Starting phenix.real_space_refine
on Thu Mar 13 20:38:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vgn_43212/03_2025/8vgn_43212.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vgn_43212/03_2025/8vgn_43212.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vgn_43212/03_2025/8vgn_43212.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vgn_43212/03_2025/8vgn_43212.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vgn_43212/03_2025/8vgn_43212.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vgn_43212/03_2025/8vgn_43212.cif"
  }
  resolution = 2.5
  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=   0.001 sd=   1.031
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      54      5.16       5
     C    5836      2.51       5
     N    1500      2.21       5
     O    1760      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9150
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1668
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 13, 'TRANS': 210}
    Chain: "B"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1623
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199}
    Chain: "G"
      Number of atoms: 1284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1284
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 7, 'TRANS': 157}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1668
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 13, 'TRANS': 210}
    Chain: "I"
      Number of atoms: 1284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1284
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 7, 'TRANS': 157}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1623
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199}
  Time building chain proxies: 6.61, per 1000 atoms: 0.72
  Number of scatterers: 9150
  At special positions: 0
  Unit cell: (62.6919, 154.39, 124.448, 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      54     16.00
     O    1760      8.00
     N    1500      7.00
     C    5836      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 144 " - pdb=" SG  CYS A 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS B 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 167 " - pdb=" SG  CYS G 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 220 " - pdb=" SG  CYS L 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 167 " - pdb=" SG  CYS I 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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: 2.24
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2224

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 22 sheets defined
      29.7% alpha, 37.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.686A  pdb=" N   TYR A  32 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 64
    Processing helix  chain 'A' and resid 83 through 87
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 160 through 162
      No H-bonds generated for 'chain 'A' and resid 160 through 162'
    Processing helix  chain 'A' and resid 191 through 196
      removed outlier: 4.386A  pdb=" N   THR A 195 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 208
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.518A  pdb=" N   ALA B  83 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
    Processing helix  chain 'B' and resid 183 through 187
    Processing helix  chain 'G' and resid 48 through 71
    Processing helix  chain 'G' and resid 79 through 84
    Processing helix  chain 'G' and resid 85 through 98
    Processing helix  chain 'G' and resid 99 through 102
    Processing helix  chain 'G' and resid 114 through 143
    Processing helix  chain 'G' and resid 152 through 157
    Processing helix  chain 'G' and resid 171 through 176
      removed outlier: 3.832A  pdb=" N   ASN G 176 " --> pdb=" O   SER G 173 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 177 through 219
      removed outlier: 4.569A  pdb=" N   ASN G 214 " --> pdb=" O   GLY G 210 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.686A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'H' and resid 131 through 133
      No H-bonds generated for 'chain 'H' and resid 131 through 133'
    Processing helix  chain 'H' and resid 160 through 162
      No H-bonds generated for 'chain 'H' and resid 160 through 162'
    Processing helix  chain 'H' and resid 191 through 196
      removed outlier: 4.388A  pdb=" N   THR H 195 " --> pdb=" O   SER H 191 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 205 through 208
    Processing helix  chain 'I' and resid 48 through 71
    Processing helix  chain 'I' and resid 79 through 84
    Processing helix  chain 'I' and resid 85 through 98
    Processing helix  chain 'I' and resid 99 through 102
    Processing helix  chain 'I' and resid 114 through 143
    Processing helix  chain 'I' and resid 152 through 157
    Processing helix  chain 'I' and resid 171 through 176
      removed outlier: 3.831A  pdb=" N   ASN I 176 " --> pdb=" O   SER I 173 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 177 through 219
      removed outlier: 4.562A  pdb=" N   ASN I 214 " --> pdb=" O   GLY I 210 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.518A  pdb=" N   ALA L  83 " --> pdb=" O   ALA L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 126
    Processing helix  chain 'L' and resid 183 through 187
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12
      removed outlier: 4.021A  pdb=" N   ASN A  33 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   MET A  34 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ALA A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP A  36 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12
      removed outlier: 7.034A  pdb=" N   CYS A  92 " --> pdb=" O   TRP A 103 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   TRP A 103 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ARG A  94 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASP A 100A" --> pdb=" O   TYR A  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 128
      removed outlier: 5.710A  pdb=" N   TYR A 180 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 136
      removed outlier: 5.710A  pdb=" N   TYR A 180 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 158
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.243A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   GLN B  37 " --> pdb=" O   PRO B  46 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.243A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118
      removed outlier: 5.061A  pdb=" N   SER B 131 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LEU B 181 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   VAL B 133 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   LEU B 179 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   LEU B 135 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   SER B 177 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   ASN B 137 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU B 175 " --> pdb=" O   ASN B 137 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154
    Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12
      removed outlier: 4.023A  pdb=" N   ASN H  33 " --> pdb=" O   SER H  95 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   MET H  34 " --> pdb=" O   ALA H  50 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   ALA H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 9 through 12
      removed outlier: 7.036A  pdb=" N   CYS H  92 " --> pdb=" O   TRP H 103 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   TRP H 103 " --> pdb=" O   CYS H  92 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ARG H  94 " --> pdb=" O   ASN H 101 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP H 100A" --> pdb=" O   TYR H  98 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 128
      removed outlier: 5.709A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 135 through 136
      removed outlier: 5.709A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 155 through 158
    Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.245A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   GLN L  37 " --> pdb=" O   PRO L  46 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.245A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.064A  pdb=" N   SER L 131 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   LEU L 181 " --> pdb=" O   SER L 131 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LEU L 179 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 177 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   SER L 177 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   ASN L 137 " --> pdb=" O   LEU L 175 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU L 175 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 153 through 154

    514 hydrogen bonds defined for protein.
    1332 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: 2.90

  Time building geometry restraints manager: 2.67 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: 2828
        1.34 -     1.46: 2141
        1.46 -     1.58: 4323
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 9374
  Sorted by residual:
  bond pdb=" C   GLU A 216 "
       pdb=" N   PRO A 217 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.019 8.40e-03 1.42e+04 4.92e+00
  bond pdb=" C   GLU H 216 "
       pdb=" N   PRO H 217 "
    ideal  model  delta    sigma   weight residual
    1.334  1.351 -0.017 8.40e-03 1.42e+04 4.23e+00
  bond pdb=" CG1 ILE G  95 "
       pdb=" CD1 ILE G  95 "
    ideal  model  delta    sigma   weight residual
    1.513  1.457  0.056 3.90e-02 6.57e+02 2.04e+00
  bond pdb=" CG1 ILE I  95 "
       pdb=" CD1 ILE I  95 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.91e+00
  bond pdb=" CB  ARG L  61 "
       pdb=" CG  ARG L  61 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.50e+00
  ... (remaining 9369 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 11954
        1.59 -     3.18: 659
        3.18 -     4.76: 109
        4.76 -     6.35: 14
        6.35 -     7.94: 10
  Bond angle restraints: 12746
  Sorted by residual:
  angle pdb=" N   GLY G  75 "
        pdb=" CA  GLY G  75 "
        pdb=" C   GLY G  75 "
      ideal   model   delta    sigma   weight residual
     111.52  118.49   -6.97 1.31e+00 5.83e-01 2.83e+01
  angle pdb=" N   GLY I  75 "
        pdb=" CA  GLY I  75 "
        pdb=" C   GLY I  75 "
      ideal   model   delta    sigma   weight residual
     111.52  118.34   -6.82 1.31e+00 5.83e-01 2.71e+01
  angle pdb=" N   GLY G  91 "
        pdb=" CA  GLY G  91 "
        pdb=" C   GLY G  91 "
      ideal   model   delta    sigma   weight residual
     112.64  116.80   -4.16 1.21e+00 6.83e-01 1.18e+01
  angle pdb=" N   GLY I  91 "
        pdb=" CA  GLY I  91 "
        pdb=" C   GLY I  91 "
      ideal   model   delta    sigma   weight residual
     112.64  116.71   -4.07 1.21e+00 6.83e-01 1.13e+01
  angle pdb=" N   LYS I 142 "
        pdb=" CA  LYS I 142 "
        pdb=" C   LYS I 142 "
      ideal   model   delta    sigma   weight residual
     113.72  117.63   -3.91 1.30e+00 5.92e-01 9.04e+00
  ... (remaining 12741 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 5123
       17.26 -    34.53: 369
       34.53 -    51.79: 62
       51.79 -    69.06: 28
       69.06 -    86.32: 16
  Dihedral angle restraints: 5598
    sinusoidal: 2120
      harmonic: 3478
  Sorted by residual:
  dihedral pdb=" CA  PRO A 153 "
           pdb=" C   PRO A 153 "
           pdb=" N   VAL A 154 "
           pdb=" CA  VAL A 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.44   28.56     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  PRO H 153 "
           pdb=" C   PRO H 153 "
           pdb=" N   VAL H 154 "
           pdb=" CA  VAL H 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.47   28.53     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  LYS H 218 "
           pdb=" C   LYS H 218 "
           pdb=" N   SER H 219 "
           pdb=" CA  SER H 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.99   28.01     0      5.00e+00 4.00e-02 3.14e+01
  ... (remaining 5595 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1120
       0.058 -    0.115: 276
       0.115 -    0.173: 45
       0.173 -    0.231: 1
       0.231 -    0.288: 2
  Chirality restraints: 1444
  Sorted by residual:
  chirality pdb=" CA  PHE H 150 "
            pdb=" N   PHE H 150 "
            pdb=" C   PHE H 150 "
            pdb=" CB  PHE H 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  PHE A 150 "
            pdb=" N   PHE A 150 "
            pdb=" C   PHE A 150 "
            pdb=" CB  PHE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  PRO L 141 "
            pdb=" N   PRO L 141 "
            pdb=" C   PRO L 141 "
            pdb=" CB  PRO L 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.53e-01
  ... (remaining 1441 not shown)

  Planarity restraints: 1598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 142 "   -0.315 9.50e-02 1.11e+02   1.42e-01 1.56e+01
        pdb=" NE  ARG B 142 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 142 "   -0.028 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 142 "    0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 142 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L 142 "   -0.317 9.50e-02 1.11e+02   1.43e-01 1.56e+01
        pdb=" NE  ARG L 142 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG L 142 "   -0.028 2.00e-02 2.50e+03
        pdb=" NH1 ARG L 142 "    0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG L 142 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  52 "   -0.002 2.00e-02 2.50e+03   2.37e-02 1.12e+01
        pdb=" CG  TYR A  52 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  52 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  52 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  52 "    0.034 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  52 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  52 "    0.032 2.00e-02 2.50e+03
        pdb=" OH  TYR A  52 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 1595 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2495
        2.81 -     3.33: 8974
        3.33 -     3.86: 16041
        3.86 -     4.38: 19495
        4.38 -     4.90: 32489
  Nonbonded interactions: 79494
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU L 123 "
            pdb=" NZ  LYS L 126 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE2 GLU B 123 "
            pdb=" NZ  LYS B 126 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE1 GLU I 150 "
            pdb=" NH1 ARG I 156 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" OE1 GLU G 150 "
            pdb=" NH1 ARG G 156 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" OE2 GLU I 213 "
            pdb=" NZ  LYS I 217 "
     model   vdw
     2.365 3.120
  ... (remaining 79489 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'I'
}

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:             4.880
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.510
  Find NCS groups from input model:        0.260
  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:13.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
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      :  0.006   0.056   9374  Z= 0.363
  Angle     :  0.832   7.940  12746  Z= 0.466
  Chirality :  0.051   0.288   1444
  Planarity :  0.008   0.143   1598
  Dihedral  : 14.287  86.319   3338
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.13 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  3.52 %
    Favored  : 95.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.56 (0.23), residues: 1188
  helix: -0.92 (0.26), residues: 270
  sheet:  0.31 (0.25), residues: 418
  loop : -0.48 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP L  91 
 HIS   0.007   0.001   HIS B  34 
 PHE   0.038   0.003   PHE H 100D
 TYR   0.034   0.008   TYR H  52 
 ARG   0.032   0.004   ARG B 142 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 167
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8008 (t0) cc_final: 0.7565 (t70)
REVERT: G   49 SER cc_start: 0.8224 (m) cc_final: 0.7982 (p)
REVERT: G  117 MET cc_start: 0.8221 (mtp) cc_final: 0.7627 (mmm)
REVERT: G  119 MET cc_start: 0.7190 (mmt) cc_final: 0.6540 (tpt)
REVERT: G  149 MET cc_start: 0.8089 (mmt) cc_final: 0.7859 (mmp)
REVERT: G  213 GLU cc_start: 0.8559 (tp30) cc_final: 0.8188 (tm-30)
REVERT: G  215 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: G  216 TRP cc_start: 0.7980 (m100) cc_final: 0.7339 (m-10)
REVERT: H    3 GLN cc_start: 0.8799 (tt0) cc_final: 0.8544 (tt0)
REVERT: H    5 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8318 (tp40)
REVERT: H   72 ASP cc_start: 0.7999 (t0) cc_final: 0.7542 (t70)
REVERT: I   49 SER cc_start: 0.8232 (m) cc_final: 0.7877 (p)
REVERT: I  117 MET cc_start: 0.8248 (mtp) cc_final: 0.7244 (mmm)
REVERT: I  119 MET cc_start: 0.7100 (mmt) cc_final: 0.6883 (mmt)
REVERT: I  149 MET cc_start: 0.8076 (mmt) cc_final: 0.7840 (mmp)
REVERT: I  213 GLU cc_start: 0.8544 (tp30) cc_final: 0.8181 (tm-30)
REVERT: I  216 TRP cc_start: 0.7990 (m100) cc_final: 0.7340 (m-10)
  outliers start: 8
  outliers final: 0
  residues processed: 173
  average time/residue: 1.4861
  time to fit residues: 273.0264
Evaluate side-chains
  114 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0870
   chunk 47 optimal weight:    0.2980
   chunk 92 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
B  53 ASN
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 171 ASN
G 204 GLN
H  61 GLN
** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 204 GLN
L  53 ASN
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.125712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.075205 restraints weight = 14622.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.37
r_work: 0.2855 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9374  Z= 0.227
  Angle     :  0.680   6.528  12746  Z= 0.357
  Chirality :  0.045   0.152   1444
  Planarity :  0.005   0.049   1598
  Dihedral  :  5.585  28.556   1278
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.47 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.74 (0.25), residues: 1188
  helix:  1.48 (0.30), residues: 270
  sheet:  0.43 (0.24), residues: 426
  loop :  0.13 (0.30), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP I  89 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.019   0.002   PHE H 100D
 TYR   0.021   0.002   TYR G  86 
 ARG   0.011   0.001   ARG B  24 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8115 (t0) cc_final: 0.7838 (t70)
REVERT: A  199 ILE cc_start: 0.8291 (tp) cc_final: 0.8077 (tp)
REVERT: B  170 ASP cc_start: 0.8289 (t0) cc_final: 0.7993 (t0)
REVERT: G   49 SER cc_start: 0.8260 (m) cc_final: 0.8056 (p)
REVERT: G   71 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8638 (mtp)
REVERT: G  117 MET cc_start: 0.8005 (mtp) cc_final: 0.6821 (mmm)
REVERT: G  118 ILE cc_start: 0.8406 (mm) cc_final: 0.8158 (mp)
REVERT: G  119 MET cc_start: 0.7283 (mmt) cc_final: 0.6826 (tpt)
REVERT: G  149 MET cc_start: 0.8219 (mmt) cc_final: 0.7960 (mmp)
REVERT: G  213 GLU cc_start: 0.8190 (tp30) cc_final: 0.7822 (tm-30)
REVERT: G  215 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: G  216 TRP cc_start: 0.8073 (m100) cc_final: 0.7166 (m-10)
REVERT: H   72 ASP cc_start: 0.8108 (t0) cc_final: 0.7789 (t70)
REVERT: H  212 ASP cc_start: 0.9160 (m-30) cc_final: 0.8923 (m-30)
REVERT: I  117 MET cc_start: 0.8191 (mtp) cc_final: 0.7005 (mmm)
REVERT: I  118 ILE cc_start: 0.8509 (mm) cc_final: 0.8175 (mp)
REVERT: I  119 MET cc_start: 0.7344 (mmt) cc_final: 0.6870 (tpt)
REVERT: I  149 MET cc_start: 0.8215 (mmt) cc_final: 0.7903 (mmp)
REVERT: I  213 GLU cc_start: 0.8186 (tp30) cc_final: 0.7864 (tm-30)
REVERT: I  215 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7530 (mm-30)
REVERT: I  216 TRP cc_start: 0.8079 (m100) cc_final: 0.7198 (m-10)
REVERT: L   79 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7749 (mp0)
REVERT: L  170 ASP cc_start: 0.8288 (t0) cc_final: 0.7982 (t0)
  outliers start: 18
  outliers final: 0
  residues processed: 158
  average time/residue: 1.4476
  time to fit residues: 242.2213
Evaluate side-chains
  118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 MET
Chi-restraints excluded: chain L residue   79 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 73 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 171 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.124011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.072051 restraints weight = 14626.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 2.41
r_work: 0.2756 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9374  Z= 0.319
  Angle     :  0.684   7.834  12746  Z= 0.354
  Chirality :  0.045   0.152   1444
  Planarity :  0.004   0.034   1598
  Dihedral  :  5.181  21.200   1278
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.23 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.25), residues: 1188
  helix:  1.80 (0.31), residues: 272
  sheet:  0.57 (0.24), residues: 428
  loop :  0.07 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP I  89 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.021   0.002   PHE L 116 
 TYR   0.023   0.002   TYR I  86 
 ARG   0.009   0.001   ARG I  47 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8077 (t0) cc_final: 0.7738 (t70)
REVERT: A  216 GLU cc_start: 0.8386 (pm20) cc_final: 0.8105 (pp20)
REVERT: B  170 ASP cc_start: 0.8307 (t0) cc_final: 0.7941 (t0)
REVERT: G   46 MET cc_start: 0.5357 (ttp) cc_final: 0.4362 (mpt)
REVERT: G   48 GLU cc_start: 0.6907 (mm-30) cc_final: 0.5971 (mp0)
REVERT: G   49 SER cc_start: 0.8313 (m) cc_final: 0.7981 (p)
REVERT: G   71 MET cc_start: 0.8906 (mtm) cc_final: 0.8550 (mtp)
REVERT: G  117 MET cc_start: 0.7968 (mtp) cc_final: 0.6819 (mmm)
REVERT: G  118 ILE cc_start: 0.8353 (mm) cc_final: 0.8105 (mp)
REVERT: G  149 MET cc_start: 0.8069 (mmt) cc_final: 0.7781 (mmp)
REVERT: G  213 GLU cc_start: 0.8262 (tp30) cc_final: 0.7925 (tm-30)
REVERT: G  215 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7514 (mm-30)
REVERT: G  216 TRP cc_start: 0.8165 (m100) cc_final: 0.7220 (m-10)
REVERT: G  217 LYS cc_start: 0.7956 (mmpt) cc_final: 0.7752 (mmpt)
REVERT: H   72 ASP cc_start: 0.8052 (t0) cc_final: 0.7688 (t70)
REVERT: H  201 ASN cc_start: 0.8443 (m-40) cc_final: 0.8238 (m-40)
REVERT: H  216 GLU cc_start: 0.8427 (pm20) cc_final: 0.8136 (pp20)
REVERT: I   93 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8072 (mtp)
REVERT: I  117 MET cc_start: 0.8030 (mtp) cc_final: 0.6908 (mmm)
REVERT: I  118 ILE cc_start: 0.8390 (mm) cc_final: 0.8176 (mp)
REVERT: I  119 MET cc_start: 0.7168 (mmt) cc_final: 0.6714 (tpt)
REVERT: I  149 MET cc_start: 0.8079 (mmt) cc_final: 0.7833 (mmp)
REVERT: I  213 GLU cc_start: 0.8238 (tp30) cc_final: 0.7914 (tm-30)
REVERT: I  215 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7565 (mm-30)
REVERT: I  216 TRP cc_start: 0.8159 (m100) cc_final: 0.7212 (m-10)
REVERT: I  217 LYS cc_start: 0.7933 (mmpt) cc_final: 0.7731 (mmpt)
REVERT: L   79 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7905 (mp0)
REVERT: L  170 ASP cc_start: 0.8343 (t0) cc_final: 0.8023 (t0)
  outliers start: 25
  outliers final: 6
  residues processed: 146
  average time/residue: 1.5316
  time to fit residues: 238.2518
Evaluate side-chains
  126 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain G residue   93 MET
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  151 SER
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   79 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A  61 GLN
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
H  61 GLN
** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.124683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.072933 restraints weight = 14507.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.39
r_work: 0.2832 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9374  Z= 0.256
  Angle     :  0.626   8.594  12746  Z= 0.323
  Chirality :  0.044   0.155   1444
  Planarity :  0.004   0.035   1598
  Dihedral  :  4.862  20.036   1278
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.52 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.05 (0.25), residues: 1188
  helix:  2.12 (0.32), residues: 272
  sheet:  0.64 (0.24), residues: 428
  loop :  0.04 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP I  89 
 HIS   0.004   0.001   HIS L 189 
 PHE   0.015   0.002   PHE L 116 
 TYR   0.020   0.002   TYR I  86 
 ARG   0.009   0.001   ARG L  24 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8704 (mm-30)
REVERT: A   72 ASP cc_start: 0.8112 (t0) cc_final: 0.7752 (t70)
REVERT: A  216 GLU cc_start: 0.8399 (pm20) cc_final: 0.8164 (pp20)
REVERT: B   79 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8225 (mm-30)
REVERT: B  167 ASP cc_start: 0.8242 (t0) cc_final: 0.7926 (t0)
REVERT: B  169 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8574 (pptt)
REVERT: B  170 ASP cc_start: 0.8512 (t0) cc_final: 0.8052 (t0)
REVERT: G   46 MET cc_start: 0.5436 (ttp) cc_final: 0.4211 (mpt)
REVERT: G   48 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6091 (mp0)
REVERT: G   71 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8571 (mtp)
REVERT: G  117 MET cc_start: 0.8074 (mtp) cc_final: 0.7057 (mmm)
REVERT: G  149 MET cc_start: 0.8068 (mmt) cc_final: 0.7792 (mmp)
REVERT: G  213 GLU cc_start: 0.8349 (tp30) cc_final: 0.8022 (tm-30)
REVERT: G  215 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7498 (mm-30)
REVERT: G  216 TRP cc_start: 0.8112 (m100) cc_final: 0.7166 (m-10)
REVERT: H   10 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8712 (mm-30)
REVERT: H   72 ASP cc_start: 0.8138 (t0) cc_final: 0.7726 (t70)
REVERT: H  216 GLU cc_start: 0.8453 (pm20) cc_final: 0.8181 (pp20)
REVERT: I  117 MET cc_start: 0.7892 (mtp) cc_final: 0.6794 (mmm)
REVERT: I  118 ILE cc_start: 0.8331 (mm) cc_final: 0.8117 (mp)
REVERT: I  119 MET cc_start: 0.7190 (mmt) cc_final: 0.6776 (tpt)
REVERT: I  149 MET cc_start: 0.8025 (mmt) cc_final: 0.7750 (mmp)
REVERT: I  213 GLU cc_start: 0.8314 (tp30) cc_final: 0.8024 (tm-30)
REVERT: I  215 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7589 (mm-30)
REVERT: I  216 TRP cc_start: 0.8084 (m100) cc_final: 0.7053 (m-10)
REVERT: L  167 ASP cc_start: 0.8429 (t0) cc_final: 0.7990 (t0)
REVERT: L  169 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8569 (pptt)
REVERT: L  170 ASP cc_start: 0.8547 (t0) cc_final: 0.8029 (t0)
  outliers start: 22
  outliers final: 8
  residues processed: 138
  average time/residue: 1.4272
  time to fit residues: 208.9515
Evaluate side-chains
  130 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain G residue   71 MET
Chi-restraints excluded: chain G residue   93 MET
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain I residue   49 SER
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   33 ILE
Chi-restraints excluded: chain L residue  169 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 96 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 36 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A 168 HIS
B 137 ASN
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 163 ASN
G 166 ASN
H   3 GLN
I 163 ASN
I 166 ASN
** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 189 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.124841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.073015 restraints weight = 14457.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.40
r_work: 0.2830 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9374  Z= 0.241
  Angle     :  0.615   6.988  12746  Z= 0.316
  Chirality :  0.043   0.160   1444
  Planarity :  0.004   0.036   1598
  Dihedral  :  4.736  19.659   1278
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.11 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.17 (0.25), residues: 1188
  helix:  2.26 (0.32), residues: 272
  sheet:  0.74 (0.24), residues: 428
  loop :  0.04 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP I  89 
 HIS   0.008   0.001   HIS L 189 
 PHE   0.014   0.001   PHE G 200 
 TYR   0.020   0.002   TYR I  86 
 ARG   0.011   0.001   ARG B  24 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8703 (mm-30)
REVERT: A   72 ASP cc_start: 0.8129 (t0) cc_final: 0.7725 (t70)
REVERT: B   79 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8203 (mm-30)
REVERT: B  167 ASP cc_start: 0.8245 (t0) cc_final: 0.7930 (t0)
REVERT: B  169 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8817 (pptt)
REVERT: B  170 ASP cc_start: 0.8551 (t0) cc_final: 0.8067 (t0)
REVERT: G   46 MET cc_start: 0.5466 (ttp) cc_final: 0.4120 (mpt)
REVERT: G   48 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6156 (mp0)
REVERT: G   71 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8581 (mtp)
REVERT: G  117 MET cc_start: 0.7933 (mtp) cc_final: 0.7130 (mmm)
REVERT: G  119 MET cc_start: 0.7622 (tpp) cc_final: 0.7279 (tpt)
REVERT: G  149 MET cc_start: 0.7986 (mmt) cc_final: 0.7737 (mmp)
REVERT: G  213 GLU cc_start: 0.8314 (tp30) cc_final: 0.8047 (tm-30)
REVERT: G  216 TRP cc_start: 0.8096 (m100) cc_final: 0.7022 (m-10)
REVERT: H    3 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8534 (tt0)
REVERT: H   10 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8705 (mm-30)
REVERT: H   72 ASP cc_start: 0.8162 (t0) cc_final: 0.7693 (t70)
REVERT: H  216 GLU cc_start: 0.8463 (pm20) cc_final: 0.8215 (pp20)
REVERT: I  117 MET cc_start: 0.7845 (mtp) cc_final: 0.7023 (mmm)
REVERT: I  118 ILE cc_start: 0.8276 (mm) cc_final: 0.8047 (mp)
REVERT: I  119 MET cc_start: 0.7122 (mmt) cc_final: 0.6700 (tpt)
REVERT: I  149 MET cc_start: 0.7944 (mmt) cc_final: 0.7703 (mmp)
REVERT: I  213 GLU cc_start: 0.8280 (tp30) cc_final: 0.8019 (tm-30)
REVERT: I  216 TRP cc_start: 0.8111 (m100) cc_final: 0.7068 (m-10)
REVERT: L  169 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8747 (pptt)
REVERT: L  170 ASP cc_start: 0.8599 (t0) cc_final: 0.8036 (t0)
  outliers start: 21
  outliers final: 8
  residues processed: 141
  average time/residue: 1.3506
  time to fit residues: 202.3828
Evaluate side-chains
  131 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain G residue   71 MET
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain I residue   49 SER
Chi-restraints excluded: chain I residue  100 LEU
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  169 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 15 optimal weight:    0.2980
   chunk 53 optimal weight:    2.9990
   chunk 94 optimal weight:    0.5980
   chunk 41 optimal weight:    8.9990
   chunk 104 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 113 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A   5 GLN
A  61 GLN
A 168 HIS
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 140 ASN
H  61 GLN
I 140 ASN
** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.124141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.072325 restraints weight = 14464.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.38
r_work: 0.2814 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9374  Z= 0.288
  Angle     :  0.632   7.244  12746  Z= 0.324
  Chirality :  0.044   0.158   1444
  Planarity :  0.004   0.042   1598
  Dihedral  :  4.770  20.445   1278
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.99 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.23 (0.25), residues: 1188
  helix:  2.23 (0.31), residues: 272
  sheet:  0.82 (0.24), residues: 434
  loop :  0.07 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP G  89 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.016   0.002   PHE G 200 
 TYR   0.021   0.002   TYR G  86 
 ARG   0.011   0.001   ARG L  24 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8716 (mm-30)
REVERT: A   72 ASP cc_start: 0.8151 (t0) cc_final: 0.7740 (t70)
REVERT: A  216 GLU cc_start: 0.8337 (pm20) cc_final: 0.8104 (pp20)
REVERT: B   79 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8144 (mm-30)
REVERT: B  169 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8758 (pptt)
REVERT: B  170 ASP cc_start: 0.8606 (t0) cc_final: 0.8115 (t0)
REVERT: G   46 MET cc_start: 0.5896 (ttp) cc_final: 0.5268 (mpt)
REVERT: G   48 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6318 (mp0)
REVERT: G   71 MET cc_start: 0.8942 (mtm) cc_final: 0.8541 (mtp)
REVERT: G   76 ILE cc_start: 0.8278 (mm) cc_final: 0.8075 (pt)
REVERT: G   93 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8045 (mtp)
REVERT: G  117 MET cc_start: 0.7934 (mtp) cc_final: 0.7148 (mmm)
REVERT: G  119 MET cc_start: 0.7664 (tpp) cc_final: 0.7273 (tpt)
REVERT: G  149 MET cc_start: 0.7934 (mmt) cc_final: 0.7699 (mmp)
REVERT: G  166 ASN cc_start: 0.7882 (t0) cc_final: 0.7670 (t160)
REVERT: G  213 GLU cc_start: 0.8308 (tp30) cc_final: 0.8055 (tm-30)
REVERT: G  216 TRP cc_start: 0.8102 (m100) cc_final: 0.7097 (m-10)
REVERT: H    5 GLN cc_start: 0.8774 (tp40) cc_final: 0.8301 (mp10)
REVERT: H   10 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8713 (mm-30)
REVERT: H   72 ASP cc_start: 0.8211 (t0) cc_final: 0.7737 (t70)
REVERT: H  216 GLU cc_start: 0.8477 (pm20) cc_final: 0.8235 (pp20)
REVERT: I   93 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8006 (mtp)
REVERT: I  117 MET cc_start: 0.7811 (mtp) cc_final: 0.7059 (mmm)
REVERT: I  119 MET cc_start: 0.7172 (mmt) cc_final: 0.6698 (tpt)
REVERT: I  149 MET cc_start: 0.7884 (mmt) cc_final: 0.7652 (mmp)
REVERT: I  213 GLU cc_start: 0.8287 (tp30) cc_final: 0.8040 (tm-30)
REVERT: I  216 TRP cc_start: 0.8111 (m100) cc_final: 0.7099 (m-10)
REVERT: L  169 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8760 (pptt)
REVERT: L  170 ASP cc_start: 0.8654 (t0) cc_final: 0.8123 (t0)
  outliers start: 22
  outliers final: 10
  residues processed: 139
  average time/residue: 1.4563
  time to fit residues: 214.6969
Evaluate side-chains
  127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain G residue   93 MET
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  142 LYS
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  118 ILE
Chi-restraints excluded: chain I residue  142 LYS
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  169 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 83 optimal weight:    0.0370
   chunk 112 optimal weight:    9.9990
   chunk 106 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 41 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.7460

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A   5 GLN
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 199 GLN
I 166 ASN
** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.124837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.072579 restraints weight = 14549.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.39
r_work: 0.2825 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9374  Z= 0.257
  Angle     :  0.624   6.985  12746  Z= 0.319
  Chirality :  0.043   0.148   1444
  Planarity :  0.004   0.046   1598
  Dihedral  :  4.688  20.190   1278
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 14.36 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.26 (0.25), residues: 1188
  helix:  2.31 (0.31), residues: 272
  sheet:  0.81 (0.24), residues: 424
  loop :  0.11 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP I  89 
 HIS   0.006   0.001   HIS L 189 
 PHE   0.015   0.001   PHE G 200 
 TYR   0.019   0.002   TYR I  86 
 ARG   0.012   0.001   ARG B  24 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8703 (mm-30)
REVERT: A   72 ASP cc_start: 0.8140 (t0) cc_final: 0.7708 (t70)
REVERT: A  216 GLU cc_start: 0.8429 (pm20) cc_final: 0.8202 (pp20)
REVERT: B   79 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8163 (mm-30)
REVERT: B  169 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8760 (pptt)
REVERT: B  170 ASP cc_start: 0.8677 (t0) cc_final: 0.8149 (t0)
REVERT: G   48 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6124 (mp0)
REVERT: G   71 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8543 (mtp)
REVERT: G  117 MET cc_start: 0.7918 (mtp) cc_final: 0.7179 (mmm)
REVERT: G  119 MET cc_start: 0.7667 (tpp) cc_final: 0.7333 (tpt)
REVERT: G  149 MET cc_start: 0.7842 (mmt) cc_final: 0.7613 (mmp)
REVERT: G  213 GLU cc_start: 0.8299 (tp30) cc_final: 0.8051 (tm-30)
REVERT: G  216 TRP cc_start: 0.8088 (m100) cc_final: 0.7113 (m-10)
REVERT: H    5 GLN cc_start: 0.8784 (tp40) cc_final: 0.8523 (mm110)
REVERT: H   10 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8714 (mm-30)
REVERT: H   72 ASP cc_start: 0.8210 (t0) cc_final: 0.7715 (t70)
REVERT: H  159 ASN cc_start: 0.7834 (m-40) cc_final: 0.7622 (m110)
REVERT: H  199 ILE cc_start: 0.8777 (pp) cc_final: 0.8556 (tp)
REVERT: H  216 GLU cc_start: 0.8495 (pm20) cc_final: 0.8274 (pp20)
REVERT: I  117 MET cc_start: 0.7789 (mtp) cc_final: 0.7040 (mmm)
REVERT: I  119 MET cc_start: 0.7205 (mmt) cc_final: 0.6751 (tpt)
REVERT: I  149 MET cc_start: 0.7870 (mmt) cc_final: 0.7550 (mmp)
REVERT: I  213 GLU cc_start: 0.8280 (tp30) cc_final: 0.8040 (tm-30)
REVERT: I  216 TRP cc_start: 0.8091 (m100) cc_final: 0.7114 (m-10)
REVERT: L  169 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8759 (pptt)
REVERT: L  170 ASP cc_start: 0.8678 (t0) cc_final: 0.8141 (t0)
  outliers start: 14
  outliers final: 4
  residues processed: 125
  average time/residue: 1.5242
  time to fit residues: 202.2921
Evaluate side-chains
  121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  199 GLN
Chi-restraints excluded: chain G residue   71 MET
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  169 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 60 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 1 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0670
   chunk 0 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8724

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
A  61 GLN
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 199 GLN
H  61 GLN
H 168 HIS
** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 137 ASN
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.124016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.072060 restraints weight = 14767.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 2.42
r_work: 0.2812 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9374  Z= 0.286
  Angle     :  0.634   7.418  12746  Z= 0.323
  Chirality :  0.043   0.148   1444
  Planarity :  0.004   0.054   1598
  Dihedral  :  4.685  21.048   1278
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.16 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.37 (0.25), residues: 1188
  helix:  2.30 (0.31), residues: 272
  sheet:  1.01 (0.24), residues: 434
  loop :  0.08 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP I  89 
 HIS   0.007   0.001   HIS L 189 
 PHE   0.016   0.002   PHE G 200 
 TYR   0.020   0.002   TYR I  86 
 ARG   0.013   0.001   ARG B  24 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8716 (mm-30)
REVERT: A   72 ASP cc_start: 0.8216 (t0) cc_final: 0.7753 (t70)
REVERT: A  216 GLU cc_start: 0.8471 (pm20) cc_final: 0.8255 (pp20)
REVERT: B   79 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8161 (mm-30)
REVERT: B  145 LYS cc_start: 0.8826 (ptmm) cc_final: 0.8245 (pptt)
REVERT: B  169 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8760 (pptt)
REVERT: B  170 ASP cc_start: 0.8706 (t0) cc_final: 0.8166 (t0)
REVERT: G   48 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6091 (mp0)
REVERT: G   49 SER cc_start: 0.8356 (m) cc_final: 0.7912 (t)
REVERT: G   71 MET cc_start: 0.8946 (mtm) cc_final: 0.8545 (mtp)
REVERT: G  117 MET cc_start: 0.7904 (mtp) cc_final: 0.7227 (mmm)
REVERT: G  119 MET cc_start: 0.7634 (tpp) cc_final: 0.7326 (tpt)
REVERT: G  149 MET cc_start: 0.7828 (mmt) cc_final: 0.7593 (mmp)
REVERT: G  213 GLU cc_start: 0.8288 (tp30) cc_final: 0.8068 (tm-30)
REVERT: G  216 TRP cc_start: 0.8093 (m100) cc_final: 0.7078 (m-10)
REVERT: H    5 GLN cc_start: 0.8779 (tp40) cc_final: 0.8551 (mm110)
REVERT: H   10 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8724 (mm-30)
REVERT: H   72 ASP cc_start: 0.8223 (t0) cc_final: 0.7737 (t70)
REVERT: H  199 ILE cc_start: 0.8616 (pp) cc_final: 0.8402 (tp)
REVERT: H  216 GLU cc_start: 0.8525 (pm20) cc_final: 0.8317 (pp20)
REVERT: I   50 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8548 (mttm)
REVERT: I  117 MET cc_start: 0.7782 (mtp) cc_final: 0.7326 (tpp)
REVERT: I  149 MET cc_start: 0.7871 (mmt) cc_final: 0.7665 (mmp)
REVERT: I  213 GLU cc_start: 0.8291 (tp30) cc_final: 0.8046 (tm-30)
REVERT: I  216 TRP cc_start: 0.8088 (m100) cc_final: 0.7117 (m-10)
REVERT: L  137 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7938 (t0)
REVERT: L  169 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8765 (pptt)
REVERT: L  170 ASP cc_start: 0.8717 (t0) cc_final: 0.8165 (t0)
  outliers start: 17
  outliers final: 7
  residues processed: 126
  average time/residue: 1.8016
  time to fit residues: 240.2374
Evaluate side-chains
  121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain I residue  142 LYS
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  137 ASN
Chi-restraints excluded: chain L residue  169 LYS
Chi-restraints excluded: chain L residue  199 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   chunk 53 optimal weight:    0.5980
   chunk 70 optimal weight:    0.2980
   chunk 44 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 116 optimal weight:    8.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
H 159 ASN
** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.125320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.073896 restraints weight = 14376.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.38
r_work: 0.2848 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9374  Z= 0.205
  Angle     :  0.610   7.291  12746  Z= 0.312
  Chirality :  0.042   0.148   1444
  Planarity :  0.004   0.056   1598
  Dihedral  :  4.547  20.050   1278
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 14.94 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.35 (0.24), residues: 1188
  helix:  2.36 (0.31), residues: 272
  sheet:  0.91 (0.24), residues: 424
  loop :  0.14 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP I  89 
 HIS   0.006   0.001   HIS L 189 
 PHE   0.013   0.001   PHE G 200 
 TYR   0.017   0.001   TYR I  86 
 ARG   0.014   0.001   ARG B  24 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8728 (mm-30)
REVERT: A   72 ASP cc_start: 0.8197 (t0) cc_final: 0.7737 (t70)
REVERT: A  216 GLU cc_start: 0.8455 (pm20) cc_final: 0.8246 (pp20)
REVERT: B   79 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8153 (mm-30)
REVERT: B  169 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8895 (pptt)
REVERT: B  170 ASP cc_start: 0.8716 (t0) cc_final: 0.8202 (t0)
REVERT: G   48 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6105 (mp0)
REVERT: G   49 SER cc_start: 0.8338 (m) cc_final: 0.8017 (p)
REVERT: G   71 MET cc_start: 0.8957 (mtm) cc_final: 0.8594 (mtp)
REVERT: G  117 MET cc_start: 0.7870 (mtp) cc_final: 0.7091 (mmm)
REVERT: G  119 MET cc_start: 0.7584 (tpp) cc_final: 0.7191 (tpt)
REVERT: G  149 MET cc_start: 0.7878 (mmt) cc_final: 0.7650 (mmp)
REVERT: G  213 GLU cc_start: 0.8291 (tp30) cc_final: 0.8059 (tm-30)
REVERT: G  216 TRP cc_start: 0.8068 (m100) cc_final: 0.7102 (m-10)
REVERT: H    5 GLN cc_start: 0.8761 (tp40) cc_final: 0.8553 (mm110)
REVERT: H   10 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8705 (mm-30)
REVERT: H   72 ASP cc_start: 0.8197 (t0) cc_final: 0.7708 (t70)
REVERT: I   50 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8555 (mttm)
REVERT: I  117 MET cc_start: 0.8011 (mtp) cc_final: 0.7682 (tpp)
REVERT: I  119 MET cc_start: 0.7776 (tpp) cc_final: 0.7330 (tpt)
REVERT: I  149 MET cc_start: 0.7890 (mmt) cc_final: 0.7547 (mmp)
REVERT: I  213 GLU cc_start: 0.8267 (tp30) cc_final: 0.8040 (tm-30)
REVERT: I  216 TRP cc_start: 0.8071 (m100) cc_final: 0.7022 (m-10)
REVERT: L  169 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8911 (pptt)
REVERT: L  170 ASP cc_start: 0.8719 (t0) cc_final: 0.8191 (t0)
  outliers start: 10
  outliers final: 4
  residues processed: 126
  average time/residue: 1.4903
  time to fit residues: 198.7233
Evaluate side-chains
  119 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  169 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 57 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 111 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
A  61 GLN
B 199 GLN
H  61 GLN
H 168 HIS
I 171 ASN
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.123224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.070982 restraints weight = 14629.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.43
r_work: 0.2792 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   9374  Z= 0.361
  Angle     :  0.679   7.918  12746  Z= 0.347
  Chirality :  0.044   0.153   1444
  Planarity :  0.005   0.058   1598
  Dihedral  :  4.796  22.880   1278
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 15.43 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.33 (0.24), residues: 1188
  helix:  2.22 (0.30), residues: 270
  sheet:  1.02 (0.24), residues: 432
  loop :  0.06 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP G  89 
 HIS   0.010   0.002   HIS B 189 
 PHE   0.018   0.002   PHE G 200 
 TYR   0.021   0.002   TYR G  86 
 ARG   0.015   0.001   ARG B  24 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8743 (mm-30)
REVERT: A   72 ASP cc_start: 0.8237 (t0) cc_final: 0.7788 (t70)
REVERT: A   81 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8774 (tt0)
REVERT: A  159 ASN cc_start: 0.7978 (m-40) cc_final: 0.7764 (m110)
REVERT: A  199 ILE cc_start: 0.8724 (pp) cc_final: 0.8487 (tp)
REVERT: A  200 CYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8784 (p)
REVERT: A  216 GLU cc_start: 0.8468 (pm20) cc_final: 0.8259 (pp20)
REVERT: B   79 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8196 (mm-30)
REVERT: B  169 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8810 (pptt)
REVERT: B  170 ASP cc_start: 0.8739 (t0) cc_final: 0.8200 (t0)
REVERT: G   49 SER cc_start: 0.8414 (m) cc_final: 0.8063 (p)
REVERT: G   71 MET cc_start: 0.8924 (mtm) cc_final: 0.8518 (mtp)
REVERT: G  117 MET cc_start: 0.7908 (mtp) cc_final: 0.7273 (mmm)
REVERT: G  149 MET cc_start: 0.7829 (mmt) cc_final: 0.7606 (mmp)
REVERT: G  213 GLU cc_start: 0.8337 (tp30) cc_final: 0.8095 (tm-30)
REVERT: G  216 TRP cc_start: 0.8092 (m100) cc_final: 0.7138 (m-10)
REVERT: H    5 GLN cc_start: 0.8831 (tp40) cc_final: 0.8572 (mm110)
REVERT: H   10 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8740 (mm-30)
REVERT: H   72 ASP cc_start: 0.8253 (t0) cc_final: 0.7764 (t70)
REVERT: I   46 MET cc_start: 0.6586 (ttt) cc_final: 0.4444 (mpt)
REVERT: I  117 MET cc_start: 0.8226 (mtp) cc_final: 0.7810 (tpp)
REVERT: I  119 MET cc_start: 0.7786 (tpp) cc_final: 0.7460 (tpt)
REVERT: I  213 GLU cc_start: 0.8306 (tp30) cc_final: 0.8079 (tm-30)
REVERT: I  216 TRP cc_start: 0.8066 (m100) cc_final: 0.7039 (m-10)
REVERT: L  169 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8787 (pptt)
REVERT: L  170 ASP cc_start: 0.8741 (t0) cc_final: 0.8193 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 120
  average time/residue: 1.4700
  time to fit residues: 186.7145
Evaluate side-chains
  118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  142 LYS
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  169 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 48 optimal weight:    0.2980
   chunk 17 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
G 166 ASN
H 168 HIS
L 137 ASN
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.124523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.072758 restraints weight = 14591.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 2.42
r_work: 0.2824 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9374  Z= 0.248
  Angle     :  0.638   7.443  12746  Z= 0.327
  Chirality :  0.042   0.144   1444
  Planarity :  0.005   0.058   1598
  Dihedral  :  4.653  21.058   1278
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 15.62 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.24), residues: 1188
  helix:  2.36 (0.30), residues: 270
  sheet:  1.05 (0.24), residues: 432
  loop :  0.07 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP I  89 
 HIS   0.010   0.001   HIS B 189 
 PHE   0.015   0.001   PHE G 200 
 TYR   0.019   0.001   TYR G  86 
 ARG   0.015   0.001   ARG B  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10361.75 seconds
wall clock time: 182 minutes 26.15 seconds (10946.15 seconds total)