}
          Chain breaks: 1
    Chain: "n"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1736
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 11, 'TRANS': 201}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 1576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1576
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 8, 'TRANS': 190}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1736
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 11, 'TRANS': 201}
          Chain breaks: 1
  Time building chain proxies: 4.40, per 1000 atoms: 0.66
  Number of scatterers: 6624
  At special positions: 0
  Unit cell: (81.525, 84.786, 133.701, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O    1240      8.00
     N    1114      7.00
     C    4244      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS m  43 " - pdb=" SG  CYS m 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS m 157 " - pdb=" SG  CYS m 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS n  26 " - pdb=" SG  CYS n  98 " distance=2.04
    Simple disulfide: pdb=" SG  CYS n 156 " - pdb=" SG  CYS n 212 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M  43 " - pdb=" SG  CYS M 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 157 " - pdb=" SG  CYS M 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  26 " - pdb=" SG  CYS N  98 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 156 " - pdb=" SG  CYS N 212 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 964.1 milliseconds
  

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 20 sheets defined
      3.9% alpha, 36.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'm' and resid 211 through 215
      removed outlier: 4.341A  pdb=" N   ASN m 214 " --> pdb=" O   GLN m 211 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 89 through 93
      removed outlier: 3.919A  pdb=" N   SER n  93 " --> pdb=" O   GLU n  90 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 144 through 149
      removed outlier: 3.833A  pdb=" N   LEU n 148 " --> pdb=" O   ALA n 144 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 211 through 215
      removed outlier: 4.341A  pdb=" N   ASN M 214 " --> pdb=" O   GLN M 211 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 89 through 93
      removed outlier: 3.919A  pdb=" N   SER N  93 " --> pdb=" O   GLU N  90 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 144 through 149
      removed outlier: 3.833A  pdb=" N   LEU N 148 " --> pdb=" O   ALA N 144 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'm' and resid 23 through 25
      removed outlier: 3.581A  pdb=" N   VAL m  39 " --> pdb=" O   ILE m  98 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   SER m  93 " --> pdb=" O   LYS m  88 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR m  83 " --> pdb=" O   SER m  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'm' and resid 30 through 34
      removed outlier: 6.442A  pdb=" N   VAL m  31 " --> pdb=" O   THR m 133 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   GLU m 135 " --> pdb=" O   VAL m  31 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   MET m  33 " --> pdb=" O   GLU m 135 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA m 107 " --> pdb=" O   VAL m 132 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE m  54 " --> pdb=" O   ARG m  70 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ARG m  70 " --> pdb=" O   ILE m  54 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   TRP m  56 " --> pdb=" O   LEU m  68 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'm' and resid 30 through 34
      removed outlier: 6.442A  pdb=" N   VAL m  31 " --> pdb=" O   THR m 133 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   GLU m 135 " --> pdb=" O   VAL m  31 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   MET m  33 " --> pdb=" O   GLU m 135 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA m 107 " --> pdb=" O   VAL m 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'm' and resid 146 through 150
      removed outlier: 3.994A  pdb=" N   GLU m 161 " --> pdb=" O   TYR m 192 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   TYR m 192 " --> pdb=" O   GLU m 161 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL m 195 " --> pdb=" O   ALA m 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'n' and resid 13 through 14
      removed outlier: 5.391A  pdb=" N   TRP n 101 " --> pdb=" O   TYR n  35 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   TYR n  35 " --> pdb=" O   TRP n 101 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ILE n  36 " --> pdb=" O   TYR n  52 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   TYR n  52 " --> pdb=" O   ILE n  36 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   TRP n  38 " --> pdb=" O   LEU n  50 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS n  59 " --> pdb=" O   ASP n  54 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'n' and resid 13 through 14
    Processing sheet with id=AA7, first strand: chain 'n' and resid 21 through 25
    Processing sheet with id=AA8, first strand: chain 'n' and resid 152 through 153
      removed outlier: 3.548A  pdb=" N   GLY n 152 " --> pdb=" O   VAL n 201 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'n' and resid 156 through 159
      removed outlier: 3.560A  pdb=" N   SER n 197 " --> pdb=" O   CYS n 156 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'n' and resid 167 through 171
      removed outlier: 3.554A  pdb=" N   GLN n 171 " --> pdb=" O   ARG n 211 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25
      removed outlier: 3.581A  pdb=" N   VAL M  39 " --> pdb=" O   ILE M  98 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   SER M  93 " --> pdb=" O   LYS M  88 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR M  83 " --> pdb=" O   SER M  80 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'M' and resid 30 through 34
      removed outlier: 6.443A  pdb=" N   VAL M  31 " --> pdb=" O   THR M 133 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   GLU M 135 " --> pdb=" O   VAL M  31 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   MET M  33 " --> pdb=" O   GLU M 135 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA M 107 " --> pdb=" O   VAL M 132 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE M  54 " --> pdb=" O   ARG M  70 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ARG M  70 " --> pdb=" O   ILE M  54 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   TRP M  56 " --> pdb=" O   LEU M  68 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 30 through 34
      removed outlier: 6.443A  pdb=" N   VAL M  31 " --> pdb=" O   THR M 133 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   GLU M 135 " --> pdb=" O   VAL M  31 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   MET M  33 " --> pdb=" O   GLU M 135 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA M 107 " --> pdb=" O   VAL M 132 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'M' and resid 146 through 150
      removed outlier: 3.994A  pdb=" N   GLU M 161 " --> pdb=" O   TYR M 192 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   TYR M 192 " --> pdb=" O   GLU M 161 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL M 195 " --> pdb=" O   ALA M 183 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'N' and resid 13 through 14
      removed outlier: 5.390A  pdb=" N   TRP N 101 " --> pdb=" O   TYR N  35 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   TYR N  35 " --> pdb=" O   TRP N 101 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   ILE N  36 " --> pdb=" O   TYR N  52 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   TYR N  52 " --> pdb=" O   ILE N  36 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   TRP N  38 " --> pdb=" O   LEU N  50 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS N  59 " --> pdb=" O   ASP N  54 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14
    Processing sheet with id=AB8, first strand: chain 'N' and resid 21 through 25
    Processing sheet with id=AB9, first strand: chain 'N' and resid 152 through 153
      removed outlier: 3.548A  pdb=" N   GLY N 152 " --> pdb=" O   VAL N 201 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'N' and resid 156 through 159
      removed outlier: 3.559A  pdb=" N   SER N 197 " --> pdb=" O   CYS N 156 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'N' and resid 167 through 171
      removed outlier: 3.553A  pdb=" N   GLN N 171 " --> pdb=" O   ARG N 211 " (cutoff:3.500A)

    178 hydrogen bonds defined for protein.
    444 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1391
        1.33 -     1.45: 1713
        1.45 -     1.58: 3636
        1.58 -     1.70: 4
        1.70 -     1.83: 36
  Bond restraints: 6780
  Sorted by residual:
  bond pdb=" CB  GLU m 104 "
       pdb=" CG  GLU m 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.596 -0.076 3.00e-02 1.11e+03 6.50e+00
  bond pdb=" CB  GLU M 104 "
       pdb=" CG  GLU M 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.596 -0.076 3.00e-02 1.11e+03 6.47e+00
  bond pdb=" CB  ASP n 164 "
       pdb=" CG  ASP n 164 "
    ideal  model  delta    sigma   weight residual
    1.516  1.461  0.055 2.50e-02 1.60e+03 4.80e+00
  bond pdb=" CB  ASP N 164 "
       pdb=" CG  ASP N 164 "
    ideal  model  delta    sigma   weight residual
    1.516  1.462  0.054 2.50e-02 1.60e+03 4.67e+00
  bond pdb=" CB  GLU n 209 "
       pdb=" CG  GLU n 209 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.064 3.00e-02 1.11e+03 4.51e+00
  ... (remaining 6775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.33: 9052
        3.33 -     6.67: 103
        6.67 -    10.00: 18
       10.00 -    13.34: 7
       13.34 -    16.67: 4
  Bond angle restraints: 9184
  Sorted by residual:
  angle pdb=" CA  GLU M 104 "
        pdb=" CB  GLU M 104 "
        pdb=" CG  GLU M 104 "
      ideal   model   delta    sigma   weight residual
     114.10  129.38  -15.28 2.00e+00 2.50e-01 5.84e+01
  angle pdb=" CA  GLU m 104 "
        pdb=" CB  GLU m 104 "
        pdb=" CG  GLU m 104 "
      ideal   model   delta    sigma   weight residual
     114.10  129.37  -15.27 2.00e+00 2.50e-01 5.83e+01
  angle pdb=" C   ASN n 219 "
        pdb=" CA  ASN n 219 "
        pdb=" CB  ASN n 219 "
      ideal   model   delta    sigma   weight residual
     110.19   98.47   11.72 1.62e+00 3.81e-01 5.23e+01
  angle pdb=" CA  GLU N 209 "
        pdb=" CB  GLU N 209 "
        pdb=" CG  GLU N 209 "
      ideal   model   delta    sigma   weight residual
     114.10  125.46  -11.36 2.00e+00 2.50e-01 3.23e+01
  angle pdb=" CA  GLU n 209 "
        pdb=" CB  GLU n 209 "
        pdb=" CG  GLU n 209 "
      ideal   model   delta    sigma   weight residual
     114.10  125.46  -11.36 2.00e+00 2.50e-01 3.23e+01
  ... (remaining 9179 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 3579
       17.98 -    35.96: 299
       35.96 -    53.94: 160
       53.94 -    71.91: 58
       71.91 -    89.89: 8
  Dihedral angle restraints: 4104
    sinusoidal: 1672
      harmonic: 2432
  Sorted by residual:
  dihedral pdb=" C   ASN n 219 "
           pdb=" N   ASN n 219 "
           pdb=" CA  ASN n 219 "
           pdb=" CB  ASN n 219 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -106.18  -16.42     0      2.50e+00 1.60e-01 4.31e+01
  dihedral pdb=" CA  THR N 146 "
           pdb=" C   THR N 146 "
           pdb=" N   LYS N 147 "
           pdb=" CA  LYS N 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  THR n 146 "
           pdb=" C   THR n 146 "
           pdb=" N   LYS n 147 "
           pdb=" CA  LYS n 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.24   22.76     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 4101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 813
       0.073 -    0.146: 178
       0.146 -    0.218: 29
       0.218 -    0.291: 5
       0.291 -    0.364: 3
  Chirality restraints: 1028
  Sorted by residual:
  chirality pdb=" CA  ASN n 219 "
            pdb=" N   ASN n 219 "
            pdb=" C   ASN n 219 "
            pdb=" CB  ASN n 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CA  PHE N 162 "
            pdb=" N   PHE N 162 "
            pdb=" C   PHE N 162 "
            pdb=" CB  PHE N 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  PHE n 162 "
            pdb=" N   PHE n 162 "
            pdb=" C   PHE n 162 "
            pdb=" CB  PHE n 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 1025 not shown)

  Planarity restraints: 1144
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN n 219 "    0.012 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   ASN n 219 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASN n 219 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LYS n 220 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO N 230 "   -0.041 5.00e-02 4.00e+02   6.26e-02 6.28e+00
        pdb=" N   PRO N 231 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO N 231 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO N 231 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO n 230 "    0.041 5.00e-02 4.00e+02   6.26e-02 6.27e+00
        pdb=" N   PRO n 231 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO n 231 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO n 231 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1141 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1181
        2.77 -     3.30: 5072
        3.30 -     3.83: 10302
        3.83 -     4.37: 11547
        4.37 -     4.90: 21304
  Nonbonded interactions: 49406
  Sorted by model distance:
  nonbonded pdb=" OG1 THR n 153 "
            pdb=" OG1 THR n 200 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG1 THR N 153 "
            pdb=" OG1 THR N 200 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   SER m 145 "
            pdb=" OG  SER m 145 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   SER M 145 "
            pdb=" OG  SER M 145 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   SER N 205 "
            pdb=" OG  SER N 205 "
     model   vdw
     2.257 3.040
  ... (remaining 49401 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'M'
  selection = chain 'm'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'n'
}

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 individual isotropic
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:             0.770
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.780
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
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      :  0.008   0.076   6780  Z= 0.525
  Angle     :  1.122  16.669   9184  Z= 0.616
  Chirality :  0.065   0.364   1028
  Planarity :  0.008   0.063   1144
  Dihedral  : 18.530  89.893   2504
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers : 14.93 %
    Allowed  :  7.73 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.31 (0.26), residues: 808
  helix:  None (None), residues: 0
  sheet: -1.27 (0.26), residues: 390
  loop : -3.22 (0.22), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP N  38 
 HIS   0.004   0.001   HIS N  74 
 PHE   0.023   0.003   PHE n 162 
 TYR   0.022   0.003   TYR N  52 
 ARG   0.004   0.001   ARG m  36 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 112
    poor density    : 149
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: m   30 SER cc_start: 0.7233 (OUTLIER) cc_final: 0.6890 (m)
REVERT: m   32 SER cc_start: 0.6091 (OUTLIER) cc_final: 0.5785 (m)
REVERT: m   46 GLU cc_start: 0.8186 (tt0) cc_final: 0.7975 (tt0)
REVERT: m   53 TYR cc_start: 0.8034 (m-80) cc_final: 0.7782 (m-80)
REVERT: m  125 ILE cc_start: 0.8249 (mt) cc_final: 0.7985 (mt)
REVERT: m  205 SER cc_start: 0.6889 (OUTLIER) cc_final: 0.6642 (m)
REVERT: M   65 MET cc_start: 0.7849 (mmt) cc_final: 0.7626 (tpp)
REVERT: M  220 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6578 (m)
REVERT: N  173 LYS cc_start: 0.5510 (OUTLIER) cc_final: 0.5206 (ptmt)
REVERT: N  209 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6197 (tt0)
  outliers start: 112
  outliers final: 17
  residues processed: 237
  average time/residue: 0.2051
  time to fit residues: 61.9544
Evaluate side-chains
  129 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   30 SER
Chi-restraints excluded: chain m residue   32 SER
Chi-restraints excluded: chain m residue  133 THR
Chi-restraints excluded: chain m residue  174 SER
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  205 SER
Chi-restraints excluded: chain m residue  207 THR
Chi-restraints excluded: chain m residue  224 VAL
Chi-restraints excluded: chain n residue   30 VAL
Chi-restraints excluded: chain n residue  124 THR
Chi-restraints excluded: chain n residue  205 SER
Chi-restraints excluded: chain M residue   44 LEU
Chi-restraints excluded: chain M residue  104 GLU
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain M residue  220 THR
Chi-restraints excluded: chain N residue   15 THR
Chi-restraints excluded: chain N residue   18 THR
Chi-restraints excluded: chain N residue  100 THR
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  148 LEU
Chi-restraints excluded: chain N residue  173 LYS
Chi-restraints excluded: chain N residue  189 THR
Chi-restraints excluded: chain N residue  209 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
m  28 GLN
m  42 ASN
m  77 ASN
m 102 GLN
m 139 GLN
m 193 ASN
m 218 HIS
n  37 HIS
n 169 HIS
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  28 GLN
M  42 ASN
M  77 ASN
M 102 GLN
N  32 ASN
N  37 HIS
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6780  Z= 0.229
  Angle     :  0.655  11.336   9184  Z= 0.341
  Chirality :  0.048   0.158   1028
  Planarity :  0.006   0.041   1144
  Dihedral  :  8.338  57.642    916
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 17.07 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.99 (0.27), residues: 808
  helix: -4.57 (0.47), residues: 22
  sheet: -1.01 (0.25), residues: 418
  loop : -3.00 (0.25), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP n  79 
 HIS   0.002   0.001   HIS n 210 
 PHE   0.016   0.002   PHE M 162 
 TYR   0.012   0.002   TYR N  52 
 ARG   0.003   0.001   ARG m 137 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 113
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
REVERT: m   46 GLU cc_start: 0.8333 (tt0) cc_final: 0.8112 (tt0)
REVERT: m  105 ASP cc_start: 0.7424 (m-30) cc_final: 0.7153 (m-30)
REVERT: m  125 ILE cc_start: 0.8211 (mt) cc_final: 0.7995 (mt)
REVERT: n  111 TYR cc_start: 0.6186 (OUTLIER) cc_final: 0.4983 (t80)
REVERT: M  220 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.6975 (m)
  outliers start: 37
  outliers final: 28
  residues processed: 141
  average time/residue: 0.1976
  time to fit residues: 36.7220
Evaluate side-chains
  133 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  133 THR
Chi-restraints excluded: chain m residue  149 MET
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  206 VAL
Chi-restraints excluded: chain m residue  207 THR
Chi-restraints excluded: chain m residue  224 VAL
Chi-restraints excluded: chain n residue   15 THR
Chi-restraints excluded: chain n residue   18 THR
Chi-restraints excluded: chain n residue   30 VAL
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   77 ARG
Chi-restraints excluded: chain n residue   87 ASN
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue  111 TYR
Chi-restraints excluded: chain n residue  124 THR
Chi-restraints excluded: chain n residue  171 GLN
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain M residue  220 THR
Chi-restraints excluded: chain N residue   18 THR
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  153 THR
Chi-restraints excluded: chain N residue  209 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0270
   chunk 60 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.1244

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

Flipped N/Q/H residues before XYZ refinement:
m 193 ASN
m 218 HIS
n  32 ASN
n  91 ASN
n 182 GLN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 218 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6780  Z= 0.273
  Angle     :  0.662  12.317   9184  Z= 0.344
  Chirality :  0.049   0.187   1028
  Planarity :  0.005   0.051   1144
  Dihedral  :  6.905  59.202    897
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 18.80 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.67 (0.27), residues: 808
  helix: -4.47 (0.49), residues: 22
  sheet: -0.66 (0.26), residues: 410
  loop : -2.95 (0.25), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP M  49 
 HIS   0.003   0.001   HIS n  37 
 PHE   0.016   0.002   PHE M 162 
 TYR   0.015   0.002   TYR n  53 
 ARG   0.003   0.000   ARG m 137 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 112
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: m   46 GLU cc_start: 0.8232 (tt0) cc_final: 0.7990 (tt0)
REVERT: m  105 ASP cc_start: 0.7596 (m-30) cc_final: 0.7315 (m-30)
REVERT: m  125 ILE cc_start: 0.8142 (mt) cc_final: 0.7924 (mt)
REVERT: n  111 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.5156 (t80)
REVERT: N   16 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7503 (mmt180)
  outliers start: 38
  outliers final: 27
  residues processed: 139
  average time/residue: 0.1865
  time to fit residues: 34.3214
Evaluate side-chains
  131 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  133 THR
Chi-restraints excluded: chain m residue  146 VAL
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  207 THR
Chi-restraints excluded: chain m residue  224 VAL
Chi-restraints excluded: chain n residue   15 THR
Chi-restraints excluded: chain n residue   25 THR
Chi-restraints excluded: chain n residue   56 SER
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   87 ASN
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue  111 TYR
Chi-restraints excluded: chain n residue  124 THR
Chi-restraints excluded: chain n residue  171 GLN
Chi-restraints excluded: chain n residue  181 SER
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   30 SER
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  146 VAL
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  153 THR
Chi-restraints excluded: chain N residue  189 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 48 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 77 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
m 218 HIS
n  32 ASN
n  91 ASN
n 182 GLN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  22 GLN
M 120 ASN
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6780  Z= 0.187
  Angle     :  0.579   9.835   9184  Z= 0.302
  Chirality :  0.047   0.187   1028
  Planarity :  0.005   0.048   1144
  Dihedral  :  5.643  59.055    890
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 18.13 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.38 (0.28), residues: 808
  helix: -4.06 (0.60), residues: 22
  sheet: -0.39 (0.27), residues: 412
  loop : -2.87 (0.26), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP M  49 
 HIS   0.003   0.001   HIS n 169 
 PHE   0.010   0.001   PHE m  67 
 TYR   0.013   0.001   TYR n  53 
 ARG   0.003   0.000   ARG m 137 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 107
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
REVERT: m   46 GLU cc_start: 0.8227 (tt0) cc_final: 0.7968 (tt0)
REVERT: m  105 ASP cc_start: 0.7603 (m-30) cc_final: 0.7318 (m-30)
REVERT: n  111 TYR cc_start: 0.6192 (OUTLIER) cc_final: 0.5133 (t80)
REVERT: N   16 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.7468 (mmt180)
  outliers start: 42
  outliers final: 32
  residues processed: 133
  average time/residue: 0.2024
  time to fit residues: 35.5932
Evaluate side-chains
  134 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   25 THR
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  133 THR
Chi-restraints excluded: chain m residue  146 VAL
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  206 VAL
Chi-restraints excluded: chain m residue  207 THR
Chi-restraints excluded: chain m residue  217 VAL
Chi-restraints excluded: chain m residue  224 VAL
Chi-restraints excluded: chain n residue   15 THR
Chi-restraints excluded: chain n residue   25 THR
Chi-restraints excluded: chain n residue   30 VAL
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   77 ARG
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue  111 TYR
Chi-restraints excluded: chain n residue  124 THR
Chi-restraints excluded: chain n residue  128 LEU
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   25 THR
Chi-restraints excluded: chain M residue   30 SER
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  120 ASN
Chi-restraints excluded: chain M residue  146 VAL
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   48 GLN
Chi-restraints excluded: chain N residue   98 CYS
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  189 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 57 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0570
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
m 193 ASN
m 218 HIS
n  32 ASN
n  91 ASN
n 182 GLN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  22 GLN
M 120 ASN
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6780  Z= 0.171
  Angle     :  0.555   9.050   9184  Z= 0.290
  Chirality :  0.046   0.195   1028
  Planarity :  0.005   0.047   1144
  Dihedral  :  5.200  54.640    890
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 18.00 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.20 (0.28), residues: 808
  helix: -3.72 (0.73), residues: 22
  sheet: -0.28 (0.27), residues: 414
  loop : -2.77 (0.26), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP n 198 
 HIS   0.004   0.001   HIS n 169 
 PHE   0.012   0.001   PHE m 180 
 TYR   0.016   0.001   TYR m 192 
 ARG   0.004   0.000   ARG m 137 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 109
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
REVERT: m   33 MET cc_start: 0.7164 (tpp) cc_final: 0.6948 (tpp)
REVERT: m   46 GLU cc_start: 0.8239 (tt0) cc_final: 0.7959 (tt0)
REVERT: n  111 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5130 (t80)
REVERT: N   16 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7427 (mmt180)
  outliers start: 46
  outliers final: 38
  residues processed: 140
  average time/residue: 0.2526
  time to fit residues: 48.2710
Evaluate side-chains
  143 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 104
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   25 THR
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue  103 LEU
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  146 VAL
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  206 VAL
Chi-restraints excluded: chain m residue  207 THR
Chi-restraints excluded: chain m residue  217 VAL
Chi-restraints excluded: chain m residue  224 VAL
Chi-restraints excluded: chain n residue   15 THR
Chi-restraints excluded: chain n residue   25 THR
Chi-restraints excluded: chain n residue   56 SER
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   77 ARG
Chi-restraints excluded: chain n residue   87 ASN
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue  111 TYR
Chi-restraints excluded: chain n residue  124 THR
Chi-restraints excluded: chain n residue  128 LEU
Chi-restraints excluded: chain n residue  159 GLU
Chi-restraints excluded: chain n residue  171 GLN
Chi-restraints excluded: chain n residue  181 SER
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   22 GLN
Chi-restraints excluded: chain M residue   25 THR
Chi-restraints excluded: chain M residue   30 SER
Chi-restraints excluded: chain M residue   47 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  146 VAL
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain M residue  210 VAL
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   48 GLN
Chi-restraints excluded: chain N residue   98 CYS
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  153 THR
Chi-restraints excluded: chain N residue  189 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
m 218 HIS
n  91 ASN
n 182 GLN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  22 GLN
M 120 ASN
N 210 HIS
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6780  Z= 0.203
  Angle     :  0.578   9.641   9184  Z= 0.302
  Chirality :  0.047   0.205   1028
  Planarity :  0.005   0.050   1144
  Dihedral  :  4.910  43.512    888
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 19.07 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.12 (0.28), residues: 808
  helix: -3.36 (0.81), residues: 22
  sheet: -0.18 (0.27), residues: 408
  loop : -2.77 (0.26), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP n 198 
 HIS   0.005   0.001   HIS n 169 
 PHE   0.011   0.002   PHE N 196 
 TYR   0.015   0.001   TYR N  52 
 ARG   0.003   0.000   ARG N  49 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 105
  time to evaluate  : 0.837 
Fit side-chains
REVERT: m   33 MET cc_start: 0.7200 (tpp) cc_final: 0.6949 (tpp)
REVERT: m   46 GLU cc_start: 0.8246 (tt0) cc_final: 0.7950 (tt0)
REVERT: n  111 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5161 (t80)
REVERT: N   16 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.7468 (mmt180)
  outliers start: 45
  outliers final: 37
  residues processed: 139
  average time/residue: 0.1819
  time to fit residues: 33.8123
Evaluate side-chains
  135 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 97
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   25 THR
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue  103 LEU
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  146 VAL
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  206 VAL
Chi-restraints excluded: chain m residue  217 VAL
Chi-restraints excluded: chain n residue   15 THR
Chi-restraints excluded: chain n residue   25 THR
Chi-restraints excluded: chain n residue   56 SER
Chi-restraints excluded: chain n residue   62 LEU
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   77 ARG
Chi-restraints excluded: chain n residue   87 ASN
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue   98 CYS
Chi-restraints excluded: chain n residue  111 TYR
Chi-restraints excluded: chain n residue  128 LEU
Chi-restraints excluded: chain n residue  159 GLU
Chi-restraints excluded: chain n residue  171 GLN
Chi-restraints excluded: chain n residue  181 SER
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   22 GLN
Chi-restraints excluded: chain M residue   30 SER
Chi-restraints excluded: chain M residue   47 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  146 VAL
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain M residue  210 VAL
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   48 GLN
Chi-restraints excluded: chain N residue   98 CYS
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  153 THR
Chi-restraints excluded: chain N residue  189 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
m 193 ASN
m 218 HIS
n  91 ASN
n 182 GLN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  22 GLN
M 120 ASN
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.3966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6780  Z= 0.204
  Angle     :  0.584   9.429   9184  Z= 0.303
  Chirality :  0.047   0.216   1028
  Planarity :  0.005   0.049   1144
  Dihedral  :  4.631  26.855    885
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 19.07 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.11 (0.28), residues: 808
  helix: -3.22 (0.82), residues: 22
  sheet: -0.25 (0.27), residues: 414
  loop : -2.71 (0.26), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP M  49 
 HIS   0.004   0.001   HIS n 169 
 PHE   0.014   0.002   PHE n 162 
 TYR   0.016   0.001   TYR n  53 
 ARG   0.007   0.000   ARG m 137 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 103
  time to evaluate  : 0.887 
Fit side-chains
REVERT: m   46 GLU cc_start: 0.8253 (tt0) cc_final: 0.7948 (tt0)
REVERT: n  111 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5166 (t80)
REVERT: M  125 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8720 (mp)
REVERT: N   16 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7478 (mmt180)
  outliers start: 46
  outliers final: 43
  residues processed: 138
  average time/residue: 0.1762
  time to fit residues: 32.9781
Evaluate side-chains
  144 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 99
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   25 THR
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue  103 LEU
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  146 VAL
Chi-restraints excluded: chain m residue  149 MET
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  206 VAL
Chi-restraints excluded: chain m residue  217 VAL
Chi-restraints excluded: chain n residue   25 THR
Chi-restraints excluded: chain n residue   56 SER
Chi-restraints excluded: chain n residue   62 LEU
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   77 ARG
Chi-restraints excluded: chain n residue   87 ASN
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue   91 ASN
Chi-restraints excluded: chain n residue   98 CYS
Chi-restraints excluded: chain n residue  111 TYR
Chi-restraints excluded: chain n residue  128 LEU
Chi-restraints excluded: chain n residue  159 GLU
Chi-restraints excluded: chain n residue  171 GLN
Chi-restraints excluded: chain n residue  181 SER
Chi-restraints excluded: chain n residue  194 MET
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   22 GLN
Chi-restraints excluded: chain M residue   25 THR
Chi-restraints excluded: chain M residue   30 SER
Chi-restraints excluded: chain M residue   43 CYS
Chi-restraints excluded: chain M residue   47 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  119 LEU
Chi-restraints excluded: chain M residue  120 ASN
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  146 VAL
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain M residue  210 VAL
Chi-restraints excluded: chain N residue   15 THR
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   98 CYS
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  153 THR
Chi-restraints excluded: chain N residue  189 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0040
   chunk 49 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 67 optimal weight:    4.9990
   overall best weight:    1.0996

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

Flipped N/Q/H residues before XYZ refinement:
m 218 HIS
n  91 ASN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
n 218 ASN
M  22 GLN
M 102 GLN
M 120 ASN
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6780  Z= 0.261
  Angle     :  0.627  10.922   9184  Z= 0.325
  Chirality :  0.049   0.213   1028
  Planarity :  0.005   0.052   1144
  Dihedral  :  4.849  31.992    885
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 19.33 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.14 (0.28), residues: 808
  helix: -2.96 (0.88), residues: 22
  sheet: -0.31 (0.27), residues: 414
  loop : -2.69 (0.26), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP n 198 
 HIS   0.006   0.001   HIS n 169 
 PHE   0.015   0.002   PHE N 162 
 TYR   0.018   0.002   TYR n  53 
 ARG   0.007   0.001   ARG m 137 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 102
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
REVERT: m   46 GLU cc_start: 0.8268 (tt0) cc_final: 0.7961 (tt0)
REVERT: n  111 TYR cc_start: 0.6301 (OUTLIER) cc_final: 0.5264 (t80)
REVERT: M  125 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8730 (mp)
  outliers start: 47
  outliers final: 42
  residues processed: 138
  average time/residue: 0.1490
  time to fit residues: 27.7936
Evaluate side-chains
  144 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 100
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   25 THR
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue   98 ILE
Chi-restraints excluded: chain m residue  103 LEU
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  146 VAL
Chi-restraints excluded: chain m residue  149 MET
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  206 VAL
Chi-restraints excluded: chain m residue  217 VAL
Chi-restraints excluded: chain n residue   25 THR
Chi-restraints excluded: chain n residue   56 SER
Chi-restraints excluded: chain n residue   62 LEU
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   77 ARG
Chi-restraints excluded: chain n residue   87 ASN
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue   91 ASN
Chi-restraints excluded: chain n residue   98 CYS
Chi-restraints excluded: chain n residue  111 TYR
Chi-restraints excluded: chain n residue  128 LEU
Chi-restraints excluded: chain n residue  159 GLU
Chi-restraints excluded: chain n residue  171 GLN
Chi-restraints excluded: chain n residue  194 MET
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   22 GLN
Chi-restraints excluded: chain M residue   30 SER
Chi-restraints excluded: chain M residue   43 CYS
Chi-restraints excluded: chain M residue   47 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  133 THR
Chi-restraints excluded: chain M residue  146 VAL
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain M residue  210 VAL
Chi-restraints excluded: chain N residue   18 THR
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   98 CYS
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  153 THR
Chi-restraints excluded: chain N residue  159 GLU
Chi-restraints excluded: chain N residue  189 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
m 218 HIS
n  91 ASN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  77 ASN
M 120 ASN
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6780  Z= 0.336
  Angle     :  0.695  12.916   9184  Z= 0.359
  Chirality :  0.050   0.220   1028
  Planarity :  0.005   0.056   1144
  Dihedral  :  5.167  31.441    885
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 19.60 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.22 (0.28), residues: 808
  helix: -2.86 (0.91), residues: 22
  sheet: -0.36 (0.26), residues: 412
  loop : -2.75 (0.25), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP n 198 
 HIS   0.005   0.001   HIS n 169 
 PHE   0.018   0.002   PHE N 196 
 TYR   0.021   0.002   TYR n  53 
 ARG   0.007   0.001   ARG m 137 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 99
  time to evaluate  : 0.897 
Fit side-chains
REVERT: m   46 GLU cc_start: 0.8290 (tt0) cc_final: 0.7981 (tt0)
REVERT: M   76 GLN cc_start: 0.7539 (tt0) cc_final: 0.7248 (tt0)
REVERT: M  125 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8727 (mp)
REVERT: M  161 GLU cc_start: 0.6276 (mt-10) cc_final: 0.5843 (mt-10)
REVERT: M  191 LYS cc_start: 0.6808 (mppt) cc_final: 0.6282 (mppt)
  outliers start: 44
  outliers final: 42
  residues processed: 134
  average time/residue: 0.1910
  time to fit residues: 34.3697
Evaluate side-chains
  138 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 95
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   25 THR
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue   98 ILE
Chi-restraints excluded: chain m residue  103 LEU
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  146 VAL
Chi-restraints excluded: chain m residue  149 MET
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  206 VAL
Chi-restraints excluded: chain m residue  217 VAL
Chi-restraints excluded: chain n residue   25 THR
Chi-restraints excluded: chain n residue   56 SER
Chi-restraints excluded: chain n residue   62 LEU
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   77 ARG
Chi-restraints excluded: chain n residue   87 ASN
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue   91 ASN
Chi-restraints excluded: chain n residue   98 CYS
Chi-restraints excluded: chain n residue  159 GLU
Chi-restraints excluded: chain n residue  171 GLN
Chi-restraints excluded: chain n residue  194 MET
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   30 SER
Chi-restraints excluded: chain M residue   43 CYS
Chi-restraints excluded: chain M residue   47 THR
Chi-restraints excluded: chain M residue   77 ASN
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  120 ASN
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  133 THR
Chi-restraints excluded: chain M residue  146 VAL
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain M residue  210 VAL
Chi-restraints excluded: chain N residue   18 THR
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   98 CYS
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  153 THR
Chi-restraints excluded: chain N residue  159 GLU
Chi-restraints excluded: chain N residue  189 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 73 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0970
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
n  91 ASN
n 182 GLN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 120 ASN
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6780  Z= 0.180
  Angle     :  0.599  10.576   9184  Z= 0.313
  Chirality :  0.047   0.234   1028
  Planarity :  0.005   0.048   1144
  Dihedral  :  4.785  36.656    885
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 20.53 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.95 (0.28), residues: 808
  helix: -2.52 (0.99), residues: 22
  sheet: -0.23 (0.27), residues: 400
  loop : -2.44 (0.26), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP n 198 
 HIS   0.005   0.001   HIS n 169 
 PHE   0.015   0.001   PHE m 180 
 TYR   0.017   0.001   TYR n  53 
 ARG   0.007   0.000   ARG m 137 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 0.760 
Fit side-chains
REVERT: m   46 GLU cc_start: 0.8268 (tt0) cc_final: 0.7959 (tt0)
REVERT: M   75 GLU cc_start: 0.6996 (tp30) cc_final: 0.6742 (tp30)
REVERT: M   76 GLN cc_start: 0.7556 (tt0) cc_final: 0.7289 (tt0)
REVERT: M  125 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8720 (mp)
REVERT: M  161 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5821 (mt-10)
  outliers start: 37
  outliers final: 34
  residues processed: 131
  average time/residue: 0.1858
  time to fit residues: 32.9696
Evaluate side-chains
  134 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 99
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain m residue   25 THR
Chi-restraints excluded: chain m residue   31 VAL
Chi-restraints excluded: chain m residue   98 ILE
Chi-restraints excluded: chain m residue  103 LEU
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  121 THR
Chi-restraints excluded: chain m residue  146 VAL
Chi-restraints excluded: chain m residue  149 MET
Chi-restraints excluded: chain m residue  178 THR
Chi-restraints excluded: chain m residue  206 VAL
Chi-restraints excluded: chain m residue  217 VAL
Chi-restraints excluded: chain n residue   25 THR
Chi-restraints excluded: chain n residue   56 SER
Chi-restraints excluded: chain n residue   62 LEU
Chi-restraints excluded: chain n residue   66 LEU
Chi-restraints excluded: chain n residue   77 ARG
Chi-restraints excluded: chain n residue   87 ASN
Chi-restraints excluded: chain n residue   89 ILE
Chi-restraints excluded: chain n residue   98 CYS
Chi-restraints excluded: chain n residue  159 GLU
Chi-restraints excluded: chain n residue  171 GLN
Chi-restraints excluded: chain n residue  200 THR
Chi-restraints excluded: chain M residue   43 CYS
Chi-restraints excluded: chain M residue   47 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  133 THR
Chi-restraints excluded: chain M residue  146 VAL
Chi-restraints excluded: chain M residue  187 SER
Chi-restraints excluded: chain M residue  210 VAL
Chi-restraints excluded: chain N residue   98 CYS
Chi-restraints excluded: chain N residue  124 THR
Chi-restraints excluded: chain N residue  142 SER
Chi-restraints excluded: chain N residue  159 GLU
Chi-restraints excluded: chain N residue  189 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0870
   chunk 17 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 65 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
n  91 ASN
** n 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 120 ASN
** N 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.173643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.148580 restraints weight = 8662.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.77
r_work: 0.3525 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3524
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.4243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6780  Z= 0.172
  Angle     :  0.569   9.408   9184  Z= 0.297
  Chirality :  0.047   0.234   1028
  Planarity :  0.005   0.047   1144
  Dihedral  :  4.532  33.832    885
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 20.27 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.79 (0.29), residues: 808
  helix: -2.18 (1.07), residues: 22
  sheet: -0.13 (0.27), residues: 402
  loop : -2.36 (0.26), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP n 198 
 HIS   0.005   0.001   HIS n 169 
 PHE   0.015   0.001   PHE m 180 
 TYR   0.015   0.001   TYR n  53 
 ARG   0.007   0.000   ARG m 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1807.38 seconds
wall clock time: 37 minutes 40.47 seconds (2260.47 seconds total)