Starting phenix.real_space_refine
on Tue Feb 11 17:51:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fja_29220/02_2025/8fja_29220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fja_29220/02_2025/8fja_29220.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fja_29220/02_2025/8fja_29220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fja_29220/02_2025/8fja_29220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fja_29220/02_2025/8fja_29220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fja_29220/02_2025/8fja_29220.cif"
  }
  resolution = 3.0
  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=   0.000 sd=   1.000
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      27      5.16       5
     C    4024      2.51       5
     N    1117      2.21       5
     O    1251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6419
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 1645
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 214, 1645
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203}
    Chain: "E"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1620
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2237
          Classifications: {'peptide': 274}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 262}
    Chain: "B"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 837
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94}
    Chain: "C"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 80
          Classifications: {'peptide': 10}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 9}
  Time building chain proxies: 4.96, per 1000 atoms: 0.77
  Number of scatterers: 6419
  At special positions: 0
  Unit cell: (138.55, 103.7, 68.85, 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      27     16.00
     O    1251      8.00
     N    1117      7.00
     C    4024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 134 " - pdb=" SG  CYS D 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 214 " - pdb=" SG  CYS E 135 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 148 " - pdb=" SG  CYS E 204 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 101 " - pdb=" SG  CYS A 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 259 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  80 " distance=2.03

  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: 1.31
  Conformation dependent library (CDL) restraints added in 863.6 milliseconds
  

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1510

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 19 sheets defined
      13.2% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'D' and resid 121 through 125
      removed outlier: 3.618A  pdb=" N   LEU D 125 " --> pdb=" O   ASP D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 186
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.861A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.074A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 193 through 197
      removed outlier: 3.703A  pdb=" N   LEU E 197 " --> pdb=" O   SER E 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 53
      removed outlier: 3.545A  pdb=" N   ILE A  52 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU A  53 " --> pdb=" O   PRO A  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 49 through 53'
    Processing helix  chain 'A' and resid 56 through 85
      removed outlier: 3.620A  pdb=" N   TRP A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 149
      removed outlier: 4.173A  pdb=" N   THR A 142 " --> pdb=" O   MET A 138 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   THR A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 161
      removed outlier: 4.045A  pdb=" N   GLN A 155 " --> pdb=" O   HIS A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 175
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 252 through 255
      removed outlier: 4.498A  pdb=" N   GLN A 255 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 252 through 255'
    Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.937A  pdb=" N   ASP D  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER D  67 " --> pdb=" O   ASP D  70 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.512A  pdb=" N   ALA D  13 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 54
      removed outlier: 6.735A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   TYR D  49 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   LEU D  33 " --> pdb=" O   TYR D  49 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR D  97 " --> pdb=" O   GLN D  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 115
      removed outlier: 4.281A  pdb=" N   SER D 114 " --> pdb=" O   ASN D 137 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ASN D 137 " --> pdb=" O   SER D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 145 through 149
      removed outlier: 4.351A  pdb=" N   LYS D 145 " --> pdb=" O   THR D 197 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR D 197 " --> pdb=" O   LYS D 145 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LYS D 149 " --> pdb=" O   ALA D 193 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA D 193 " --> pdb=" O   LYS D 149 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 159 through 160
    Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 164
      removed outlier: 4.076A  pdb=" N   SER D 174 " --> pdb=" O   THR D 164 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.871A  pdb=" N   MET E  34 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   GLY E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.530A  pdb=" N   VAL E 110 " --> pdb=" O   LYS E  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 131
      removed outlier: 3.521A  pdb=" N   SER E 128 " --> pdb=" O   LYS E 151 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ALA E 145 " --> pdb=" O   VAL E 192 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL E 192 " --> pdb=" O   ALA E 145 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   GLY E 147 " --> pdb=" O   VAL E 190 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   VAL E 190 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
      removed outlier: 5.720A  pdb=" N   LEU E 149 " --> pdb=" O   SER E 188 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   SER E 188 " --> pdb=" O   LEU E 149 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   LYS E 151 " --> pdb=" O   LEU E 186 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   LEU E 186 " --> pdb=" O   LYS E 151 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   TYR E 153 " --> pdb=" O   TYR E 184 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   SER E 187 " --> pdb=" O   PRO E 175 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   VAL E 189 " --> pdb=" O   THR E 173 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   THR E 173 " --> pdb=" O   VAL E 189 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 161 through 162
      removed outlier: 4.269A  pdb=" N   CYS E 204 " --> pdb=" O   LYS E 217 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   LYS E 217 " --> pdb=" O   CYS E 204 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 46 through 47
      removed outlier: 6.861A  pdb=" N   GLY A  26 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ALA A  24 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ASP A  37 " --> pdb=" O   PHE A  22 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   PHE A  22 " --> pdb=" O   ASP A  37 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG A 111 " --> pdb=" O   ASP A 102 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   HIS A 114 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE A 124 " --> pdb=" O   TYR A 116 " (cutoff:3.500A)
      removed outlier: 5.388A  pdb=" N   TYR A 118 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   ASP A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 186 through 193
      removed outlier: 3.573A  pdb=" N   HIS A 188 " --> pdb=" O   TRP A 204 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   PHE A 241 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 186 through 193
      removed outlier: 3.573A  pdb=" N   HIS A 188 " --> pdb=" O   TRP A 204 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   PHE A 241 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 222 through 223
      removed outlier: 3.536A  pdb=" N   VAL A 261 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 6 through 11
      removed outlier: 5.772A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 6 through 11
      removed outlier: 5.772A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   SER B  55 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 44 through 45

    259 hydrogen bonds defined for protein.
    660 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: 1.79

  Time building geometry restraints manager: 1.55 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: 2110
        1.34 -     1.46: 1654
        1.46 -     1.58: 2778
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 6580
  Sorted by residual:
  bond pdb=" CG  ARG A   6 "
       pdb=" CD  ARG A   6 "
    ideal  model  delta    sigma   weight residual
    1.520  1.478  0.042 3.00e-02 1.11e+03 2.00e+00
  bond pdb=" CB  PRO B  32 "
       pdb=" CG  PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.506  1.453  0.053 3.90e-02 6.57e+02 1.82e+00
  bond pdb=" SD  MET E 108 "
       pdb=" CE  MET E 108 "
    ideal  model  delta    sigma   weight residual
    1.791  1.758  0.033 2.50e-02 1.60e+03 1.79e+00
  bond pdb=" CD  LYS B  19 "
       pdb=" CE  LYS B  19 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.73e+00
  bond pdb=" CB  PRO A 210 "
       pdb=" CG  PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.506  1.457  0.049 3.90e-02 6.57e+02 1.56e+00
  ... (remaining 6575 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 8557
        1.78 -     3.56: 308
        3.56 -     5.34: 47
        5.34 -     7.13: 12
        7.13 -     8.91: 9
  Bond angle restraints: 8933
  Sorted by residual:
  angle pdb=" CA  ARG E 218 "
        pdb=" CB  ARG E 218 "
        pdb=" CG  ARG E 218 "
      ideal   model   delta    sigma   weight residual
     114.10  122.84   -8.74 2.00e+00 2.50e-01 1.91e+01
  angle pdb=" N   ARG A  17 "
        pdb=" CA  ARG A  17 "
        pdb=" C   ARG A  17 "
      ideal   model   delta    sigma   weight residual
     107.49  116.40   -8.91 2.16e+00 2.14e-01 1.70e+01
  angle pdb=" C   GLU B  16 "
        pdb=" CA  GLU B  16 "
        pdb=" CB  GLU B  16 "
      ideal   model   delta    sigma   weight residual
     109.70  117.03   -7.33 1.81e+00 3.05e-01 1.64e+01
  angle pdb=" C   LYS B  75 "
        pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
      ideal   model   delta    sigma   weight residual
     121.81  129.99   -8.18 2.16e+00 2.14e-01 1.43e+01
  angle pdb=" N   ASN B  17 "
        pdb=" CA  ASN B  17 "
        pdb=" C   ASN B  17 "
      ideal   model   delta    sigma   weight residual
     110.10  115.20   -5.10 1.49e+00 4.50e-01 1.17e+01
  ... (remaining 8928 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 3561
       16.59 -    33.19: 283
       33.19 -    49.78: 45
       49.78 -    66.38: 11
       66.38 -    82.97: 8
  Dihedral angle restraints: 3908
    sinusoidal: 1554
      harmonic: 2354
  Sorted by residual:
  dihedral pdb=" CB  CYS E 148 "
           pdb=" SG  CYS E 148 "
           pdb=" SG  CYS E 204 "
           pdb=" CB  CYS E 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.03  -50.03     1      1.00e+01 1.00e-02 3.43e+01
  dihedral pdb=" CB  CYS D  23 "
           pdb=" SG  CYS D  23 "
           pdb=" SG  CYS D  88 "
           pdb=" CB  CYS D  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.16   40.84     1      1.00e+01 1.00e-02 2.34e+01
  dihedral pdb=" CB  CYS B  25 "
           pdb=" SG  CYS B  25 "
           pdb=" SG  CYS B  80 "
           pdb=" CB  CYS B  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -113.49   27.49     1      1.00e+01 1.00e-02 1.08e+01
  ... (remaining 3905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 587
       0.040 -    0.080: 266
       0.080 -    0.119: 68
       0.119 -    0.159: 29
       0.159 -    0.199: 7
  Chirality restraints: 957
  Sorted by residual:
  chirality pdb=" CA  LYS B  19 "
            pdb=" N   LYS B  19 "
            pdb=" C   LYS B  19 "
            pdb=" CB  LYS B  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" CB  THR E 173 "
            pdb=" CA  THR E 173 "
            pdb=" OG1 THR E 173 "
            pdb=" CG2 THR E 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" CB  ILE D 106 "
            pdb=" CA  ILE D 106 "
            pdb=" CG1 ILE D 106 "
            pdb=" CG2 ILE D 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 954 not shown)

  Planarity restraints: 1157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 174 "   -0.064 5.00e-02 4.00e+02   9.64e-02 1.49e+01
        pdb=" N   PRO E 175 "    0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO E 175 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO E 175 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D  79 "    0.061 5.00e-02 4.00e+02   9.21e-02 1.36e+01
        pdb=" N   PRO D  80 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO D  80 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO D  80 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  19 "    0.044 5.00e-02 4.00e+02   6.69e-02 7.16e+00
        pdb=" N   PRO A  20 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A  20 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  20 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1154 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 914
        2.76 -     3.29: 5434
        3.29 -     3.83: 9750
        3.83 -     4.36: 12022
        4.36 -     4.90: 21803
  Nonbonded interactions: 49923
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 255 "
            pdb=" NH2 ARG A 273 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" NE2 GLN D 147 "
            pdb=" O   GLN D 155 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OD2 ASP A 220 "
            pdb=" NH1 ARG A 256 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   SER E 196 "
            pdb=" OG  SER E 196 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   GLN D 124 "
            pdb=" OG  SER D 127 "
     model   vdw
     2.331 3.040
  ... (remaining 49918 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 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:             1.910
  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:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     18.630
  Find NCS groups from input model:        0.070
  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:13.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
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      :  0.007   0.053   6580  Z= 0.453
  Angle     :  0.818   8.907   8933  Z= 0.432
  Chirality :  0.051   0.199    957
  Planarity :  0.006   0.096   1157
  Dihedral  : 12.620  82.970   2374
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    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: -2.60 (0.27), residues: 800
  helix: -1.37 (0.52), residues: 79
  sheet: -1.37 (0.27), residues: 333
  loop : -2.06 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP E 100 
 HIS   0.007   0.001   HIS E 208 
 PHE   0.031   0.002   PHE B  70 
 TYR   0.025   0.002   TYR A 113 
 ARG   0.014   0.001   ARG A   6 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: E   73 ASP cc_start: 0.8497 (t70) cc_final: 0.8252 (t70)
REVERT: E  108 MET cc_start: 0.8701 (mpp) cc_final: 0.8219 (mpt)
REVERT: A  173 GLU cc_start: 0.8080 (tp30) cc_final: 0.7730 (tp30)
REVERT: A  219 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8290 (ttt-90)
REVERT: A  255 GLN cc_start: 0.9172 (mm110) cc_final: 0.8836 (mm110)
REVERT: B   76 ASP cc_start: 0.8614 (m-30) cc_final: 0.8387 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 1.7671
  time to fit residues: 152.0890
Evaluate side-chains
  76 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  72 GLN
A 224 GLN
B  17 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.141920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.076936 restraints weight = 8508.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.77
r_work: 0.2695 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2544 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2592 r_free = 0.2592    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2591 r_free = 0.2591    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6580  Z= 0.241
  Angle     :  0.604   6.657   8933  Z= 0.321
  Chirality :  0.044   0.148    957
  Planarity :  0.005   0.069   1157
  Dihedral  :  4.740  21.889    890
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.40 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    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: -1.59 (0.29), residues: 800
  helix: -0.39 (0.57), residues: 78
  sheet: -0.68 (0.28), residues: 339
  loop : -1.47 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 100 
 HIS   0.004   0.001   HIS E 208 
 PHE   0.014   0.001   PHE B  70 
 TYR   0.014   0.001   TYR A  99 
 ARG   0.004   0.001   ARG D  40 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.734 
Fit side-chains
REVERT: D  165 GLU cc_start: 0.8091 (pt0) cc_final: 0.7875 (pt0)
REVERT: E    3 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8181 (mm-40)
REVERT: A   58 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7467 (mp0)
REVERT: A  113 TYR cc_start: 0.8429 (m-80) cc_final: 0.8161 (m-80)
REVERT: A  121 LYS cc_start: 0.9108 (ptpp) cc_final: 0.8789 (ptpp)
REVERT: A  173 GLU cc_start: 0.8753 (tp30) cc_final: 0.8355 (tp30)
REVERT: A  212 GLU cc_start: 0.9003 (tt0) cc_final: 0.8787 (tp30)
REVERT: A  255 GLN cc_start: 0.9321 (mm110) cc_final: 0.8861 (mm110)
REVERT: B   76 ASP cc_start: 0.8907 (m-30) cc_final: 0.8701 (m-30)
  outliers start: 7
  outliers final: 1
  residues processed: 72
  average time/residue: 1.8954
  time to fit residues: 141.8024
Evaluate side-chains
  69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 19 optimal weight:   20.0000
   chunk 68 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.139738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.078726 restraints weight = 8653.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 3.44
r_work: 0.2643 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2491 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2491
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2536 r_free = 0.2536    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2536 r_free = 0.2536    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
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   0.031   6580  Z= 0.284
  Angle     :  0.576   6.110   8933  Z= 0.305
  Chirality :  0.044   0.157    957
  Planarity :  0.005   0.063   1157
  Dihedral  :  4.637  23.497    890
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.67 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    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 (0.29), residues: 800
  helix: -0.07 (0.59), residues: 78
  sheet: -0.27 (0.28), residues: 335
  loop : -1.24 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 100 
 HIS   0.004   0.001   HIS E  95 
 PHE   0.014   0.002   PHE B  70 
 TYR   0.013   0.001   TYR A  99 
 ARG   0.003   0.000   ARG B  81 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7540 (mp0)
REVERT: A  113 TYR cc_start: 0.8522 (m-80) cc_final: 0.8083 (m-80)
REVERT: A  121 LYS cc_start: 0.9111 (ptpp) cc_final: 0.8819 (ptpp)
REVERT: A  173 GLU cc_start: 0.8837 (tp30) cc_final: 0.8426 (tp30)
REVERT: A  212 GLU cc_start: 0.9067 (tt0) cc_final: 0.8846 (tp30)
REVERT: A  255 GLN cc_start: 0.9319 (mm110) cc_final: 0.8864 (mm110)
REVERT: B   19 LYS cc_start: 0.9095 (ptpp) cc_final: 0.8870 (ptpp)
REVERT: B   76 ASP cc_start: 0.8897 (m-30) cc_final: 0.8640 (m-30)
  outliers start: 8
  outliers final: 2
  residues processed: 71
  average time/residue: 1.8034
  time to fit residues: 132.9907
Evaluate side-chains
  67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9980
   chunk 15 optimal weight:   20.0000
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   chunk 49 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.140294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.077377 restraints weight = 8675.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.70
r_work: 0.2705 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2558 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2604
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2604 r_free = 0.2604    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2604 r_free = 0.2604    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6580  Z= 0.207
  Angle     :  0.525   5.423   8933  Z= 0.279
  Chirality :  0.042   0.142    957
  Planarity :  0.004   0.063   1157
  Dihedral  :  4.424  22.868    890
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.24 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.30), residues: 800
  helix: -0.12 (0.57), residues: 84
  sheet: -0.03 (0.29), residues: 335
  loop : -1.13 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 100 
 HIS   0.003   0.001   HIS E 208 
 PHE   0.010   0.001   PHE D  91 
 TYR   0.011   0.001   TYR A  99 
 ARG   0.004   0.000   ARG E  16 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  183 LEU cc_start: 0.8569 (mm) cc_final: 0.8302 (mm)
REVERT: A   58 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7563 (mp0)
REVERT: A  113 TYR cc_start: 0.8409 (m-80) cc_final: 0.7897 (m-80)
REVERT: A  121 LYS cc_start: 0.9029 (ptpp) cc_final: 0.8783 (ptpp)
REVERT: A  212 GLU cc_start: 0.8961 (tt0) cc_final: 0.8736 (tp30)
REVERT: A  255 GLN cc_start: 0.9283 (mm110) cc_final: 0.8844 (mm110)
REVERT: A  256 ARG cc_start: 0.8815 (mtm180) cc_final: 0.8508 (mtm110)
REVERT: B   76 ASP cc_start: 0.8868 (m-30) cc_final: 0.8626 (m-30)
  outliers start: 9
  outliers final: 3
  residues processed: 70
  average time/residue: 1.9691
  time to fit residues: 143.4955
Evaluate side-chains
  67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  225 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.139681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.076441 restraints weight = 8590.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.69
r_work: 0.2691 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2544 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2592 r_free = 0.2592    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2592 r_free = 0.2592    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6580  Z= 0.233
  Angle     :  0.524   5.327   8933  Z= 0.279
  Chirality :  0.042   0.147    957
  Planarity :  0.004   0.058   1157
  Dihedral  :  4.385  23.900    890
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 12.38 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.30), residues: 800
  helix: -0.03 (0.57), residues: 84
  sheet:  0.13 (0.28), residues: 335
  loop : -1.09 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 100 
 HIS   0.003   0.001   HIS E  95 
 PHE   0.011   0.001   PHE D  91 
 TYR   0.012   0.001   TYR B  63 
 ARG   0.003   0.000   ARG E  16 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: D  165 GLU cc_start: 0.7956 (pt0) cc_final: 0.7686 (pt0)
REVERT: E  104 ASN cc_start: 0.8983 (m110) cc_final: 0.8631 (m110)
REVERT: E  183 LEU cc_start: 0.8510 (mm) cc_final: 0.8251 (mm)
REVERT: A   58 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7571 (mp0)
REVERT: A  113 TYR cc_start: 0.8393 (m-80) cc_final: 0.7861 (m-80)
REVERT: A  121 LYS cc_start: 0.9058 (ptpp) cc_final: 0.8806 (ptpp)
REVERT: B   76 ASP cc_start: 0.8869 (m-30) cc_final: 0.8641 (m-30)
REVERT: B   94 LYS cc_start: 0.9253 (mttt) cc_final: 0.9004 (mttm)
  outliers start: 5
  outliers final: 3
  residues processed: 68
  average time/residue: 1.7793
  time to fit residues: 125.6346
Evaluate side-chains
  63 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 61 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 39 optimal weight:   20.0000
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 13 optimal weight:   20.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.141729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.077397 restraints weight = 8545.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.71
r_work: 0.2702 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2551 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2551
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2599 r_free = 0.2599    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2599 r_free = 0.2599    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6580  Z= 0.183
  Angle     :  0.499   5.207   8933  Z= 0.266
  Chirality :  0.041   0.141    957
  Planarity :  0.004   0.055   1157
  Dihedral  :  4.269  22.744    890
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.66 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.30), residues: 800
  helix:  0.15 (0.58), residues: 84
  sheet:  0.21 (0.29), residues: 333
  loop : -1.00 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 100 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.009   0.001   PHE D  91 
 TYR   0.010   0.001   TYR A  99 
 ARG   0.004   0.000   ARG E  16 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.708 
Fit side-chains
REVERT: D  165 GLU cc_start: 0.7962 (pt0) cc_final: 0.7702 (pt0)
REVERT: E  104 ASN cc_start: 0.8993 (m110) cc_final: 0.8693 (m110)
REVERT: E  183 LEU cc_start: 0.8563 (mm) cc_final: 0.8328 (mm)
REVERT: A   58 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7598 (mp0)
REVERT: A  113 TYR cc_start: 0.8394 (m-80) cc_final: 0.7886 (m-80)
REVERT: A  121 LYS cc_start: 0.9077 (ptpp) cc_final: 0.8846 (ptpp)
REVERT: B   76 ASP cc_start: 0.8868 (m-30) cc_final: 0.8631 (m-30)
REVERT: B   94 LYS cc_start: 0.9270 (mttt) cc_final: 0.8940 (mttm)
  outliers start: 9
  outliers final: 3
  residues processed: 67
  average time/residue: 1.7760
  time to fit residues: 123.7917
Evaluate side-chains
  61 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  116 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0020
   chunk 79 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.141638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.078456 restraints weight = 8609.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 2.68
r_work: 0.2729 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6580  Z= 0.157
  Angle     :  0.489   5.066   8933  Z= 0.260
  Chirality :  0.041   0.140    957
  Planarity :  0.004   0.053   1157
  Dihedral  :  4.118  21.924    890
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.09 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.30), residues: 800
  helix:  0.28 (0.59), residues: 84
  sheet:  0.34 (0.29), residues: 332
  loop : -0.85 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 100 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.008   0.001   PHE D  91 
 TYR   0.011   0.001   TYR A  99 
 ARG   0.003   0.000   ARG E  16 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.695 
Fit side-chains
REVERT: D  165 GLU cc_start: 0.7954 (pt0) cc_final: 0.7709 (pt0)
REVERT: E  104 ASN cc_start: 0.8973 (m110) cc_final: 0.8681 (m110)
REVERT: E  183 LEU cc_start: 0.8499 (mm) cc_final: 0.8270 (mm)
REVERT: A   58 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7528 (mp0)
REVERT: A  113 TYR cc_start: 0.8295 (m-80) cc_final: 0.7793 (m-80)
REVERT: A  121 LYS cc_start: 0.8969 (ptpp) cc_final: 0.8725 (ptpp)
REVERT: B   76 ASP cc_start: 0.8791 (m-30) cc_final: 0.8549 (m-30)
REVERT: B   94 LYS cc_start: 0.9252 (mttt) cc_final: 0.8920 (mttm)
  outliers start: 7
  outliers final: 5
  residues processed: 64
  average time/residue: 1.6865
  time to fit residues: 112.3327
Evaluate side-chains
  64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  172 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  116 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 26 optimal weight:    0.2980
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0070
   chunk 63 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.4604

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.138569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.075416 restraints weight = 8694.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 2.64
r_work: 0.2670 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2519 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2519
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2566 r_free = 0.2566    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2566 r_free = 0.2566    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   6580  Z= 0.342
  Angle     :  0.553   5.274   8933  Z= 0.293
  Chirality :  0.044   0.163    957
  Planarity :  0.005   0.051   1157
  Dihedral  :  4.412  26.121    890
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.37 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.30), residues: 800
  helix: -0.03 (0.57), residues: 84
  sheet:  0.26 (0.28), residues: 345
  loop : -0.83 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 100 
 HIS   0.004   0.001   HIS E  95 
 PHE   0.015   0.002   PHE D  91 
 TYR   0.015   0.001   TYR B  63 
 ARG   0.004   0.000   ARG E  16 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.687 
Fit side-chains
REVERT: D  165 GLU cc_start: 0.8055 (pt0) cc_final: 0.7792 (pt0)
REVERT: E  104 ASN cc_start: 0.9016 (m110) cc_final: 0.8652 (m110)
REVERT: E  183 LEU cc_start: 0.8498 (mm) cc_final: 0.8261 (mm)
REVERT: A   58 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7492 (mp0)
REVERT: A  113 TYR cc_start: 0.8453 (m-80) cc_final: 0.7863 (m-80)
REVERT: A  121 LYS cc_start: 0.9060 (ptpp) cc_final: 0.8777 (ptpp)
REVERT: B   76 ASP cc_start: 0.8845 (m-30) cc_final: 0.8635 (m-30)
REVERT: B   94 LYS cc_start: 0.9261 (mttt) cc_final: 0.8927 (mttm)
  outliers start: 8
  outliers final: 3
  residues processed: 63
  average time/residue: 1.7610
  time to fit residues: 115.2798
Evaluate side-chains
  62 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  116 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 58 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0970
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.140991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.077811 restraints weight = 8617.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 2.70
r_work: 0.2712 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2565 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6580  Z= 0.163
  Angle     :  0.491   5.304   8933  Z= 0.261
  Chirality :  0.041   0.140    957
  Planarity :  0.004   0.052   1157
  Dihedral  :  4.180  23.105    890
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.37 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.30), residues: 800
  helix:  0.31 (0.59), residues: 84
  sheet:  0.42 (0.29), residues: 332
  loop : -0.79 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 100 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.008   0.001   PHE D  91 
 TYR   0.010   0.001   TYR A  99 
 ARG   0.005   0.000   ARG D 108 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.694 
Fit side-chains
REVERT: D  165 GLU cc_start: 0.8032 (pt0) cc_final: 0.7711 (pt0)
REVERT: E  104 ASN cc_start: 0.9010 (m110) cc_final: 0.8719 (m110)
REVERT: E  183 LEU cc_start: 0.8544 (mm) cc_final: 0.8313 (mm)
REVERT: A   58 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7552 (mp0)
REVERT: A  113 TYR cc_start: 0.8370 (m-80) cc_final: 0.7875 (m-80)
REVERT: A  121 LYS cc_start: 0.8994 (ptpp) cc_final: 0.8749 (ptpp)
REVERT: B   76 ASP cc_start: 0.8786 (m-30) cc_final: 0.8530 (m-30)
REVERT: B   94 LYS cc_start: 0.9258 (mttt) cc_final: 0.8934 (mttm)
  outliers start: 6
  outliers final: 5
  residues processed: 61
  average time/residue: 1.7850
  time to fit residues: 113.3640
Evaluate side-chains
  62 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  116 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 71 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0770
   chunk 58 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.142813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.077237 restraints weight = 8862.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 2.80
r_work: 0.2695 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2542 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2591 r_free = 0.2591    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2591 r_free = 0.2591    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6580  Z= 0.195
  Angle     :  0.500   5.189   8933  Z= 0.265
  Chirality :  0.041   0.140    957
  Planarity :  0.004   0.051   1157
  Dihedral  :  4.156  22.219    890
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.80 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.30), residues: 800
  helix:  0.29 (0.59), residues: 84
  sheet:  0.44 (0.29), residues: 332
  loop : -0.72 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 100 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.010   0.001   PHE D  91 
 TYR   0.011   0.001   TYR B  63 
 ARG   0.005   0.000   ARG E  16 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.668 
Fit side-chains
REVERT: D  165 GLU cc_start: 0.8018 (pt0) cc_final: 0.7787 (pt0)
REVERT: E  104 ASN cc_start: 0.9013 (m110) cc_final: 0.8724 (m110)
REVERT: E  183 LEU cc_start: 0.8559 (mm) cc_final: 0.8336 (mm)
REVERT: A   58 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7631 (mp0)
REVERT: A  113 TYR cc_start: 0.8435 (m-80) cc_final: 0.7958 (m-80)
REVERT: A  121 LYS cc_start: 0.9065 (ptpp) cc_final: 0.8708 (ptpp)
REVERT: B   76 ASP cc_start: 0.8814 (m-30) cc_final: 0.8592 (m-30)
REVERT: B   94 LYS cc_start: 0.9282 (mttt) cc_final: 0.8977 (mttm)
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 1.7305
  time to fit residues: 108.0770
Evaluate side-chains
  62 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  116 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 47 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9990
   chunk 69 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0040
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.143171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.078487 restraints weight = 8900.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 2.79
r_work: 0.2739 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2590 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2590
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6580  Z= 0.135
  Angle     :  0.470   5.113   8933  Z= 0.250
  Chirality :  0.040   0.138    957
  Planarity :  0.004   0.052   1157
  Dihedral  :  3.960  18.753    890
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.66 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 19.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.31), residues: 800
  helix:  0.47 (0.60), residues: 84
  sheet:  0.43 (0.29), residues: 332
  loop : -0.53 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 244 
 HIS   0.002   0.000   HIS E  35 
 PHE   0.007   0.001   PHE A  33 
 TYR   0.010   0.001   TYR A  99 
 ARG   0.005   0.000   ARG E  16 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5967.22 seconds
wall clock time: 105 minutes 37.12 seconds (6337.12 seconds total)