Starting phenix.real_space_refine
on Thu Mar 13 20:31:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vgo_43216/03_2025/8vgo_43216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vgo_43216/03_2025/8vgo_43216.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vgo_43216/03_2025/8vgo_43216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vgo_43216/03_2025/8vgo_43216.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vgo_43216/03_2025/8vgo_43216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vgo_43216/03_2025/8vgo_43216.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.004
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      70      5.16       5
     C    5822      2.51       5
     N    1502      2.21       5
     O    1754      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9148
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1670
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 12, 'TRANS': 212}
    Chain: "B"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1620
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200}
    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: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1670
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 12, 'TRANS': 212}
    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: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1620
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200}
  Time building chain proxies: 6.28, per 1000 atoms: 0.69
  Number of scatterers: 9148
  At special positions: 0
  Unit cell: (100.12, 126.319, 130.998, 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      70     16.00
     O    1754      8.00
     N    1502      7.00
     C    5822      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  11 " - pdb=" SG  CYS A 151 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 108 " - pdb=" SG  CYS A 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 144 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 221 " - 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  40 " - pdb=" SG  CYS B 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  80 " - pdb=" SG  CYS B 171 " distance=2.03
    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  11 " - pdb=" SG  CYS H 151 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 108 " - pdb=" SG  CYS H 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 221 " - 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  40 " - pdb=" SG  CYS L 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  80 " - pdb=" SG  CYS L 171 " distance=2.03
    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: 2.09
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2228

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 22 sheets defined
      28.9% alpha, 38.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.671A  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 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 192 through 195
      removed outlier: 3.631A  pdb=" N   GLY A 195 " --> pdb=" O   SER A 192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 192 through 195'
    Processing helix  chain 'A' and resid 206 through 209
    Processing helix  chain 'B' and resid 79 through 83
    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 97
    Processing helix  chain 'G' and resid 98 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: 3.698A  pdb=" N   ASN G 176 " --> pdb=" O   SER G 173 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 177 through 216
      removed outlier: 5.106A  pdb=" N   ASN G 214 " --> pdb=" O   GLY G 210 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.627A  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 161 through 163
      No H-bonds generated for 'chain 'H' and resid 161 through 163'
    Processing helix  chain 'H' and resid 192 through 195
      removed outlier: 3.628A  pdb=" N   GLY H 195 " --> pdb=" O   SER H 192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 192 through 195'
    Processing helix  chain 'H' and resid 206 through 209
    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 97
    Processing helix  chain 'I' and resid 98 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: 3.696A  pdb=" N   ASN I 176 " --> pdb=" O   SER I 173 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 177 through 216
      removed outlier: 5.103A  pdb=" N   ASN I 214 " --> pdb=" O   GLY I 210 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
    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: 4.068A  pdb=" N   ASN A  33 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   MET A  34 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ALA A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.701A  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: 7.037A  pdb=" N   CYS A  92 " --> pdb=" O   TRP A 103 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   TRP A 103 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ARG A  94 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 128
      removed outlier: 5.576A  pdb=" N   TYR A 181 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 136
      removed outlier: 5.576A  pdb=" N   TYR A 181 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 159
      removed outlier: 4.105A  pdb=" N   TYR A 199 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    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: 6.431A  pdb=" N   TRP B  35 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13
    Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118
      removed outlier: 5.802A  pdb=" N   TYR B 173 " --> pdb=" O   ASN B 138 " (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: 4.063A  pdb=" N   ASN H  33 " --> pdb=" O   SER H  95 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   MET H  34 " --> pdb=" O   ALA H  50 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ALA H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.723A  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: 4.850A  pdb=" N   TRP H 103 " --> pdb=" O   CYS H  92 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   ARG H  94 " --> pdb=" O   ASN H 101 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 128
      removed outlier: 5.576A  pdb=" N   TYR H 181 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 135 through 136
      removed outlier: 5.576A  pdb=" N   TYR H 181 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 156 through 159
      removed outlier: 4.105A  pdb=" N   TYR H 199 " --> pdb=" O   VAL H 216 " (cutoff:3.500A)
    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: 6.421A  pdb=" N   TRP L  35 " --> pdb=" O   TRP L  47 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AC3, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.800A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 153 through 154

    548 hydrogen bonds defined for protein.
    1410 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.93

  Time building geometry restraints manager: 2.53 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: 2842
        1.34 -     1.46: 2162
        1.46 -     1.58: 4266
        1.58 -     1.70: 0
        1.70 -     1.82: 98
  Bond restraints: 9368
  Sorted by residual:
  bond pdb=" CB  ILE I 162 "
       pdb=" CG1 ILE I 162 "
    ideal  model  delta    sigma   weight residual
    1.530  1.512  0.018 2.00e-02 2.50e+03 7.83e-01
  bond pdb=" CB  ILE G 162 "
       pdb=" CG1 ILE G 162 "
    ideal  model  delta    sigma   weight residual
    1.530  1.513  0.017 2.00e-02 2.50e+03 7.18e-01
  bond pdb=" CB  GLU G 150 "
       pdb=" CG  GLU G 150 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.03e-01
  bond pdb=" CB  GLU I 150 "
       pdb=" CG  GLU I 150 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.88e-01
  bond pdb=" CB  VAL L  19 "
       pdb=" CG1 VAL L  19 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.34e-01
  ... (remaining 9363 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 12024
        1.30 -     2.60: 572
        2.60 -     3.90: 104
        3.90 -     5.20: 13
        5.20 -     6.50: 17
  Bond angle restraints: 12730
  Sorted by residual:
  angle pdb=" C   PHE A 150 "
        pdb=" N   CYS A 151 "
        pdb=" CA  CYS A 151 "
      ideal   model   delta    sigma   weight residual
     121.54  128.04   -6.50 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" C   PHE H 150 "
        pdb=" N   CYS H 151 "
        pdb=" CA  CYS H 151 "
      ideal   model   delta    sigma   weight residual
     121.54  128.04   -6.50 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" CA  TYR G 182 "
        pdb=" CB  TYR G 182 "
        pdb=" CG  TYR G 182 "
      ideal   model   delta    sigma   weight residual
     113.90  119.58   -5.68 1.80e+00 3.09e-01 9.95e+00
  angle pdb=" CA  TYR I 182 "
        pdb=" CB  TYR I 182 "
        pdb=" CG  TYR I 182 "
      ideal   model   delta    sigma   weight residual
     113.90  119.54   -5.64 1.80e+00 3.09e-01 9.83e+00
  angle pdb=" C   SER L  26 "
        pdb=" N   SER L  28 "
        pdb=" CA  SER L  28 "
      ideal   model   delta    sigma   weight residual
     121.54  127.47   -5.93 1.91e+00 2.74e-01 9.63e+00
  ... (remaining 12725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 5163
       17.55 -    35.09: 375
       35.09 -    52.64: 43
       52.64 -    70.19: 21
       70.19 -    87.74: 16
  Dihedral angle restraints: 5618
    sinusoidal: 2134
      harmonic: 3484
  Sorted by residual:
  dihedral pdb=" CA  PHE H 150 "
           pdb=" C   PHE H 150 "
           pdb=" N   CYS H 151 "
           pdb=" CA  CYS H 151 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.78  -26.22     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" CA  PHE A 150 "
           pdb=" C   PHE A 150 "
           pdb=" N   CYS A 151 "
           pdb=" CA  CYS A 151 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.85  -26.15     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  LYS H 219 "
           pdb=" C   LYS H 219 "
           pdb=" N   SER H 220 "
           pdb=" CA  SER H 220 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.85   26.15     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 5615 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 766
       0.029 -    0.058: 422
       0.058 -    0.086: 150
       0.086 -    0.115: 82
       0.115 -    0.144: 22
  Chirality restraints: 1442
  Sorted by residual:
  chirality pdb=" CA  ILE L   2 "
            pdb=" N   ILE L   2 "
            pdb=" C   ILE L   2 "
            pdb=" CB  ILE L   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  ILE B   2 "
            pdb=" N   ILE B   2 "
            pdb=" C   ILE B   2 "
            pdb=" CB  ILE B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CB  ILE G 162 "
            pdb=" CA  ILE G 162 "
            pdb=" CG1 ILE G 162 "
            pdb=" CG2 ILE G 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 1439 not shown)

  Planarity restraints: 1594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  77 "    0.364 9.50e-02 1.11e+02   1.65e-01 2.11e+01
        pdb=" NE  ARG B  77 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  77 "    0.034 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  77 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  77 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L  77 "   -0.365 9.50e-02 1.11e+02   1.65e-01 2.10e+01
        pdb=" NE  ARG L  77 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG L  77 "   -0.033 2.00e-02 2.50e+03
        pdb=" NH1 ARG L  77 "    0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG L  77 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  52 "    0.001 2.00e-02 2.50e+03   2.97e-02 1.77e+01
        pdb=" CG  TYR A  52 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  52 "    0.042 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  52 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  52 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  52 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  52 "   -0.042 2.00e-02 2.50e+03
        pdb=" OH  TYR A  52 "    0.042 2.00e-02 2.50e+03
  ... (remaining 1591 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2790
        2.83 -     3.35: 8686
        3.35 -     3.86: 16018
        3.86 -     4.38: 19300
        4.38 -     4.90: 32252
  Nonbonded interactions: 79046
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU L 105 "
            pdb=" OH  TYR L 173 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OE1 GLU B 105 "
            pdb=" OH  TYR B 173 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR H  97 "
            pdb=" OE1 GLU I 174 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" NZ  LYS H 215 "
            pdb=" OE1 GLU H 217 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NZ  LYS A 215 "
            pdb=" OE1 GLU A 217 "
     model   vdw
     2.322 3.120
  ... (remaining 79041 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:             3.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.220
  Find NCS groups from input model:        0.260
  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:             0.010
  Load rotamer database and sin/cos tables:11.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
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      :  0.003   0.041   9368  Z= 0.201
  Angle     :  0.676   6.503  12730  Z= 0.374
  Chirality :  0.044   0.144   1442
  Planarity :  0.008   0.165   1594
  Dihedral  : 13.676  87.737   3330
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  4.79 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.53 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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: -0.28 (0.24), residues: 1190
  helix: -1.16 (0.25), residues: 270
  sheet:  0.80 (0.24), residues: 418
  loop : -0.34 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP G  89 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.027   0.002   PHE H 100D
 TYR   0.042   0.005   TYR A  52 
 ARG   0.038   0.005   ARG B  77 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 220
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 GLU cc_start: 0.8144 (tt0) cc_final: 0.7943 (tm-30)
REVERT: G   76 ILE cc_start: 0.7825 (mt) cc_final: 0.7584 (tp)
REVERT: G  137 ASP cc_start: 0.7669 (m-30) cc_final: 0.7168 (m-30)
REVERT: G  203 PHE cc_start: 0.8010 (t80) cc_final: 0.7737 (t80)
REVERT: I   76 ILE cc_start: 0.7824 (mt) cc_final: 0.7536 (tp)
REVERT: I   85 TRP cc_start: 0.8183 (m100) cc_final: 0.7979 (m100)
REVERT: I  137 ASP cc_start: 0.7611 (m-30) cc_final: 0.7136 (m-30)
REVERT: I  203 PHE cc_start: 0.8012 (t80) cc_final: 0.7705 (t80)
REVERT: L   17 GLU cc_start: 0.8605 (tt0) cc_final: 0.8386 (tt0)
  outliers start: 2
  outliers final: 0
  residues processed: 221
  average time/residue: 1.4544
  time to fit residues: 339.7383
Evaluate side-chains
  148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0670
   chunk 30 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   chunk 47 optimal weight:    0.5980
   chunk 92 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A 202 ASN
B 138 ASN
G  56 GLN
G 171 ASN
H 202 ASN
I  56 GLN
I 171 ASN
L 138 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.106625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.073755 restraints weight = 15022.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.47
r_work: 0.2871 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9368  Z= 0.211
  Angle     :  0.646   6.604  12730  Z= 0.344
  Chirality :  0.044   0.151   1442
  Planarity :  0.005   0.050   1594
  Dihedral  :  5.682  39.563   1280
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.18 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.80 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1190
  helix:  1.20 (0.31), residues: 268
  sheet:  1.03 (0.23), residues: 424
  loop :  0.34 (0.30), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP G  89 
 HIS   0.003   0.001   HIS A  35 
 PHE   0.020   0.002   PHE A 100D
 TYR   0.018   0.002   TYR H  98 
 ARG   0.011   0.001   ARG B  24 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.8811 (tt0) cc_final: 0.8586 (tm-30)
REVERT: A  152 GLU cc_start: 0.8226 (tt0) cc_final: 0.7876 (tm-30)
REVERT: B  123 GLU cc_start: 0.8341 (mp0) cc_final: 0.8126 (mp0)
REVERT: B  147 GLN cc_start: 0.9071 (tp40) cc_final: 0.8824 (mt0)
REVERT: B  187 GLU cc_start: 0.9244 (mt-10) cc_final: 0.9041 (mm-30)
REVERT: G   76 ILE cc_start: 0.7964 (mt) cc_final: 0.7683 (tp)
REVERT: G  117 MET cc_start: 0.6026 (tmm) cc_final: 0.5547 (mtt)
REVERT: G  137 ASP cc_start: 0.7669 (m-30) cc_final: 0.7065 (m-30)
REVERT: G  203 PHE cc_start: 0.7680 (t80) cc_final: 0.7383 (t80)
REVERT: H    3 GLN cc_start: 0.8793 (tt0) cc_final: 0.8576 (tm-30)
REVERT: H   72 ASP cc_start: 0.8563 (t0) cc_final: 0.8230 (t0)
REVERT: H  152 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7669 (tm-30)
REVERT: I   76 ILE cc_start: 0.8116 (mt) cc_final: 0.7770 (tp)
REVERT: I   85 TRP cc_start: 0.8209 (m100) cc_final: 0.7981 (m100)
REVERT: I  117 MET cc_start: 0.6010 (tmm) cc_final: 0.5481 (mtt)
REVERT: I  137 ASP cc_start: 0.7666 (m-30) cc_final: 0.7071 (m-30)
REVERT: I  203 PHE cc_start: 0.7676 (t80) cc_final: 0.7390 (t80)
REVERT: L  123 GLU cc_start: 0.8336 (mp0) cc_final: 0.8132 (mp0)
REVERT: L  147 GLN cc_start: 0.9082 (tp40) cc_final: 0.8848 (mt0)
REVERT: L  187 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9031 (mm-30)
  outliers start: 14
  outliers final: 4
  residues processed: 157
  average time/residue: 1.2395
  time to fit residues: 207.2539
Evaluate side-chains
  146 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 142
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain I residue   51 THR
Chi-restraints excluded: chain L residue  154 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 113 optimal weight:    0.1980
   chunk 50 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
G  56 GLN
I  56 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.102210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.067756 restraints weight = 15333.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 2.57
r_work: 0.2776 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2641 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078   9368  Z= 0.384
  Angle     :  0.662   6.175  12730  Z= 0.353
  Chirality :  0.046   0.200   1442
  Planarity :  0.005   0.039   1594
  Dihedral  :  5.580  36.225   1280
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.02 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.28 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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 (0.24), residues: 1190
  helix:  1.21 (0.31), residues: 280
  sheet:  1.08 (0.24), residues: 422
  loop :  0.06 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP G  89 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.019   0.002   PHE H 100D
 TYR   0.020   0.002   TYR A  98 
 ARG   0.008   0.001   ARG L 142 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 GLU cc_start: 0.8218 (tt0) cc_final: 0.7892 (tm-30)
REVERT: B  123 GLU cc_start: 0.8319 (mp0) cc_final: 0.8065 (mp0)
REVERT: B  142 ARG cc_start: 0.8627 (ttt-90) cc_final: 0.7798 (tmt170)
REVERT: B  147 GLN cc_start: 0.9038 (tp40) cc_final: 0.8768 (mt0)
REVERT: B  170 ASP cc_start: 0.8004 (t0) cc_final: 0.7590 (t0)
REVERT: G   76 ILE cc_start: 0.8117 (mt) cc_final: 0.7886 (tp)
REVERT: G  137 ASP cc_start: 0.7533 (m-30) cc_final: 0.7112 (m-30)
REVERT: G  203 PHE cc_start: 0.7820 (t80) cc_final: 0.7564 (t80)
REVERT: H  152 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: I   76 ILE cc_start: 0.8118 (mt) cc_final: 0.7866 (tp)
REVERT: I   85 TRP cc_start: 0.8323 (m100) cc_final: 0.8094 (m100)
REVERT: I  137 ASP cc_start: 0.7625 (m-30) cc_final: 0.7210 (m-30)
REVERT: I  203 PHE cc_start: 0.7816 (t80) cc_final: 0.7535 (t80)
REVERT: L  123 GLU cc_start: 0.8317 (mp0) cc_final: 0.8064 (mp0)
REVERT: L  142 ARG cc_start: 0.8645 (ttt-90) cc_final: 0.7818 (tmt170)
REVERT: L  147 GLN cc_start: 0.9082 (tt0) cc_final: 0.8837 (mt0)
REVERT: L  170 ASP cc_start: 0.8015 (t0) cc_final: 0.7596 (t0)
  outliers start: 23
  outliers final: 5
  residues processed: 162
  average time/residue: 1.4220
  time to fit residues: 245.6615
Evaluate side-chains
  148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 143
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain I residue   51 THR
Chi-restraints excluded: chain I residue  162 ILE
Chi-restraints excluded: chain L residue  154 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0980
   chunk 47 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
A 202 ASN
A 204 ASN
G  56 GLN
H   5 GLN
H 202 ASN
H 204 ASN
I  56 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.103764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.070055 restraints weight = 14855.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.49
r_work: 0.2802 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9368  Z= 0.222
  Angle     :  0.612   7.919  12730  Z= 0.322
  Chirality :  0.043   0.173   1442
  Planarity :  0.004   0.055   1594
  Dihedral  :  5.167  29.508   1280
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.52 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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:  1.14 (0.24), residues: 1190
  helix:  1.43 (0.31), residues: 282
  sheet:  1.16 (0.24), residues: 422
  loop :  0.06 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP G  89 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.015   0.002   PHE H 100D
 TYR   0.016   0.001   TYR I  86 
 ARG   0.014   0.001   ARG B  24 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 GLU cc_start: 0.8064 (tt0) cc_final: 0.7710 (tm-30)
REVERT: B  123 GLU cc_start: 0.8243 (mp0) cc_final: 0.7974 (mp0)
REVERT: B  142 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.7710 (tmt170)
REVERT: B  147 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8700 (mt0)
REVERT: B  183 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7755 (tttm)
REVERT: G  117 MET cc_start: 0.5961 (tmm) cc_final: 0.5451 (mtt)
REVERT: G  137 ASP cc_start: 0.7597 (m-30) cc_final: 0.6939 (m-30)
REVERT: G  203 PHE cc_start: 0.7619 (t80) cc_final: 0.7331 (t80)
REVERT: H  152 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: I   76 ILE cc_start: 0.7940 (mt) cc_final: 0.7703 (tp)
REVERT: I  117 MET cc_start: 0.6000 (tmm) cc_final: 0.5423 (mtt)
REVERT: I  137 ASP cc_start: 0.7655 (m-30) cc_final: 0.6994 (m-30)
REVERT: I  203 PHE cc_start: 0.7588 (t80) cc_final: 0.7298 (t80)
REVERT: L  123 GLU cc_start: 0.8241 (mp0) cc_final: 0.7973 (mp0)
REVERT: L  142 ARG cc_start: 0.8622 (ttt-90) cc_final: 0.7705 (tmt170)
REVERT: L  147 GLN cc_start: 0.8972 (tt0) cc_final: 0.8733 (mt0)
REVERT: L  183 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7778 (tttm)
  outliers start: 23
  outliers final: 2
  residues processed: 164
  average time/residue: 1.6362
  time to fit residues: 285.1717
Evaluate side-chains
  143 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  183 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 78 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 96 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A 204 ASN
G  56 GLN
H   3 GLN
H 204 ASN
I  56 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.106322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.074005 restraints weight = 14960.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.38
r_work: 0.2867 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9368  Z= 0.267
  Angle     :  0.616   6.395  12730  Z= 0.326
  Chirality :  0.044   0.148   1442
  Planarity :  0.004   0.042   1594
  Dihedral  :  5.130  25.254   1280
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.11 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.72 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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:  1.22 (0.24), residues: 1190
  helix:  1.70 (0.31), residues: 272
  sheet:  1.25 (0.24), residues: 420
  loop : -0.01 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP G  89 
 HIS   0.002   0.001   HIS A  35 
 PHE   0.016   0.002   PHE G  62 
 TYR   0.019   0.002   TYR G 182 
 ARG   0.010   0.001   ARG L  24 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 1.023 
Fit side-chains
REVERT: B  123 GLU cc_start: 0.8380 (mp0) cc_final: 0.8105 (mp0)
REVERT: B  147 GLN cc_start: 0.9034 (tp40) cc_final: 0.8764 (mt0)
REVERT: G  117 MET cc_start: 0.6197 (tmm) cc_final: 0.5593 (mtt)
REVERT: G  137 ASP cc_start: 0.7596 (m-30) cc_final: 0.7143 (m-30)
REVERT: G  203 PHE cc_start: 0.7789 (t80) cc_final: 0.7499 (t80)
REVERT: H    3 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8493 (tm-30)
REVERT: H    5 GLN cc_start: 0.8748 (mm110) cc_final: 0.8451 (mm110)
REVERT: H  152 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7859 (tm-30)
REVERT: I  137 ASP cc_start: 0.7630 (m-30) cc_final: 0.7206 (m-30)
REVERT: I  203 PHE cc_start: 0.7785 (t80) cc_final: 0.7509 (t80)
REVERT: L   40 CYS cc_start: 0.8090 (m) cc_final: 0.7801 (m)
REVERT: L  123 GLU cc_start: 0.8385 (mp0) cc_final: 0.8112 (mp0)
REVERT: L  147 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8829 (mt0)
  outliers start: 25
  outliers final: 2
  residues processed: 156
  average time/residue: 1.5048
  time to fit residues: 250.0260
Evaluate side-chains
  142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 138
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  154 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 6 optimal weight:    0.0970
   chunk 20 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 112 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 204 ASN
G  56 GLN
H 202 ASN
H 204 ASN
I  56 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.108837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.077864 restraints weight = 15861.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.43
r_work: 0.3059 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9368  Z= 0.238
  Angle     :  0.625   8.512  12730  Z= 0.329
  Chirality :  0.043   0.156   1442
  Planarity :  0.004   0.069   1594
  Dihedral  :  5.027  20.211   1280
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.69 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.24), residues: 1190
  helix:  1.78 (0.31), residues: 272
  sheet:  1.22 (0.24), residues: 428
  loop :  0.06 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP G  89 
 HIS   0.002   0.001   HIS A  35 
 PHE   0.014   0.001   PHE A 100D
 TYR   0.016   0.001   TYR I  86 
 ARG   0.015   0.002   ARG B  24 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8426 (tm-30)
REVERT: A    5 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8226 (mm110)
REVERT: B  123 GLU cc_start: 0.8402 (mp0) cc_final: 0.8124 (mp0)
REVERT: B  142 ARG cc_start: 0.8570 (ttt-90) cc_final: 0.7793 (tmt170)
REVERT: B  147 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8714 (mt0)
REVERT: G  137 ASP cc_start: 0.7639 (m-30) cc_final: 0.7183 (m-30)
REVERT: G  203 PHE cc_start: 0.7765 (t80) cc_final: 0.7475 (t80)
REVERT: I  117 MET cc_start: 0.6223 (tmm) cc_final: 0.5597 (mtt)
REVERT: I  137 ASP cc_start: 0.7634 (m-30) cc_final: 0.7190 (m-30)
REVERT: I  203 PHE cc_start: 0.7734 (t80) cc_final: 0.7448 (t80)
REVERT: L   40 CYS cc_start: 0.8221 (m) cc_final: 0.7919 (m)
REVERT: L  123 GLU cc_start: 0.8391 (mp0) cc_final: 0.8115 (mp0)
REVERT: L  142 ARG cc_start: 0.8572 (ttt-90) cc_final: 0.7809 (tmt170)
REVERT: L  147 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8758 (mt0)
  outliers start: 25
  outliers final: 8
  residues processed: 148
  average time/residue: 1.2903
  time to fit residues: 203.3139
Evaluate side-chains
  139 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   11 CYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  163 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 113 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 95 optimal weight:    0.5980
   chunk 116 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A 202 ASN
A 204 ASN
G  56 GLN
H   3 GLN
H   5 GLN
H 202 ASN
H 204 ASN
I  56 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.108942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.077892 restraints weight = 16052.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.45
r_work: 0.3060 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9368  Z= 0.245
  Angle     :  0.625   8.763  12730  Z= 0.328
  Chirality :  0.043   0.156   1442
  Planarity :  0.004   0.047   1594
  Dihedral  :  4.930  18.114   1280
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.98 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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:  1.31 (0.25), residues: 1190
  helix:  1.76 (0.31), residues: 272
  sheet:  1.25 (0.24), residues: 428
  loop :  0.08 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP G  89 
 HIS   0.002   0.001   HIS A  35 
 PHE   0.014   0.001   PHE H 100D
 TYR   0.017   0.002   TYR G  86 
 ARG   0.012   0.001   ARG L  24 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.953 
Fit side-chains
REVERT: B  123 GLU cc_start: 0.8377 (mp0) cc_final: 0.8112 (mp0)
REVERT: B  142 ARG cc_start: 0.8616 (ttt-90) cc_final: 0.7760 (tmt170)
REVERT: B  147 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8665 (mt0)
REVERT: B  167 ASP cc_start: 0.8717 (t0) cc_final: 0.8516 (t0)
REVERT: G  117 MET cc_start: 0.6154 (tmm) cc_final: 0.5567 (mtt)
REVERT: G  137 ASP cc_start: 0.7630 (m-30) cc_final: 0.7169 (m-30)
REVERT: G  203 PHE cc_start: 0.7741 (t80) cc_final: 0.7469 (t80)
REVERT: I  117 MET cc_start: 0.6117 (tmm) cc_final: 0.5510 (mtt)
REVERT: I  137 ASP cc_start: 0.7623 (m-30) cc_final: 0.7177 (m-30)
REVERT: I  203 PHE cc_start: 0.7706 (t80) cc_final: 0.7393 (t80)
REVERT: L  123 GLU cc_start: 0.8369 (mp0) cc_final: 0.8100 (mp0)
REVERT: L  142 ARG cc_start: 0.8611 (ttt-90) cc_final: 0.7767 (tmt170)
REVERT: L  147 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8713 (mt0)
  outliers start: 23
  outliers final: 8
  residues processed: 146
  average time/residue: 1.3256
  time to fit residues: 205.4831
Evaluate side-chains
  140 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 CYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain G residue  206 LEU
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain I residue  206 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  154 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 1 optimal weight:    0.3980
   chunk 110 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0980
   chunk 17 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 204 ASN
G  56 GLN
H   3 GLN
H   5 GLN
H 202 ASN
H 204 ASN
** I  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.107941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.076608 restraints weight = 16178.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.46
r_work: 0.3038 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9368  Z= 0.302
  Angle     :  0.653   8.549  12730  Z= 0.343
  Chirality :  0.044   0.150   1442
  Planarity :  0.005   0.075   1594
  Dihedral  :  5.018  18.077   1280
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.66 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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:  1.25 (0.24), residues: 1190
  helix:  1.73 (0.31), residues: 270
  sheet:  1.21 (0.24), residues: 428
  loop :  0.05 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP I  89 
 HIS   0.002   0.001   HIS H 169 
 PHE   0.015   0.002   PHE H 100D
 TYR   0.018   0.002   TYR G  86 
 ARG   0.018   0.002   ARG B  24 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8448 (tm-30)
REVERT: A    5 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8295 (mm110)
REVERT: B  123 GLU cc_start: 0.8432 (mp0) cc_final: 0.8162 (mp0)
REVERT: B  142 ARG cc_start: 0.8558 (ttt-90) cc_final: 0.7442 (tpt90)
REVERT: B  147 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8696 (mt0)
REVERT: G  117 MET cc_start: 0.6219 (tmm) cc_final: 0.5598 (mtt)
REVERT: G  137 ASP cc_start: 0.7646 (m-30) cc_final: 0.7207 (m-30)
REVERT: G  203 PHE cc_start: 0.7823 (t80) cc_final: 0.7559 (t80)
REVERT: H    3 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8474 (tm-30)
REVERT: H    5 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8314 (mm110)
REVERT: I  117 MET cc_start: 0.6179 (tmm) cc_final: 0.5581 (mtt)
REVERT: I  137 ASP cc_start: 0.7658 (m-30) cc_final: 0.7212 (m-30)
REVERT: I  203 PHE cc_start: 0.7801 (t80) cc_final: 0.7497 (t80)
REVERT: L  123 GLU cc_start: 0.8416 (mp0) cc_final: 0.8144 (mp0)
REVERT: L  142 ARG cc_start: 0.8615 (ttt-90) cc_final: 0.7443 (tpt90)
REVERT: L  147 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8764 (mt0)
  outliers start: 23
  outliers final: 10
  residues processed: 147
  average time/residue: 1.5301
  time to fit residues: 238.5719
Evaluate side-chains
  142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   11 CYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain G residue  206 LEU
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain I residue  206 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  163 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 69 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 108 optimal weight:    0.1980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A 204 ASN
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
H 202 ASN
H 204 ASN
** I  56 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.108392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.076507 restraints weight = 15958.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.54
r_work: 0.3010 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9368  Z= 0.237
  Angle     :  0.642   9.049  12730  Z= 0.336
  Chirality :  0.043   0.152   1442
  Planarity :  0.004   0.056   1594
  Dihedral  :  4.893  17.790   1280
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.05 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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:  1.31 (0.25), residues: 1190
  helix:  1.81 (0.31), residues: 270
  sheet:  1.24 (0.24), residues: 430
  loop :  0.08 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP G  89 
 HIS   0.002   0.001   HIS A  35 
 PHE   0.014   0.001   PHE H 100D
 TYR   0.016   0.001   TYR G  86 
 ARG   0.014   0.001   ARG L  24 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 2.384 
Fit side-chains
REVERT: B  123 GLU cc_start: 0.8368 (mp0) cc_final: 0.8098 (mp0)
REVERT: B  142 ARG cc_start: 0.8610 (ttt-90) cc_final: 0.7392 (tpt90)
REVERT: B  147 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8652 (mt0)
REVERT: G  117 MET cc_start: 0.6081 (tmm) cc_final: 0.5487 (mtt)
REVERT: G  137 ASP cc_start: 0.7611 (m-30) cc_final: 0.7135 (m-30)
REVERT: G  203 PHE cc_start: 0.7691 (t80) cc_final: 0.7416 (t80)
REVERT: H    3 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8285 (tm-30)
REVERT: H    5 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8151 (mm110)
REVERT: I  117 MET cc_start: 0.6044 (tmm) cc_final: 0.5493 (mtt)
REVERT: I  137 ASP cc_start: 0.7627 (m-30) cc_final: 0.7142 (m-30)
REVERT: I  203 PHE cc_start: 0.7676 (t80) cc_final: 0.7462 (t80)
REVERT: L  123 GLU cc_start: 0.8349 (mp0) cc_final: 0.8079 (mp0)
REVERT: L  142 ARG cc_start: 0.8615 (ttt-90) cc_final: 0.7395 (tpt90)
REVERT: L  147 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8718 (mt0)
  outliers start: 22
  outliers final: 10
  residues processed: 146
  average time/residue: 1.7366
  time to fit residues: 270.4539
Evaluate side-chains
  143 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 1.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 CYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain G residue  206 LEU
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  163 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0040
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 202 ASN
A 204 ASN
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
H 202 ASN
H 204 ASN
** I  56 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.108472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.076478 restraints weight = 16060.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.56
r_work: 0.3019 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9368  Z= 0.239
  Angle     :  0.650   9.141  12730  Z= 0.340
  Chirality :  0.043   0.151   1442
  Planarity :  0.004   0.060   1594
  Dihedral  :  4.857  17.684   1280
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.83 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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: 1190
  helix:  1.78 (0.31), residues: 270
  sheet:  1.26 (0.24), residues: 430
  loop :  0.12 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP I  89 
 HIS   0.002   0.001   HIS A  35 
 PHE   0.014   0.001   PHE H 100D
 TYR   0.017   0.001   TYR G  86 
 ARG   0.015   0.001   ARG B  24 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
REVERT: B  123 GLU cc_start: 0.8406 (mp0) cc_final: 0.8143 (mp0)
REVERT: B  142 ARG cc_start: 0.8627 (ttt-90) cc_final: 0.7438 (tpt90)
REVERT: B  147 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8710 (mt0)
REVERT: G  117 MET cc_start: 0.6115 (tmm) cc_final: 0.5505 (mtt)
REVERT: G  137 ASP cc_start: 0.7656 (m-30) cc_final: 0.7186 (m-30)
REVERT: G  203 PHE cc_start: 0.7744 (t80) cc_final: 0.7445 (t80)
REVERT: H    3 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8385 (tm-30)
REVERT: H    5 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8200 (mm110)
REVERT: I  117 MET cc_start: 0.6142 (tmm) cc_final: 0.5543 (mtt)
REVERT: I  137 ASP cc_start: 0.7661 (m-30) cc_final: 0.7195 (m-30)
REVERT: I  203 PHE cc_start: 0.7750 (t80) cc_final: 0.7463 (t80)
REVERT: L  123 GLU cc_start: 0.8395 (mp0) cc_final: 0.8131 (mp0)
REVERT: L  142 ARG cc_start: 0.8638 (ttt-90) cc_final: 0.7831 (tmt170)
REVERT: L  147 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8752 (mt0)
  outliers start: 18
  outliers final: 10
  residues processed: 146
  average time/residue: 1.6871
  time to fit residues: 262.1972
Evaluate side-chains
  142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 CYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain G residue  206 LEU
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  163 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A 204 ASN
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
H 202 ASN
H 204 ASN
** I  56 GLN ** 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 = 0.3579 r_free = 0.3579 target = 0.106105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.073943 restraints weight = 16032.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.51
r_work: 0.2976 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   9368  Z= 0.393
  Angle     :  0.703   8.793  12730  Z= 0.368
  Chirality :  0.046   0.158   1442
  Planarity :  0.005   0.058   1594
  Dihedral  :  5.088  18.209   1280
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 17.12 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    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: 1190
  helix:  1.58 (0.31), residues: 270
  sheet:  1.30 (0.24), residues: 424
  loop :  0.08 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP G  85 
 HIS   0.002   0.001   HIS H 169 
 PHE   0.016   0.002   PHE I  62 
 TYR   0.018   0.002   TYR G  86 
 ARG   0.015   0.002   ARG L  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9445.85 seconds
wall clock time: 167 minutes 29.47 seconds (10049.47 seconds total)