Starting phenix.real_space_refine
on Wed Apr 30 05:31:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vgn_43212/04_2025/8vgn_43212.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vgn_43212/04_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_43212/04_2025/8vgn_43212.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vgn_43212/04_2025/8vgn_43212.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vgn_43212/04_2025/8vgn_43212.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vgn_43212/04_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-5669/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: 6.53, per 1000 atoms: 0.71
  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: 2.58
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.59
  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: 3.20

  Time building geometry restraints manager: 3.05 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:             5.110
  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:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.130
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  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:12.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.760
-------------------------------------------------------------------------------
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   9386  Z= 0.241
  Angle     :  0.832   7.940  12770  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17546 (  478)
  hydrogen bonds       : angle       8.25395 ( 1332)
  SS BOND              : bond        0.00453 (   12)
  SS BOND              : angle       1.15736 (   24)
  covalent geometry    : bond        0.00569 ( 9374)
  covalent geometry    : angle       0.83162 (12746)

*********************** 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  : 1.055 
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: 1.3477
  time to fit residues: 247.4290
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  : 0.990 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.5958

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.125360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.074877 restraints weight = 14630.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.37
r_work: 0.2847 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9386  Z= 0.163
  Angle     :  0.685   6.453  12770  Z= 0.360
  Chirality :  0.045   0.159   1444
  Planarity :  0.005   0.050   1598
  Dihedral  :  5.643  29.435   1278
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.38 %
    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:  0.72 (0.25), residues: 1188
  helix:  1.44 (0.30), residues: 270
  sheet:  0.42 (0.24), residues: 426
  loop :  0.13 (0.30), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP I  89 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.020   0.002   PHE H 100D
 TYR   0.022   0.002   TYR G  86 
 ARG   0.010   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04277 (  478)
  hydrogen bonds       : angle       5.46956 ( 1332)
  SS BOND              : bond        0.00654 (   12)
  SS BOND              : angle       0.63510 (   24)
  covalent geometry    : bond        0.00365 ( 9374)
  covalent geometry    : angle       0.68487 (12746)

*********************** 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
  157 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8107 (t0) cc_final: 0.7791 (t70)
REVERT: A  199 ILE cc_start: 0.8300 (tp) cc_final: 0.8086 (tp)
REVERT: B  170 ASP cc_start: 0.8265 (t0) cc_final: 0.7980 (t0)
REVERT: G   49 SER cc_start: 0.8263 (m) cc_final: 0.8059 (p)
REVERT: G   71 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8651 (mtp)
REVERT: G  117 MET cc_start: 0.8008 (mtp) cc_final: 0.6826 (mmm)
REVERT: G  118 ILE cc_start: 0.8409 (mm) cc_final: 0.8157 (mp)
REVERT: G  119 MET cc_start: 0.7280 (mmt) cc_final: 0.6821 (tpt)
REVERT: G  149 MET cc_start: 0.8201 (mmt) cc_final: 0.7933 (mmp)
REVERT: G  213 GLU cc_start: 0.8201 (tp30) cc_final: 0.7839 (tm-30)
REVERT: G  215 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7533 (mm-30)
REVERT: G  216 TRP cc_start: 0.8091 (m100) cc_final: 0.7207 (m-10)
REVERT: H   72 ASP cc_start: 0.8096 (t0) cc_final: 0.7718 (t70)
REVERT: H  212 ASP cc_start: 0.9129 (m-30) cc_final: 0.8875 (m-30)
REVERT: I  117 MET cc_start: 0.8198 (mtp) cc_final: 0.7019 (mmm)
REVERT: I  118 ILE cc_start: 0.8519 (mm) cc_final: 0.8185 (mp)
REVERT: I  119 MET cc_start: 0.7300 (mmt) cc_final: 0.6834 (tpt)
REVERT: I  149 MET cc_start: 0.8212 (mmt) cc_final: 0.7898 (mmp)
REVERT: I  213 GLU cc_start: 0.8192 (tp30) cc_final: 0.7864 (tm-30)
REVERT: I  215 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7604 (mm-30)
REVERT: I  216 TRP cc_start: 0.8103 (m100) cc_final: 0.7218 (m-10)
REVERT: L   53 ASN cc_start: 0.9228 (m110) cc_final: 0.8968 (m110)
REVERT: L   79 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8016 (mp0)
REVERT: L  170 ASP cc_start: 0.8285 (t0) cc_final: 0.7992 (t0)
  outliers start: 19
  outliers final: 2
  residues processed: 154
  average time/residue: 1.9957
  time to fit residues: 325.4730
Evaluate side-chains
  121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 3.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain G residue   71 MET
Chi-restraints excluded: chain I residue  151 SER
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:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 116 optimal weight:    9.9990
   chunk 21 optimal weight:    0.1980
   chunk 73 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.124337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.073101 restraints weight = 14523.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 2.37
r_work: 0.2759 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9386  Z= 0.213
  Angle     :  0.680   7.866  12770  Z= 0.352
  Chirality :  0.046   0.188   1444
  Planarity :  0.004   0.035   1598
  Dihedral  :  5.193  21.317   1278
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.04 %
    Favored  : 86.43 %
  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:  0.89 (0.25), residues: 1188
  helix:  1.75 (0.31), residues: 272
  sheet:  0.57 (0.24), residues: 428
  loop :  0.05 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP I  89 
 HIS   0.004   0.001   HIS I 145 
 PHE   0.021   0.002   PHE L 116 
 TYR   0.023   0.002   TYR I  86 
 ARG   0.008   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  478)
  hydrogen bonds       : angle       5.18190 ( 1332)
  SS BOND              : bond        0.00469 (   12)
  SS BOND              : angle       0.66111 (   24)
  covalent geometry    : bond        0.00494 ( 9374)
  covalent geometry    : angle       0.68039 (12746)

*********************** 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
  158 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8079 (t0) cc_final: 0.7717 (t70)
REVERT: B  170 ASP cc_start: 0.8310 (t0) cc_final: 0.8001 (t0)
REVERT: G   46 MET cc_start: 0.5350 (ttp) cc_final: 0.4881 (mpt)
REVERT: G   49 SER cc_start: 0.8314 (m) cc_final: 0.8079 (p)
REVERT: G   71 MET cc_start: 0.8906 (mtm) cc_final: 0.8554 (mtp)
REVERT: G  117 MET cc_start: 0.7977 (mtp) cc_final: 0.6822 (mmm)
REVERT: G  118 ILE cc_start: 0.8349 (mm) cc_final: 0.8105 (mp)
REVERT: G  149 MET cc_start: 0.8075 (mmt) cc_final: 0.7735 (mmp)
REVERT: G  213 GLU cc_start: 0.8278 (tp30) cc_final: 0.7901 (tm-30)
REVERT: G  215 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7518 (mm-30)
REVERT: G  216 TRP cc_start: 0.8153 (m100) cc_final: 0.7207 (m-10)
REVERT: H   72 ASP cc_start: 0.8066 (t0) cc_final: 0.7722 (t70)
REVERT: H  201 ASN cc_start: 0.8437 (m-40) cc_final: 0.8231 (m-40)
REVERT: H  216 GLU cc_start: 0.8394 (pm20) cc_final: 0.8108 (pp20)
REVERT: I   93 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8121 (mtp)
REVERT: I  117 MET cc_start: 0.8032 (mtp) cc_final: 0.6904 (mmm)
REVERT: I  118 ILE cc_start: 0.8387 (mm) cc_final: 0.8169 (mp)
REVERT: I  119 MET cc_start: 0.7140 (mmt) cc_final: 0.6671 (tpt)
REVERT: I  149 MET cc_start: 0.8082 (mmt) cc_final: 0.7831 (mmp)
REVERT: I  213 GLU cc_start: 0.8264 (tp30) cc_final: 0.7924 (tm-30)
REVERT: I  215 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7553 (mm-30)
REVERT: I  216 TRP cc_start: 0.8166 (m100) cc_final: 0.7222 (m-10)
REVERT: L  170 ASP cc_start: 0.8355 (t0) cc_final: 0.8039 (t0)
  outliers start: 26
  outliers final: 6
  residues processed: 150
  average time/residue: 1.4827
  time to fit residues: 236.1180
Evaluate side-chains
  124 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain G residue   93 MET
Chi-restraints excluded: chain G residue  151 SER
Chi-restraints excluded: chain I residue   49 SER
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  151 SER
Chi-restraints excluded: chain L residue   12 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.124452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.072634 restraints weight = 14495.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.38
r_work: 0.2828 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9386  Z= 0.183
  Angle     :  0.644   8.508  12770  Z= 0.332
  Chirality :  0.044   0.177   1444
  Planarity :  0.004   0.038   1598
  Dihedral  :  4.892  20.446   1278
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.01 %
    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:  0.99 (0.25), residues: 1188
  helix:  2.06 (0.32), residues: 272
  sheet:  0.61 (0.24), residues: 428
  loop : -0.00 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP I  89 
 HIS   0.004   0.001   HIS L 189 
 PHE   0.015   0.002   PHE G 200 
 TYR   0.021   0.002   TYR G  86 
 ARG   0.011   0.001   ARG G  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03870 (  478)
  hydrogen bonds       : angle       4.89296 ( 1332)
  SS BOND              : bond        0.00479 (   12)
  SS BOND              : angle       0.63540 (   24)
  covalent geometry    : bond        0.00425 ( 9374)
  covalent geometry    : angle       0.64420 (12746)

*********************** 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
  145 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8721 (mm-30)
REVERT: A   72 ASP cc_start: 0.8148 (t0) cc_final: 0.7734 (t70)
REVERT: B   79 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8226 (mm-30)
REVERT: B  167 ASP cc_start: 0.8439 (t0) cc_final: 0.8064 (t0)
REVERT: B  169 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8568 (pptt)
REVERT: B  170 ASP cc_start: 0.8549 (t0) cc_final: 0.8049 (t0)
REVERT: G   46 MET cc_start: 0.5397 (ttp) cc_final: 0.5154 (mpt)
REVERT: G   48 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6075 (mp0)
REVERT: G   71 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8574 (mtp)
REVERT: G  117 MET cc_start: 0.8078 (mtp) cc_final: 0.7076 (mmm)
REVERT: G  118 ILE cc_start: 0.8315 (mm) cc_final: 0.8102 (mp)
REVERT: G  149 MET cc_start: 0.8057 (mmt) cc_final: 0.7778 (mmp)
REVERT: G  213 GLU cc_start: 0.8314 (tp30) cc_final: 0.8102 (tm-30)
REVERT: G  215 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7678 (mm-30)
REVERT: G  216 TRP cc_start: 0.8076 (m100) cc_final: 0.7097 (m-10)
REVERT: H   72 ASP cc_start: 0.8131 (t0) cc_final: 0.7736 (t70)
REVERT: H  216 GLU cc_start: 0.8444 (pm20) cc_final: 0.8185 (pp20)
REVERT: I  117 MET cc_start: 0.7897 (mtp) cc_final: 0.6789 (mmm)
REVERT: I  118 ILE cc_start: 0.8333 (mm) cc_final: 0.8111 (mp)
REVERT: I  119 MET cc_start: 0.7169 (mmt) cc_final: 0.6764 (tpt)
REVERT: I  149 MET cc_start: 0.7945 (mmt) cc_final: 0.7675 (mmp)
REVERT: I  213 GLU cc_start: 0.8296 (tp30) cc_final: 0.8061 (tm-30)
REVERT: I  215 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7562 (mm-30)
REVERT: I  216 TRP cc_start: 0.8078 (m100) cc_final: 0.7125 (m-10)
REVERT: L   79 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8243 (mm-30)
REVERT: L  167 ASP cc_start: 0.8432 (t0) cc_final: 0.7993 (t0)
REVERT: L  169 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8564 (pptt)
REVERT: L  170 ASP cc_start: 0.8560 (t0) cc_final: 0.8046 (t0)
  outliers start: 22
  outliers final: 7
  residues processed: 137
  average time/residue: 1.5089
  time to fit residues: 218.6986
Evaluate side-chains
  125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LYS
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 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   79 GLU
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:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0570
   chunk 39 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 168 HIS
B 137 ASN
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 163 ASN
G 166 ASN
H   3 GLN
H   5 GLN
H 168 HIS
I 166 ASN
** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 137 ASN
L 189 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.125027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.073330 restraints weight = 14441.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 2.38
r_work: 0.2837 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9386  Z= 0.157
  Angle     :  0.616   6.995  12770  Z= 0.317
  Chirality :  0.043   0.170   1444
  Planarity :  0.004   0.037   1598
  Dihedral  :  4.711  19.646   1278
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.60 %
    Favored  : 85.45 %
  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:  1.18 (0.25), residues: 1188
  helix:  2.29 (0.32), residues: 272
  sheet:  0.72 (0.24), residues: 428
  loop :  0.05 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP I  89 
 HIS   0.007   0.001   HIS L 189 
 PHE   0.014   0.001   PHE G 200 
 TYR   0.019   0.001   TYR G  86 
 ARG   0.011   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03712 (  478)
  hydrogen bonds       : angle       4.74145 ( 1332)
  SS BOND              : bond        0.00419 (   12)
  SS BOND              : angle       0.49664 (   24)
  covalent geometry    : bond        0.00364 ( 9374)
  covalent geometry    : angle       0.61574 (12746)

*********************** 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: 20
    poor density    : 125
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8704 (mm-30)
REVERT: A   72 ASP cc_start: 0.8174 (t0) cc_final: 0.7695 (t70)
REVERT: B   79 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8199 (mm-30)
REVERT: B  169 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8749 (pptt)
REVERT: B  170 ASP cc_start: 0.8603 (t0) cc_final: 0.8042 (t0)
REVERT: G   46 MET cc_start: 0.5681 (ttp) cc_final: 0.4982 (mpt)
REVERT: G   48 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6115 (mp0)
REVERT: G   71 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8574 (mtp)
REVERT: G  117 MET cc_start: 0.7940 (mtp) cc_final: 0.7139 (mmm)
REVERT: G  119 MET cc_start: 0.7602 (tpp) cc_final: 0.7271 (tpt)
REVERT: G  149 MET cc_start: 0.7988 (mmt) cc_final: 0.7742 (mmp)
REVERT: G  213 GLU cc_start: 0.8324 (tp30) cc_final: 0.8059 (tm-30)
REVERT: G  216 TRP cc_start: 0.8093 (m100) cc_final: 0.7032 (m-10)
REVERT: H   10 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8715 (mm-30)
REVERT: H   72 ASP cc_start: 0.8167 (t0) cc_final: 0.7696 (t70)
REVERT: H  216 GLU cc_start: 0.8469 (pm20) cc_final: 0.8226 (pp20)
REVERT: I  117 MET cc_start: 0.7827 (mtp) cc_final: 0.7011 (mmm)
REVERT: I  118 ILE cc_start: 0.8269 (mm) cc_final: 0.8056 (mp)
REVERT: I  119 MET cc_start: 0.7113 (mmt) cc_final: 0.6693 (tpt)
REVERT: I  149 MET cc_start: 0.7937 (mmt) cc_final: 0.7693 (mmp)
REVERT: I  213 GLU cc_start: 0.8293 (tp30) cc_final: 0.8056 (tm-30)
REVERT: I  216 TRP cc_start: 0.8061 (m100) cc_final: 0.7026 (m-10)
REVERT: L   79 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8200 (mm-30)
REVERT: L  169 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8742 (pptt)
REVERT: L  170 ASP cc_start: 0.8610 (t0) cc_final: 0.8050 (t0)
  outliers start: 20
  outliers final: 4
  residues processed: 140
  average time/residue: 1.3428
  time to fit residues: 199.7606
Evaluate side-chains
  127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 I residue  100 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   79 GLU
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:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 41 optimal weight:    9.9990
   chunk 104 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 112 optimal weight:    6.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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**
B 199 GLN
G 140 ASN
H   3 GLN
H   5 GLN
H  61 GLN
H 168 HIS
I 140 ASN
I 171 ASN
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.122759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.070723 restraints weight = 14451.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 2.39
r_work: 0.2784 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   9386  Z= 0.256
  Angle     :  0.676   8.133  12770  Z= 0.345
  Chirality :  0.046   0.172   1444
  Planarity :  0.005   0.043   1598
  Dihedral  :  4.889  22.497   1278
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.70 %
    Favored  : 85.06 %
  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:  1.11 (0.24), residues: 1188
  helix:  2.12 (0.31), residues: 270
  sheet:  0.75 (0.24), residues: 434
  loop :  0.02 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP I  89 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.018   0.002   PHE G 200 
 TYR   0.022   0.002   TYR I  86 
 ARG   0.011   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04149 (  478)
  hydrogen bonds       : angle       4.88564 ( 1332)
  SS BOND              : bond        0.00510 (   12)
  SS BOND              : angle       0.60587 (   24)
  covalent geometry    : bond        0.00598 ( 9374)
  covalent geometry    : angle       0.67573 (12746)

*********************** 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
  139 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 1.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8745 (mm-30)
REVERT: A   72 ASP cc_start: 0.8242 (t0) cc_final: 0.7788 (t70)
REVERT: A  216 GLU cc_start: 0.8249 (pm20) cc_final: 0.7955 (pp20)
REVERT: B   79 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8191 (mm-30)
REVERT: B  169 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8768 (pptt)
REVERT: B  170 ASP cc_start: 0.8644 (t0) cc_final: 0.8102 (t0)
REVERT: G   46 MET cc_start: 0.6101 (ttp) cc_final: 0.5153 (mpt)
REVERT: G   48 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6153 (mp0)
REVERT: G   49 SER cc_start: 0.8352 (m) cc_final: 0.8032 (p)
REVERT: G   71 MET cc_start: 0.8955 (mtm) cc_final: 0.8558 (mtp)
REVERT: G   93 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8161 (mtp)
REVERT: G  117 MET cc_start: 0.8098 (mtp) cc_final: 0.7305 (mmm)
REVERT: G  119 MET cc_start: 0.7656 (tpp) cc_final: 0.7238 (tpt)
REVERT: G  149 MET cc_start: 0.7832 (mmt) cc_final: 0.7583 (mmp)
REVERT: G  166 ASN cc_start: 0.7932 (t0) cc_final: 0.7731 (t160)
REVERT: G  213 GLU cc_start: 0.8338 (tp30) cc_final: 0.8084 (tm-30)
REVERT: G  216 TRP cc_start: 0.8102 (m100) cc_final: 0.7099 (m-10)
REVERT: H   72 ASP cc_start: 0.8234 (t0) cc_final: 0.7773 (t70)
REVERT: I   93 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8154 (mtp)
REVERT: I  117 MET cc_start: 0.8071 (mtp) cc_final: 0.7280 (mmm)
REVERT: I  119 MET cc_start: 0.7208 (mmt) cc_final: 0.6725 (tpt)
REVERT: I  149 MET cc_start: 0.7865 (mmt) cc_final: 0.7623 (mmp)
REVERT: I  213 GLU cc_start: 0.8315 (tp30) cc_final: 0.8099 (tm-30)
REVERT: I  216 TRP cc_start: 0.8106 (m100) cc_final: 0.7105 (m-10)
REVERT: L   79 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8200 (mm-30)
REVERT: L  169 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8760 (pptt)
REVERT: L  170 ASP cc_start: 0.8651 (t0) cc_final: 0.8108 (t0)
  outliers start: 23
  outliers final: 7
  residues processed: 135
  average time/residue: 1.6867
  time to fit residues: 241.0173
Evaluate side-chains
  121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
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  142 LYS
Chi-restraints excluded: chain G residue  151 SER
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  142 LYS
Chi-restraints excluded: chain I residue  151 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   79 GLU
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:    0.0570
   chunk 112 optimal weight:    9.9990
   chunk 106 optimal weight:    0.4980
   chunk 102 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0770
   chunk 41 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.3056

-------------------------------------------------------------------------------
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**
H   3 GLN
H   5 GLN
I 166 ASN
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.126443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.075346 restraints weight = 14683.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.43
r_work: 0.2872 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9386  Z= 0.116
  Angle     :  0.590   6.631  12770  Z= 0.303
  Chirality :  0.042   0.164   1444
  Planarity :  0.004   0.045   1598
  Dihedral  :  4.500  18.648   1278
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 15.14 %
    Favored  : 83.98 %
  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:  1.34 (0.25), residues: 1188
  helix:  2.50 (0.31), residues: 272
  sheet:  0.85 (0.24), residues: 424
  loop :  0.09 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP I  89 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.012   0.001   PHE G 200 
 TYR   0.016   0.001   TYR G  86 
 ARG   0.013   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03424 (  478)
  hydrogen bonds       : angle       4.58857 ( 1332)
  SS BOND              : bond        0.00383 (   12)
  SS BOND              : angle       0.42703 (   24)
  covalent geometry    : bond        0.00262 ( 9374)
  covalent geometry    : angle       0.59023 (12746)

*********************** 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
  130 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8737 (mm-30)
REVERT: A   72 ASP cc_start: 0.8152 (t0) cc_final: 0.7642 (t70)
REVERT: B   53 ASN cc_start: 0.9155 (m110) cc_final: 0.8900 (m110)
REVERT: B   79 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8200 (mm-30)
REVERT: B  145 LYS cc_start: 0.8710 (ptmm) cc_final: 0.8006 (pptt)
REVERT: B  169 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8816 (pptt)
REVERT: B  170 ASP cc_start: 0.8699 (t0) cc_final: 0.8181 (t0)
REVERT: G   46 MET cc_start: 0.5827 (ttp) cc_final: 0.5098 (mpt)
REVERT: G   48 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6069 (mp0)
REVERT: G   49 SER cc_start: 0.8268 (m) cc_final: 0.7977 (p)
REVERT: G   71 MET cc_start: 0.8954 (mtm) cc_final: 0.8557 (mtp)
REVERT: G  117 MET cc_start: 0.7859 (mtp) cc_final: 0.7081 (mmm)
REVERT: G  119 MET cc_start: 0.7571 (tpp) cc_final: 0.7201 (tpt)
REVERT: G  149 MET cc_start: 0.7904 (mmt) cc_final: 0.7685 (mmp)
REVERT: G  213 GLU cc_start: 0.8275 (tp30) cc_final: 0.8051 (tm-30)
REVERT: G  216 TRP cc_start: 0.8080 (m100) cc_final: 0.7078 (m-10)
REVERT: H   72 ASP cc_start: 0.8144 (t0) cc_final: 0.7645 (t70)
REVERT: I  117 MET cc_start: 0.7696 (mtp) cc_final: 0.6928 (mmm)
REVERT: I  119 MET cc_start: 0.7058 (mmt) cc_final: 0.6653 (tpt)
REVERT: I  149 MET cc_start: 0.7866 (mmt) cc_final: 0.7651 (mmp)
REVERT: I  213 GLU cc_start: 0.8274 (tp30) cc_final: 0.8027 (tm-30)
REVERT: I  216 TRP cc_start: 0.8088 (m100) cc_final: 0.7108 (m-10)
REVERT: L   53 ASN cc_start: 0.9172 (m110) cc_final: 0.8922 (m110)
REVERT: L   79 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8193 (mm-30)
REVERT: L  169 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8808 (pptt)
REVERT: L  170 ASP cc_start: 0.8703 (t0) cc_final: 0.8181 (t0)
  outliers start: 9
  outliers final: 4
  residues processed: 130
  average time/residue: 1.6437
  time to fit residues: 227.7431
Evaluate side-chains
  122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
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 I residue  118 ILE
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   79 GLU
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:    3.9990
   chunk 20 optimal weight:   20.0000
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0870
   chunk 100 optimal weight:    1.9990
   chunk 1 optimal weight:    0.1980
   chunk 48 optimal weight:    0.1980
   chunk 0 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   overall best weight:    0.6560

-------------------------------------------------------------------------------
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
H   5 GLN
H  61 GLN
** 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 = 0.3808 r_free = 0.3808 target = 0.125097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.073472 restraints weight = 14868.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 2.44
r_work: 0.2833 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9386  Z= 0.160
  Angle     :  0.617   6.946  12770  Z= 0.316
  Chirality :  0.042   0.142   1444
  Planarity :  0.004   0.052   1598
  Dihedral  :  4.539  20.205   1278
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.33 %
    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:  1.38 (0.25), residues: 1188
  helix:  2.45 (0.31), residues: 272
  sheet:  0.94 (0.24), residues: 424
  loop :  0.10 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP I  89 
 HIS   0.006   0.001   HIS L 189 
 PHE   0.014   0.001   PHE G 200 
 TYR   0.019   0.001   TYR I  86 
 ARG   0.013   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03668 (  478)
  hydrogen bonds       : angle       4.59021 ( 1332)
  SS BOND              : bond        0.00353 (   12)
  SS BOND              : angle       0.50452 (   24)
  covalent geometry    : bond        0.00370 ( 9374)
  covalent geometry    : angle       0.61713 (12746)

*********************** 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
  125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8772 (mm-30)
REVERT: A   72 ASP cc_start: 0.8194 (t0) cc_final: 0.7703 (t70)
REVERT: A  159 ASN cc_start: 0.7780 (m-40) cc_final: 0.7558 (m110)
REVERT: A  199 ILE cc_start: 0.8681 (pp) cc_final: 0.8428 (tp)
REVERT: A  200 CYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8751 (p)
REVERT: B   79 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8159 (mm-30)
REVERT: B  169 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8838 (pptt)
REVERT: B  170 ASP cc_start: 0.8733 (t0) cc_final: 0.8223 (t0)
REVERT: G   46 MET cc_start: 0.6037 (ttp) cc_final: 0.5143 (mpt)
REVERT: G   48 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6084 (mp0)
REVERT: G   49 SER cc_start: 0.8317 (m) cc_final: 0.7875 (t)
REVERT: G   71 MET cc_start: 0.8898 (mtm) cc_final: 0.8490 (mtp)
REVERT: G  117 MET cc_start: 0.7798 (mtp) cc_final: 0.7425 (tpp)
REVERT: G  119 MET cc_start: 0.7697 (tpp) cc_final: 0.7341 (tpt)
REVERT: G  149 MET cc_start: 0.7887 (mmt) cc_final: 0.7664 (mmp)
REVERT: G  213 GLU cc_start: 0.8314 (tp30) cc_final: 0.8076 (tm-30)
REVERT: G  216 TRP cc_start: 0.8068 (m100) cc_final: 0.7107 (m-10)
REVERT: H   72 ASP cc_start: 0.8218 (t0) cc_final: 0.7720 (t70)
REVERT: H  159 ASN cc_start: 0.7804 (m-40) cc_final: 0.7587 (m110)
REVERT: H  199 ILE cc_start: 0.8760 (pp) cc_final: 0.8531 (tp)
REVERT: H  216 GLU cc_start: 0.8249 (pm20) cc_final: 0.7859 (pp20)
REVERT: I  117 MET cc_start: 0.7717 (mtp) cc_final: 0.7299 (tpp)
REVERT: I  119 MET cc_start: 0.7123 (mmt) cc_final: 0.6713 (tpt)
REVERT: I  149 MET cc_start: 0.7894 (mmt) cc_final: 0.7556 (mmp)
REVERT: I  213 GLU cc_start: 0.8274 (tp30) cc_final: 0.8057 (tm-30)
REVERT: I  216 TRP cc_start: 0.8086 (m100) cc_final: 0.7129 (m-10)
REVERT: L   79 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8163 (mm-30)
REVERT: L  169 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8833 (pptt)
REVERT: L  170 ASP cc_start: 0.8733 (t0) cc_final: 0.8226 (t0)
  outliers start: 11
  outliers final: 3
  residues processed: 124
  average time/residue: 1.5062
  time to fit residues: 197.8328
Evaluate side-chains
  120 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
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 I residue  118 ILE
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   79 GLU
Chi-restraints excluded: chain L residue  169 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 116 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.0184

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.123692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.071539 restraints weight = 14360.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.39
r_work: 0.2798 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2666 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9386  Z= 0.216
  Angle     :  0.666   7.982  12770  Z= 0.339
  Chirality :  0.044   0.151   1444
  Planarity :  0.005   0.056   1598
  Dihedral  :  4.721  22.128   1278
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.43 %
    Favored  : 83.50 %
  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:  1.38 (0.24), residues: 1188
  helix:  2.37 (0.30), residues: 270
  sheet:  1.04 (0.24), residues: 432
  loop :  0.03 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP I  89 
 HIS   0.007   0.001   HIS B 189 
 PHE   0.017   0.002   PHE G 200 
 TYR   0.022   0.002   TYR I  86 
 ARG   0.014   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03925 (  478)
  hydrogen bonds       : angle       4.73789 ( 1332)
  SS BOND              : bond        0.00386 (   12)
  SS BOND              : angle       0.54748 (   24)
  covalent geometry    : bond        0.00504 ( 9374)
  covalent geometry    : angle       0.66654 (12746)

*********************** 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
  123 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8730 (mm-30)
REVERT: A   72 ASP cc_start: 0.8247 (t0) cc_final: 0.7743 (t70)
REVERT: A  199 ILE cc_start: 0.8675 (pp) cc_final: 0.8452 (tp)
REVERT: A  200 CYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8691 (p)
REVERT: A  216 GLU cc_start: 0.8297 (pm20) cc_final: 0.7927 (pp20)
REVERT: B   79 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8200 (mm-30)
REVERT: B  169 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8856 (pptt)
REVERT: B  170 ASP cc_start: 0.8728 (t0) cc_final: 0.8214 (t0)
REVERT: G   46 MET cc_start: 0.6086 (ttp) cc_final: 0.4858 (mpt)
REVERT: G   48 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6166 (mp0)
REVERT: G   49 SER cc_start: 0.8336 (m) cc_final: 0.7872 (t)
REVERT: G   71 MET cc_start: 0.8921 (mtm) cc_final: 0.8522 (mtp)
REVERT: G  117 MET cc_start: 0.7915 (mtp) cc_final: 0.7581 (tpp)
REVERT: G  119 MET cc_start: 0.7684 (tpp) cc_final: 0.7360 (tpt)
REVERT: G  149 MET cc_start: 0.7846 (mmt) cc_final: 0.7624 (mmp)
REVERT: G  213 GLU cc_start: 0.8349 (tp30) cc_final: 0.8113 (tm-30)
REVERT: G  216 TRP cc_start: 0.8091 (m100) cc_final: 0.7127 (m-10)
REVERT: H   72 ASP cc_start: 0.8256 (t0) cc_final: 0.7760 (t70)
REVERT: H  199 ILE cc_start: 0.8669 (pp) cc_final: 0.8464 (tp)
REVERT: H  216 GLU cc_start: 0.8272 (pm20) cc_final: 0.7919 (pp20)
REVERT: I  117 MET cc_start: 0.7841 (mtp) cc_final: 0.7331 (tpp)
REVERT: I  213 GLU cc_start: 0.8307 (tp30) cc_final: 0.8082 (tm-30)
REVERT: I  216 TRP cc_start: 0.8089 (m100) cc_final: 0.7117 (m-10)
REVERT: L   79 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8206 (mm-30)
REVERT: L  169 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8857 (pptt)
REVERT: L  170 ASP cc_start: 0.8733 (t0) cc_final: 0.8224 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 119
  average time/residue: 1.5132
  time to fit residues: 190.4726
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  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
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 I residue  118 ILE
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   79 GLU
Chi-restraints excluded: chain L residue  169 LYS
Chi-restraints excluded: chain L residue  199 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 114 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 110 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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
A 159 ASN
B 199 GLN
H   3 GLN
H   5 GLN
H  61 GLN
** 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 = 0.3805 r_free = 0.3805 target = 0.124176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.072196 restraints weight = 14638.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.41
r_work: 0.2811 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9386  Z= 0.182
  Angle     :  0.651   7.532  12770  Z= 0.332
  Chirality :  0.043   0.146   1444
  Planarity :  0.005   0.058   1598
  Dihedral  :  4.666  21.530   1278
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 15.62 %
    Favored  : 83.40 %
  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 (0.24), residues: 1188
  helix:  2.20 (0.30), residues: 282
  sheet:  0.89 (0.24), residues: 422
  loop :  0.05 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP I  89 
 HIS   0.009   0.001   HIS B 189 
 PHE   0.016   0.001   PHE G 200 
 TYR   0.020   0.002   TYR I  86 
 ARG   0.015   0.002   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (  478)
  hydrogen bonds       : angle       4.69150 ( 1332)
  SS BOND              : bond        0.00360 (   12)
  SS BOND              : angle       0.51665 (   24)
  covalent geometry    : bond        0.00425 ( 9374)
  covalent geometry    : angle       0.65130 (12746)

********************** 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
  118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8720 (mm-30)
REVERT: A   72 ASP cc_start: 0.8258 (t0) cc_final: 0.7754 (t70)
REVERT: A  200 CYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8813 (p)
REVERT: B   79 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8179 (mm-30)
REVERT: B  170 ASP cc_start: 0.8735 (t0) cc_final: 0.8219 (t0)
REVERT: G   46 MET cc_start: 0.6054 (ttp) cc_final: 0.4841 (mpt)
REVERT: G   48 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6170 (mp0)
REVERT: G   49 SER cc_start: 0.8335 (m) cc_final: 0.7998 (p)
REVERT: G   71 MET cc_start: 0.8907 (mtm) cc_final: 0.8505 (mtp)
REVERT: G  117 MET cc_start: 0.7813 (mtp) cc_final: 0.7469 (tpp)
REVERT: G  119 MET cc_start: 0.7674 (tpp) cc_final: 0.7346 (tpt)
REVERT: G  149 MET cc_start: 0.7822 (mmt) cc_final: 0.7596 (mmp)
REVERT: G  213 GLU cc_start: 0.8317 (tp30) cc_final: 0.8095 (tm-30)
REVERT: G  216 TRP cc_start: 0.8049 (m100) cc_final: 0.7068 (m-10)
REVERT: H   72 ASP cc_start: 0.8260 (t0) cc_final: 0.7773 (t70)
REVERT: H  216 GLU cc_start: 0.8280 (pm20) cc_final: 0.7960 (pp20)
REVERT: I  117 MET cc_start: 0.7844 (mtp) cc_final: 0.7384 (tpp)
REVERT: I  213 GLU cc_start: 0.8273 (tp30) cc_final: 0.8068 (tm-30)
REVERT: I  216 TRP cc_start: 0.8070 (m100) cc_final: 0.7090 (m-10)
REVERT: L   79 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8207 (mm-30)
REVERT: L  167 ASP cc_start: 0.8472 (t0) cc_final: 0.8118 (t0)
REVERT: L  170 ASP cc_start: 0.8732 (t0) cc_final: 0.8216 (t0)
  outliers start: 10
  outliers final: 3
  residues processed: 116
  average time/residue: 1.4931
  time to fit residues: 183.4236
Evaluate side-chains
  113 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   79 GLU
Chi-restraints excluded: chain L residue  199 GLN
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:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 17 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0870
   chunk 63 optimal weight:    0.7980
   chunk 110 optimal weight:    4.9990
   overall best weight:    0.8160

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.124236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.072200 restraints weight = 14558.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.40
r_work: 0.2812 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9386  Z= 0.185
  Angle     :  0.654   7.456  12770  Z= 0.334
  Chirality :  0.043   0.147   1444
  Planarity :  0.005   0.059   1598
  Dihedral  :  4.668  21.581   1278
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 15.82 %
    Favored  : 83.20 %
  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:  2.18 (0.30), residues: 282
  sheet:  1.05 (0.24), residues: 432
  loop : -0.01 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP I  89 
 HIS   0.009   0.001   HIS B 189 
 PHE   0.016   0.001   PHE G 200 
 TYR   0.020   0.002   TYR I  86 
 ARG   0.015   0.002   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03766 (  478)
  hydrogen bonds       : angle       4.68108 ( 1332)
  SS BOND              : bond        0.00353 (   12)
  SS BOND              : angle       0.52782 (   24)
  covalent geometry    : bond        0.00432 ( 9374)
  covalent geometry    : angle       0.65451 (12746)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10556.48 seconds
wall clock time: 182 minutes 50.06 seconds (10970.06 seconds total)