Starting phenix.real_space_refine
on Fri Aug 22 22:50:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5u1c_8481/08_2025/5u1c_8481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5u1c_8481/08_2025/5u1c_8481.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5u1c_8481/08_2025/5u1c_8481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5u1c_8481/08_2025/5u1c_8481.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5u1c_8481/08_2025/5u1c_8481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5u1c_8481/08_2025/5u1c_8481.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.012
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      92      5.49       5
     Mg      2      5.21       5
     S      28      5.16       5
     C    5188      2.51       5
     N    1534      2.21       5
     O    1750      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8596
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1975
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 10, 'TRANS': 240}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1362
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 6, 'TRANS': 165}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 162
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "E"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 285
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "F"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 512
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "C"
      Number of atoms: 1975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1975
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 10, 'TRANS': 240}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1362
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 6, 'TRANS': 165}
          Chain breaks: 3
    Chain: "H"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 162
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "I"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 285
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "J"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 512
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    319  SG  CYS A  40      21.270  47.273  39.306  1.00 11.69           S
  ATOM    342  SG  CYS A  43      24.958  47.314  38.194  1.00 10.21           S
  ATOM   4615  SG  CYS C  40      65.198  83.727  39.295  1.00 12.83           S
  ATOM   4638  SG  CYS C  43      61.511  83.683  38.178  1.00 11.35           S

  Time building chain proxies: 1.86, per 1000 atoms: 0.22
  Number of scatterers: 8596
  At special positions: 0
  Unit cell: (87.77, 132.31, 83.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      28     16.00
     P      92     15.00
     Mg      2     11.99
     O    1750      8.00
     N    1534      7.00
     C    5188      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.78
  Conformation dependent library (CDL) restraints added in 252.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 500 "
        pdb="ZN    ZN A 500 " - pdb=" ND1 HIS A  16 "
        pdb="ZN    ZN A 500 " - pdb=" NE2 HIS A  12 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS A  43 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS A  40 "
      pdb="  ZN C 500 "
        pdb="ZN    ZN C 500 " - pdb=" ND1 HIS C  16 "
        pdb="ZN    ZN C 500 " - pdb=" NE2 HIS C  12 "
        pdb="ZN    ZN C 500 " - pdb=" SG  CYS C  43 "
        pdb="ZN    ZN C 500 " - pdb=" SG  CYS C  40 "
      Number of angles added : 4


  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      46.8% alpha, 18.7% beta
      42 base pairs and 70 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 16
      removed outlier: 3.585A  pdb=" N   ASP A   6 " --> pdb=" O   LEU A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 18 through 26
    Processing helix  chain 'A' and resid 29 through 40
    Processing helix  chain 'A' and resid 93 through 106
    Processing helix  chain 'A' and resid 119 through 122
    Processing helix  chain 'A' and resid 123 through 133
      removed outlier: 3.604A  pdb=" N   LYS A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 147
    Processing helix  chain 'A' and resid 148 through 166
      removed outlier: 3.868A  pdb=" N   GLN A 152 " --> pdb=" O   GLN A 148 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 156 " --> pdb=" O   GLN A 152 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN A 164 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 169
      No H-bonds generated for 'chain 'A' and resid 167 through 169'
    Processing helix  chain 'A' and resid 171 through 186
      removed outlier: 3.959A  pdb=" N   ALA A 175 " --> pdb=" O   HIS A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 204
    Processing helix  chain 'B' and resid 67 through 71
    Processing helix  chain 'B' and resid 93 through 108
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 123 through 134
      removed outlier: 3.564A  pdb=" N   LYS B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 166
    Processing helix  chain 'B' and resid 167 through 169
      No H-bonds generated for 'chain 'B' and resid 167 through 169'
    Processing helix  chain 'B' and resid 171 through 186
      removed outlier: 3.593A  pdb=" N   ALA B 175 " --> pdb=" O   HIS B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 204
      removed outlier: 3.506A  pdb=" N   ILE B 204 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 16
      removed outlier: 3.585A  pdb=" N   ASP C   6 " --> pdb=" O   LEU C   2 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 26
    Processing helix  chain 'C' and resid 29 through 40
    Processing helix  chain 'C' and resid 93 through 106
    Processing helix  chain 'C' and resid 119 through 122
    Processing helix  chain 'C' and resid 123 through 133
      removed outlier: 3.604A  pdb=" N   LYS C 127 " --> pdb=" O   SER C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 147
    Processing helix  chain 'C' and resid 148 through 166
      removed outlier: 3.866A  pdb=" N   GLN C 152 " --> pdb=" O   GLN C 148 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS C 156 " --> pdb=" O   GLN C 152 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN C 164 " --> pdb=" O   LYS C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 169
      No H-bonds generated for 'chain 'C' and resid 167 through 169'
    Processing helix  chain 'C' and resid 171 through 186
      removed outlier: 3.959A  pdb=" N   ALA C 175 " --> pdb=" O   HIS C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 204
    Processing helix  chain 'D' and resid 67 through 71
    Processing helix  chain 'D' and resid 93 through 108
    Processing helix  chain 'D' and resid 118 through 123
    Processing helix  chain 'D' and resid 123 through 134
      removed outlier: 3.564A  pdb=" N   LYS D 127 " --> pdb=" O   SER D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 152 through 166
    Processing helix  chain 'D' and resid 167 through 169
      No H-bonds generated for 'chain 'D' and resid 167 through 169'
    Processing helix  chain 'D' and resid 171 through 186
      removed outlier: 3.593A  pdb=" N   ALA D 175 " --> pdb=" O   HIS D 171 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 204
      removed outlier: 3.507A  pdb=" N   ILE D 204 " --> pdb=" O   ILE D 200 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89
      removed outlier: 4.114A  pdb=" N   VAL A  72 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   TRP A  61 " --> pdb=" O   HIS A 114 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   VAL A 113 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 227
    Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 244
      removed outlier: 6.427A  pdb=" N   VAL A 250 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   LYS A 244 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ALA A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 88
      removed outlier: 6.722A  pdb=" N   TRP B  61 " --> pdb=" O   HIS B 114 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 261
      removed outlier: 6.357A  pdb=" N   GLN B 252 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   LEU B 241 " --> pdb=" O   GLN B 252 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 89
      removed outlier: 4.114A  pdb=" N   VAL C  72 " --> pdb=" O   ILE C  89 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   TRP C  61 " --> pdb=" O   HIS C 114 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   VAL C 113 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 227
    Processing sheet with id=AA8, first strand: chain 'C' and resid 240 through 244
      removed outlier: 6.427A  pdb=" N   VAL C 250 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   LYS C 244 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   ALA C 248 " --> pdb=" O   LYS C 244 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 88
      removed outlier: 6.722A  pdb=" N   TRP D  61 " --> pdb=" O   HIS D 114 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 257 through 261
      removed outlier: 6.357A  pdb=" N   GLN D 252 " --> pdb=" O   LEU D 241 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   LEU D 241 " --> pdb=" O   GLN D 252 " (cutoff:3.500A)

    332 hydrogen bonds defined for protein.
    930 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      104 hydrogen bonds
      208 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      70 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2023
        1.33 -     1.45: 2224
        1.45 -     1.57: 4499
        1.57 -     1.69: 180
        1.69 -     1.81: 40
  Bond restraints: 8966
  Sorted by residual:
  bond pdb=" C   GLY A 118 "
       pdb=" N   SER A 119 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 1.20e-02 6.94e+03 1.56e+01
  bond pdb=" C   THR A 122 "
       pdb=" N   SER A 123 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.038 1.30e-02 5.92e+03 8.33e+00
  bond pdb=" C1'  DT E  28 "
       pdb=" N1   DT E  28 "
    ideal  model  delta    sigma   weight residual
    1.490  1.548 -0.058 3.00e-02 1.11e+03 3.69e+00
  bond pdb=" C1'  DT I  28 "
       pdb=" N1   DT I  28 "
    ideal  model  delta    sigma   weight residual
    1.490  1.547 -0.057 3.00e-02 1.11e+03 3.63e+00
  bond pdb=" C4'  DC H   6 "
       pdb=" C3'  DC H   6 "
    ideal  model  delta    sigma   weight residual
    1.523  1.560 -0.037 2.00e-02 2.50e+03 3.47e+00
  ... (remaining 8961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 12133
        2.28 -     4.57: 353
        4.57 -     6.85: 25
        6.85 -     9.13: 1
        9.13 -    11.41: 4
  Bond angle restraints: 12516
  Sorted by residual:
  angle pdb=" O   GLY C 118 "
        pdb=" C   GLY C 118 "
        pdb=" N   SER C 119 "
      ideal   model   delta    sigma   weight residual
     122.70  111.29   11.41 1.30e+00 5.92e-01 7.71e+01
  angle pdb=" O   GLY A 118 "
        pdb=" C   GLY A 118 "
        pdb=" N   SER A 119 "
      ideal   model   delta    sigma   weight residual
     122.70  111.62   11.08 1.30e+00 5.92e-01 7.26e+01
  angle pdb=" CA  GLY C 118 "
        pdb=" C   GLY C 118 "
        pdb=" N   SER C 119 "
      ideal   model   delta    sigma   weight residual
     116.69  127.81  -11.12 2.04e+00 2.40e-01 2.97e+01
  angle pdb=" CA  GLY A 118 "
        pdb=" C   GLY A 118 "
        pdb=" N   SER A 119 "
      ideal   model   delta    sigma   weight residual
     116.69  127.67  -10.98 2.04e+00 2.40e-01 2.90e+01
  angle pdb=" C   GLY C 118 "
        pdb=" N   SER C 119 "
        pdb=" CA  SER C 119 "
      ideal   model   delta    sigma   weight residual
     120.79  127.08   -6.29 1.39e+00 5.18e-01 2.05e+01
  ... (remaining 12511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.72: 4642
       33.72 -    67.44: 418
       67.44 -   101.15: 10
      101.15 -   134.87: 0
      134.87 -   168.59: 2
  Dihedral angle restraints: 5072
    sinusoidal: 2656
      harmonic: 2416
  Sorted by residual:
  dihedral pdb=" CA  GLN A 148 "
           pdb=" C   GLN A 148 "
           pdb=" N   GLY A 149 "
           pdb=" CA  GLY A 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.75  -22.25     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  GLN C 148 "
           pdb=" C   GLN C 148 "
           pdb=" N   GLY C 149 "
           pdb=" CA  GLY C 149 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.75  -22.25     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  SER C 195 "
           pdb=" C   SER C 195 "
           pdb=" N   ALA C 196 "
           pdb=" CA  ALA C 196 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 5069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 861
       0.045 -    0.091: 394
       0.091 -    0.136: 110
       0.136 -    0.182: 21
       0.182 -    0.227: 2
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CA  LYS C  46 "
            pdb=" N   LYS C  46 "
            pdb=" C   LYS C  46 "
            pdb=" CB  LYS C  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  LYS A  46 "
            pdb=" N   LYS A  46 "
            pdb=" C   LYS A  46 "
            pdb=" CB  LYS A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE A  89 "
            pdb=" N   ILE A  89 "
            pdb=" C   ILE A  89 "
            pdb=" CB  ILE A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.99e-01
  ... (remaining 1385 not shown)

  Planarity restraints: 1258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F  20 "   -0.014 2.00e-02 2.50e+03   1.47e-02 4.87e+00
        pdb=" N1   DC F  20 "    0.013 2.00e-02 2.50e+03
        pdb=" C2   DC F  20 "   -0.031 2.00e-02 2.50e+03
        pdb=" O2   DC F  20 "    0.022 2.00e-02 2.50e+03
        pdb=" N3   DC F  20 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DC F  20 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC F  20 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DC F  20 "    0.008 2.00e-02 2.50e+03
        pdb=" C6   DC F  20 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  20 "    0.014 2.00e-02 2.50e+03   1.45e-02 4.73e+00
        pdb=" N1   DC J  20 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2   DC J  20 "    0.030 2.00e-02 2.50e+03
        pdb=" O2   DC J  20 "   -0.021 2.00e-02 2.50e+03
        pdb=" N3   DC J  20 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DC J  20 "    0.005 2.00e-02 2.50e+03
        pdb=" N4   DC J  20 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DC J  20 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6   DC J  20 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  19 "   -0.026 2.00e-02 2.50e+03   1.43e-02 4.62e+00
        pdb=" N1   DC I  19 "    0.033 2.00e-02 2.50e+03
        pdb=" C2   DC I  19 "    0.001 2.00e-02 2.50e+03
        pdb=" O2   DC I  19 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DC I  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DC I  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC I  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DC I  19 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DC I  19 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1255 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 64
        2.55 -     3.14: 6733
        3.14 -     3.73: 13641
        3.73 -     4.31: 19417
        4.31 -     4.90: 30282
  Nonbonded interactions: 70137
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 228 "
            pdb=" OD1 ASP A 229 "
     model   vdw
     1.964 3.040
  nonbonded pdb=" O   ARG C 228 "
            pdb=" OD1 ASP C 229 "
     model   vdw
     1.965 3.040
  nonbonded pdb=" OD2 ASP A  64 "
            pdb="MG    MG A 501 "
     model   vdw
     1.976 2.170
  nonbonded pdb=" OD2 ASP C  64 "
            pdb="MG    MG C 501 "
     model   vdw
     1.977 2.170
  nonbonded pdb=" OG1 THR A  93 "
            pdb=" OP1  DC F  30 "
     model   vdw
     2.051 3.040
  ... (remaining 70132 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 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.020
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
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      :  0.013   0.689   8974  Z= 0.499
  Angle     :  1.066  34.856  12520  Z= 0.555
  Chirality :  0.054   0.227   1388
  Planarity :  0.005   0.035   1258
  Dihedral  : 20.206 168.589   3512
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.28 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.03 (0.24), residues: 822
  helix: -2.67 (0.22), residues: 320
  sheet: -2.02 (0.34), residues: 194
  loop : -2.86 (0.30), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 107 
 TYR   0.020   0.003   TYR B  99 
 PHE   0.024   0.003   PHE C 121 
 TRP   0.016   0.003   TRP D 235 
 HIS   0.014   0.002   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00775 ( 8966)
  covalent geometry    : angle       0.91224 (12516)
  hydrogen bonds       : bond        0.14310 (  436)
  hydrogen bonds       : angle       8.53030 ( 1138)
  metal coordination   : bond        0.36142 (    8)
  metal coordination   : angle      30.91728 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 271
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ILE cc_start: 0.8554 (mt) cc_final: 0.8231 (tp)
REVERT: C   22 MET cc_start: 0.7141 (mtm) cc_final: 0.6868 (mtp)
REVERT: C   60 ILE cc_start: 0.8428 (mt) cc_final: 0.8199 (tp)
REVERT: C   85 GLU cc_start: 0.7345 (tp30) cc_final: 0.7071 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 273
  average time/residue: 0.0972
  time to fit residues: 34.1177
Evaluate side-chains
  132 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   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 144 ASN
A 183 HIS
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN
C 144 ASN
C 183 HIS
C 252 GLN
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.121953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.103663 restraints weight = 21639.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.106049 restraints weight = 12615.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.107617 restraints weight = 8995.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.108630 restraints weight = 7281.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.109215 restraints weight = 6368.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8974  Z= 0.152
  Angle     :  0.645  10.818  12520  Z= 0.354
  Chirality :  0.044   0.158   1388
  Planarity :  0.005   0.048   1258
  Dihedral  : 25.952 179.717   1916
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 12.22 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.26), residues: 822
  helix: -0.92 (0.24), residues: 338
  sheet: -1.04 (0.34), residues: 222
  loop : -1.99 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 263 
 TYR   0.008   0.001   TYR A  99 
 PHE   0.019   0.002   PHE C 181 
 TRP   0.021   0.001   TRP C  61 
 HIS   0.007   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8966)
  covalent geometry    : angle       0.62995 (12516)
  hydrogen bonds       : bond        0.04095 (  436)
  hydrogen bonds       : angle       5.32145 ( 1138)
  metal coordination   : bond        0.00933 (    8)
  metal coordination   : angle       7.86153 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8748 (t0)
REVERT: A  178 MET cc_start: 0.8582 (mtt) cc_final: 0.6738 (mtt)
REVERT: B   87 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6823 (tm-30)
REVERT: B  132 TRP cc_start: 0.8421 (t60) cc_final: 0.8203 (t60)
REVERT: C   85 GLU cc_start: 0.7781 (tp30) cc_final: 0.7490 (mm-30)
REVERT: C  144 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8750 (t0)
REVERT: C  178 MET cc_start: 0.8607 (mtt) cc_final: 0.6762 (mtt)
REVERT: D   87 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7006 (tm-30)
REVERT: D  132 TRP cc_start: 0.8463 (t60) cc_final: 0.8253 (t60)
REVERT: D  240 LYS cc_start: 0.6180 (tptt) cc_final: 0.5716 (ptpt)
  outliers start: 22
  outliers final: 14
  residues processed: 173
  average time/residue: 0.0694
  time to fit residues: 16.7062
Evaluate side-chains
  135 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 54 optimal weight:    0.1980
   chunk 15 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 171 HIS
B 114 HIS
C 171 HIS
C 184 ASN
C 252 GLN
D 114 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.095876 restraints weight = 21449.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.098030 restraints weight = 12930.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.099505 restraints weight = 9460.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.100266 restraints weight = 7761.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.100995 restraints weight = 6924.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8974  Z= 0.236
  Angle     :  0.659   8.103  12520  Z= 0.370
  Chirality :  0.045   0.156   1388
  Planarity :  0.005   0.045   1258
  Dihedral  : 26.575 179.407   1916
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.48 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.27), residues: 822
  helix:  0.18 (0.26), residues: 340
  sheet: -0.22 (0.36), residues: 210
  loop : -1.96 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  20 
 TYR   0.024   0.002   TYR A 143 
 PHE   0.016   0.002   PHE C 100 
 TRP   0.016   0.002   TRP C  61 
 HIS   0.008   0.002   HIS D 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 8966)
  covalent geometry    : angle       0.65442 (12516)
  hydrogen bonds       : bond        0.04495 (  436)
  hydrogen bonds       : angle       5.02970 ( 1138)
  metal coordination   : bond        0.01169 (    8)
  metal coordination   : angle       4.53120 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   69 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7450 (tt0)
REVERT: A  144 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8613 (t0)
REVERT: A  178 MET cc_start: 0.8983 (mtt) cc_final: 0.7182 (mtt)
REVERT: A  230 SER cc_start: 0.7351 (m) cc_final: 0.6880 (t)
REVERT: B  132 TRP cc_start: 0.8759 (t60) cc_final: 0.8184 (t60)
REVERT: C   20 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8147 (ttm-80)
REVERT: C   69 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7467 (tt0)
REVERT: C   85 GLU cc_start: 0.7950 (tp30) cc_final: 0.7744 (mm-30)
REVERT: C  178 MET cc_start: 0.8995 (mtt) cc_final: 0.7141 (mtt)
REVERT: C  230 SER cc_start: 0.7363 (m) cc_final: 0.6895 (t)
REVERT: D  132 TRP cc_start: 0.8794 (t60) cc_final: 0.8093 (t60)
REVERT: D  178 MET cc_start: 0.8122 (tpp) cc_final: 0.7639 (tpp)
REVERT: D  263 ARG cc_start: 0.8120 (mtm110) cc_final: 0.7828 (mtm110)
  outliers start: 22
  outliers final: 16
  residues processed: 158
  average time/residue: 0.0834
  time to fit residues: 17.7098
Evaluate side-chains
  133 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 82 optimal weight:    5.9990
   chunk 68 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 222 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.115008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096454 restraints weight = 21722.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.098581 restraints weight = 13220.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.100028 restraints weight = 9689.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.100687 restraints weight = 7931.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.101459 restraints weight = 7125.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.5065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8974  Z= 0.176
  Angle     :  0.595   7.206  12520  Z= 0.337
  Chirality :  0.043   0.150   1388
  Planarity :  0.004   0.030   1258
  Dihedral  : 26.643 178.987   1916
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.05 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.28), residues: 822
  helix:  0.54 (0.26), residues: 350
  sheet: -0.07 (0.35), residues: 220
  loop : -1.92 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 107 
 TYR   0.014   0.002   TYR C 143 
 PHE   0.018   0.002   PHE D 121 
 TRP   0.011   0.001   TRP C 132 
 HIS   0.004   0.001   HIS A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8966)
  covalent geometry    : angle       0.59052 (12516)
  hydrogen bonds       : bond        0.03978 (  436)
  hydrogen bonds       : angle       4.83150 ( 1138)
  metal coordination   : bond        0.00869 (    8)
  metal coordination   : angle       4.17730 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  178 MET cc_start: 0.8895 (mtt) cc_final: 0.7098 (mtt)
REVERT: B  132 TRP cc_start: 0.8789 (t60) cc_final: 0.7877 (t60)
REVERT: C  144 ASN cc_start: 0.8983 (t0) cc_final: 0.8751 (t0)
REVERT: C  178 MET cc_start: 0.8920 (mtt) cc_final: 0.7196 (mtt)
REVERT: C  191 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7560 (mm)
REVERT: C  194 TYR cc_start: 0.7876 (m-80) cc_final: 0.7084 (m-80)
REVERT: C  230 SER cc_start: 0.7240 (m) cc_final: 0.6793 (t)
REVERT: D  132 TRP cc_start: 0.8786 (t60) cc_final: 0.7907 (t60)
REVERT: D  178 MET cc_start: 0.8051 (tpp) cc_final: 0.7465 (tpp)
  outliers start: 22
  outliers final: 16
  residues processed: 142
  average time/residue: 0.0697
  time to fit residues: 14.1608
Evaluate side-chains
  127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue   87 GLU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
C 184 ASN
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 177 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.113197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.094457 restraints weight = 21607.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.096552 restraints weight = 13190.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.097970 restraints weight = 9650.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.098838 restraints weight = 7956.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.099236 restraints weight = 7047.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.5483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8974  Z= 0.205
  Angle     :  0.620   6.254  12520  Z= 0.348
  Chirality :  0.043   0.140   1388
  Planarity :  0.004   0.031   1258
  Dihedral  : 26.789 179.694   1916
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 18.32 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.28), residues: 822
  helix:  0.72 (0.26), residues: 338
  sheet:  0.04 (0.36), residues: 206
  loop : -1.71 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 263 
 TYR   0.016   0.002   TYR C 143 
 PHE   0.023   0.002   PHE B 100 
 TRP   0.013   0.001   TRP C  61 
 HIS   0.009   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 8966)
  covalent geometry    : angle       0.61391 (12516)
  hydrogen bonds       : bond        0.04135 (  436)
  hydrogen bonds       : angle       4.83946 ( 1138)
  metal coordination   : bond        0.01629 (    8)
  metal coordination   : angle       4.74725 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  178 MET cc_start: 0.8912 (mtt) cc_final: 0.7269 (mtt)
REVERT: A  269 ARG cc_start: 0.4238 (tpt90) cc_final: 0.3814 (tpt170)
REVERT: B  132 TRP cc_start: 0.8878 (t60) cc_final: 0.7915 (t60)
REVERT: C  178 MET cc_start: 0.8930 (mtt) cc_final: 0.7262 (mtt)
REVERT: D  132 TRP cc_start: 0.8877 (t60) cc_final: 0.7917 (t60)
REVERT: D  178 MET cc_start: 0.7973 (tpp) cc_final: 0.7635 (tpp)
REVERT: D  199 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7091 (mtm-85)
  outliers start: 31
  outliers final: 20
  residues processed: 136
  average time/residue: 0.0721
  time to fit residues: 13.8559
Evaluate side-chains
  132 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  199 ARG
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 84 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
C 184 ASN
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096467 restraints weight = 21281.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.098739 restraints weight = 12018.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.100351 restraints weight = 8384.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.101260 restraints weight = 6672.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.102004 restraints weight = 5823.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.5751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8974  Z= 0.158
  Angle     :  0.580   6.327  12520  Z= 0.327
  Chirality :  0.042   0.143   1388
  Planarity :  0.004   0.032   1258
  Dihedral  : 26.696 179.838   1916
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 19.60 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.28), residues: 822
  helix:  0.84 (0.26), residues: 350
  sheet:  0.09 (0.36), residues: 216
  loop : -1.81 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 199 
 TYR   0.014   0.002   TYR A  99 
 PHE   0.013   0.001   PHE C 181 
 TRP   0.012   0.001   TRP C 132 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8966)
  covalent geometry    : angle       0.57383 (12516)
  hydrogen bonds       : bond        0.03776 (  436)
  hydrogen bonds       : angle       4.69645 ( 1138)
  metal coordination   : bond        0.01065 (    8)
  metal coordination   : angle       4.66682 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  178 MET cc_start: 0.9024 (mtt) cc_final: 0.8325 (mtt)
REVERT: B   74 LEU cc_start: 0.8396 (tp) cc_final: 0.8140 (mp)
REVERT: C  178 MET cc_start: 0.9057 (mtt) cc_final: 0.7330 (mtt)
REVERT: C  191 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7628 (mm)
REVERT: D  132 TRP cc_start: 0.8899 (t60) cc_final: 0.7709 (t60)
REVERT: D  199 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7346 (mtm-85)
  outliers start: 25
  outliers final: 18
  residues processed: 131
  average time/residue: 0.0705
  time to fit residues: 13.1293
Evaluate side-chains
  122 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  199 ARG
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 HIS
C 184 ASN
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.112178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093869 restraints weight = 21986.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.095962 restraints weight = 13211.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.097360 restraints weight = 9576.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.098041 restraints weight = 7853.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.098792 restraints weight = 7029.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8974  Z= 0.215
  Angle     :  0.626   8.792  12520  Z= 0.351
  Chirality :  0.044   0.174   1388
  Planarity :  0.004   0.034   1258
  Dihedral  : 26.937 179.710   1916
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.16 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.29), residues: 822
  helix:  0.83 (0.26), residues: 340
  sheet: -0.00 (0.36), residues: 220
  loop : -1.81 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 269 
 TYR   0.016   0.002   TYR C 143 
 PHE   0.021   0.002   PHE B 100 
 TRP   0.015   0.002   TRP C 132 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 8966)
  covalent geometry    : angle       0.62339 (12516)
  hydrogen bonds       : bond        0.04178 (  436)
  hydrogen bonds       : angle       4.79024 ( 1138)
  metal coordination   : bond        0.01981 (    8)
  metal coordination   : angle       3.12916 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  178 MET cc_start: 0.8947 (mtt) cc_final: 0.8213 (mtt)
REVERT: B  178 MET cc_start: 0.7709 (tpp) cc_final: 0.7496 (tpp)
REVERT: C   18 ASN cc_start: 0.8044 (p0) cc_final: 0.7358 (p0)
REVERT: C  178 MET cc_start: 0.8974 (mtt) cc_final: 0.8759 (mtm)
REVERT: D   87 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7164 (tm-30)
REVERT: D  199 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7356 (mtm-85)
REVERT: D  263 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7553 (mtm110)
  outliers start: 30
  outliers final: 24
  residues processed: 127
  average time/residue: 0.0548
  time to fit residues: 10.4053
Evaluate side-chains
  127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  267 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  199 ARG
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  51 HIS
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  51 HIS
C 184 ASN
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.115060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.097074 restraints weight = 21588.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.099207 restraints weight = 12889.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.100666 restraints weight = 9303.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.101576 restraints weight = 7562.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.102092 restraints weight = 6653.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.6131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8974  Z= 0.140
  Angle     :  0.591  11.357  12520  Z= 0.328
  Chirality :  0.042   0.200   1388
  Planarity :  0.003   0.034   1258
  Dihedral  : 26.691 179.714   1916
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.73 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.29), residues: 822
  helix:  0.97 (0.26), residues: 352
  sheet:  0.04 (0.37), residues: 220
  loop : -1.88 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 199 
 TYR   0.012   0.001   TYR B  83 
 PHE   0.010   0.001   PHE A 121 
 TRP   0.022   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8966)
  covalent geometry    : angle       0.58622 (12516)
  hydrogen bonds       : bond        0.03615 (  436)
  hydrogen bonds       : angle       4.64646 ( 1138)
  metal coordination   : bond        0.00858 (    8)
  metal coordination   : angle       4.41185 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  178 MET cc_start: 0.8926 (mtt) cc_final: 0.8690 (mtm)
REVERT: C   18 ASN cc_start: 0.7918 (p0) cc_final: 0.7146 (p0)
REVERT: C  178 MET cc_start: 0.8957 (mtt) cc_final: 0.8726 (mtm)
REVERT: C  191 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7845 (mm)
REVERT: D   85 GLU cc_start: 0.7695 (tt0) cc_final: 0.7168 (tt0)
REVERT: D  199 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7223 (mtm-85)
REVERT: D  263 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7491 (mtm110)
  outliers start: 27
  outliers final: 19
  residues processed: 126
  average time/residue: 0.0517
  time to fit residues: 9.6867
Evaluate side-chains
  119 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  184 ASN
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  199 ARG
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 45 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 83 optimal weight:    0.0980
   chunk 79 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.115161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.097799 restraints weight = 21440.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.099865 restraints weight = 12568.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.101312 restraints weight = 9012.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.101976 restraints weight = 7270.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.102737 restraints weight = 6456.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.6232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8974  Z= 0.151
  Angle     :  0.613  11.734  12520  Z= 0.339
  Chirality :  0.042   0.182   1388
  Planarity :  0.003   0.034   1258
  Dihedral  : 26.565 179.114   1916
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.30 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.29), residues: 822
  helix:  1.07 (0.27), residues: 352
  sheet:  0.10 (0.38), residues: 206
  loop : -1.83 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 199 
 TYR   0.015   0.002   TYR D  83 
 PHE   0.019   0.002   PHE B 100 
 TRP   0.019   0.001   TRP A 132 
 HIS   0.003   0.001   HIS A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8966)
  covalent geometry    : angle       0.60916 (12516)
  hydrogen bonds       : bond        0.03727 (  436)
  hydrogen bonds       : angle       4.64771 ( 1138)
  metal coordination   : bond        0.00956 (    8)
  metal coordination   : angle       3.66567 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  178 MET cc_start: 0.8986 (mtt) cc_final: 0.8740 (mtm)
REVERT: C   18 ASN cc_start: 0.7922 (p0) cc_final: 0.7135 (p0)
REVERT: C  178 MET cc_start: 0.9012 (mtt) cc_final: 0.8800 (mtm)
REVERT: C  191 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7765 (mm)
REVERT: C  194 TYR cc_start: 0.7766 (m-80) cc_final: 0.7242 (m-80)
REVERT: D   85 GLU cc_start: 0.7674 (tt0) cc_final: 0.7310 (tt0)
REVERT: D  199 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6788 (mmm160)
  outliers start: 26
  outliers final: 18
  residues processed: 120
  average time/residue: 0.0595
  time to fit residues: 10.6992
Evaluate side-chains
  117 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  199 ARG
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 25 optimal weight:    0.4980
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  78 HIS
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.110219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.091965 restraints weight = 21881.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.093970 restraints weight = 13081.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.095351 restraints weight = 9559.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.096219 restraints weight = 7837.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.096520 restraints weight = 6937.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.6389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   8974  Z= 0.276
  Angle     :  0.716  11.794  12520  Z= 0.398
  Chirality :  0.047   0.235   1388
  Planarity :  0.004   0.034   1258
  Dihedral  : 26.816 179.548   1916
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.59 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.29), residues: 822
  helix:  0.68 (0.26), residues: 340
  sheet: -0.39 (0.36), residues: 220
  loop : -1.90 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 107 
 TYR   0.027   0.003   TYR D  83 
 PHE   0.024   0.002   PHE D 100 
 TRP   0.026   0.002   TRP A 132 
 HIS   0.005   0.002   HIS A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 8966)
  covalent geometry    : angle       0.71464 (12516)
  hydrogen bonds       : bond        0.04696 (  436)
  hydrogen bonds       : angle       5.01450 ( 1138)
  metal coordination   : bond        0.02711 (    8)
  metal coordination   : angle       2.19558 (    4)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  178 MET cc_start: 0.8991 (mtt) cc_final: 0.8759 (mtm)
REVERT: C   18 ASN cc_start: 0.8317 (p0) cc_final: 0.7606 (p0)
REVERT: C  178 MET cc_start: 0.9002 (mtt) cc_final: 0.8283 (mtt)
REVERT: C  191 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8014 (mm)
REVERT: D   85 GLU cc_start: 0.7832 (tt0) cc_final: 0.7483 (tt0)
REVERT: D  199 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7405 (mtm-85)
REVERT: D  263 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7815 (mtm110)
  outliers start: 23
  outliers final: 19
  residues processed: 119
  average time/residue: 0.0540
  time to fit residues: 9.6794
Evaluate side-chains
  115 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  199 ARG
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 184 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 = 0.3710 r_free = 0.3710 target = 0.112326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.094374 restraints weight = 21888.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.096426 restraints weight = 13144.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.097808 restraints weight = 9545.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.098642 restraints weight = 7801.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.099105 restraints weight = 6897.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.6517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8974  Z= 0.196
  Angle     :  0.661  11.962  12520  Z= 0.368
  Chirality :  0.045   0.270   1388
  Planarity :  0.004   0.035   1258
  Dihedral  : 26.654 179.877   1916
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.30 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.29), residues: 822
  helix:  0.75 (0.26), residues: 340
  sheet: -0.38 (0.36), residues: 220
  loop : -1.85 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 199 
 TYR   0.025   0.002   TYR D  83 
 PHE   0.013   0.001   PHE A 121 
 TRP   0.014   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 8966)
  covalent geometry    : angle       0.65850 (12516)
  hydrogen bonds       : bond        0.04233 (  436)
  hydrogen bonds       : angle       4.89641 ( 1138)
  metal coordination   : bond        0.01728 (    8)
  metal coordination   : angle       3.52084 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1019.92 seconds
wall clock time: 18 minutes 19.02 seconds (1099.02 seconds total)