Starting phenix.real_space_refine
on Fri Sep 11 07:19:52 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/5u1c_8481/09_2026/5u1c_8481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5u1c_8481/09_2026/5u1c_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5u1c_8481/09_2026/5u1c_8481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5u1c_8481/09_2026/5u1c_8481.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/5u1c_8481/09_2026/5u1c_8481.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/5u1c_8481/09_2026/5u1c_8481.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5u1c_8481/09_2026/5u1c_8481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5u1c_8481/09_2026/5u1c_8481.cif"
  }
  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-2.2.1-6174/lib/python3.11/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: 1.78, per 1000 atoms: 0.21
  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: 0.65
  Conformation dependent library (CDL) restraints added in 208.8 milliseconds
  
  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: 1.01
  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: 1.23

  Time building geometry restraints manager: 0.85 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=" C1'  DT E  28 "
       pdb=" N1   DT E  28 "
    ideal  model  delta    sigma   weight residual
    1.468  1.548 -0.080 1.40e-02 5.10e+03 3.23e+01
  bond pdb=" C1'  DT I  28 "
       pdb=" N1   DT I  28 "
    ideal  model  delta    sigma   weight residual
    1.468  1.547 -0.079 1.40e-02 5.10e+03 3.20e+01
  bond pdb=" C1'  DT H   7 "
       pdb=" N1   DT H   7 "
    ideal  model  delta    sigma   weight residual
    1.468  1.545 -0.077 1.40e-02 5.10e+03 3.06e+01
  bond pdb=" C1'  DT G   7 "
       pdb=" N1   DT G   7 "
    ideal  model  delta    sigma   weight residual
    1.468  1.545 -0.077 1.40e-02 5.10e+03 3.06e+01
  bond pdb=" C1'  DT F  23 "
       pdb=" N1   DT F  23 "
    ideal  model  delta    sigma   weight residual
    1.468  1.538 -0.070 1.40e-02 5.10e+03 2.52e+01
  ... (remaining 8961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 12002
        2.28 -     4.57: 482
        4.57 -     6.85: 23
        6.85 -     9.13: 5
        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=" N3   DT J  17 "
        pdb=" C4   DT J  17 "
        pdb=" O4   DT J  17 "
      ideal   model   delta    sigma   weight residual
     119.90  123.01   -3.11 6.00e-01 2.78e+00 2.69e+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: 838
       0.045 -    0.091: 351
       0.091 -    0.136: 130
       0.136 -    0.182: 54
       0.182 -    0.227: 15
  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=" C3'  DT J  23 "
            pdb=" C4'  DT J  23 "
            pdb=" O3'  DT J  23 "
            pdb=" C2'  DT J  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.52   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (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: 0.02
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:             0.570
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.710
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
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      :  0.014   0.689   8974  Z= 0.685
  Angle     :  1.130  34.856  12520  Z= 0.729
  Chirality :  0.063   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 are 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/Z
  covalent geometry    : bond        0.00848 /  0.58 ( 8966)
  covalent geometry    : angle       0.98546 /  0.72 (12516)
  hydrogen bonds       : bond        0.14310 /  9.69 (  436)
  hydrogen bonds       : angle       8.53030 /  6.04 ( 1138)
  metal coordination   : bond        0.36142 / 17.90 (    8)
  metal coordination   : angle      30.91728 / 22.55 (    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  : 0.262 
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: 0.8227 (tp)
REVERT: C   22 MET cc_start: 0.7141 (mtm) cc_final: 0.6873 (mtp)
REVERT: C   60 ILE cc_start: 0.8427 (mt) cc_final: 0.8196 (tp)
REVERT: C   85 GLU cc_start: 0.7344 (tp30) cc_final: 0.7067 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 273
  average time/residue: 0.1146
  time to fit residues: 40.6199
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  : 0.203 
-------------------------------------------------------------------------------
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:    4.9990
   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:    0.9980
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  78 HIS
A 144 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.121290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.103251 restraints weight = 21600.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.105662 restraints weight = 12543.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.107286 restraints weight = 8859.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.108320 restraints weight = 7148.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.108769 restraints weight = 6222.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8974  Z= 0.185
  Angle     :  0.734   8.113  12520  Z= 0.416
  Chirality :  0.049   0.263   1388
  Planarity :  0.005   0.056   1258
  Dihedral  : 25.814 178.324   1916
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 12.64 %
    Favored  : 84.23 %
  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 are not related in a simple way.
  whole: -2.35 (0.26), residues: 822
  helix: -1.05 (0.24), residues: 326
  sheet: -1.26 (0.36), residues: 194
  loop : -2.14 (0.32), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 263 
 TYR   0.009   0.001   TYR C  99 
 PHE   0.016   0.002   PHE C 181 
 TRP   0.022   0.002   TRP C  61 
 HIS   0.013   0.002   HIS A  12 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.18 ( 8966)
  covalent geometry    : angle       0.72716 /  0.42 (12516)
  hydrogen bonds       : bond        0.05320 /  3.52 (  436)
  hydrogen bonds       : angle       5.85036 /  4.14 ( 1138)
  metal coordination   : bond        0.01425 /  0.69 (    8)
  metal coordination   : angle       5.73727 /  4.58 (    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
  170 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7487 (mtpt)
REVERT: A  144 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8773 (t0)
REVERT: A  178 MET cc_start: 0.8720 (mtt) cc_final: 0.7282 (mtt)
REVERT: C   15 TYR cc_start: 0.8719 (m-10) cc_final: 0.8310 (m-10)
REVERT: C   85 GLU cc_start: 0.7725 (tp30) cc_final: 0.7356 (mm-30)
REVERT: C  107 ARG cc_start: 0.6828 (mpp80) cc_final: 0.6556 (mpp80)
REVERT: C  144 ASN cc_start: 0.9106 (t0) cc_final: 0.8751 (t0)
REVERT: C  178 MET cc_start: 0.8710 (mtt) cc_final: 0.7244 (mtt)
REVERT: C  194 TYR cc_start: 0.7790 (m-80) cc_final: 0.7556 (m-80)
REVERT: C  195 SER cc_start: 0.8165 (p) cc_final: 0.6505 (m)
REVERT: D  240 LYS cc_start: 0.5752 (tptt) cc_final: 0.5445 (ptpt)
REVERT: D  263 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7820 (mtm110)
  outliers start: 22
  outliers final: 16
  residues processed: 161
  average time/residue: 0.0937
  time to fit residues: 20.6122
Evaluate side-chains
  134 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   93 THR
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  259 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  254 ASN
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  260 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   chunk 88 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 171 HIS
A 183 HIS
A 184 ASN
B 184 ASN
C  78 HIS
C 144 ASN
C 171 HIS
C 183 HIS
D 177 GLN
D 184 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.117024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.098107 restraints weight = 21269.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.100265 restraints weight = 12867.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.101719 restraints weight = 9411.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.102621 restraints weight = 7777.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.103116 restraints weight = 6903.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8974  Z= 0.242
  Angle     :  0.716   8.291  12520  Z= 0.408
  Chirality :  0.048   0.273   1388
  Planarity :  0.005   0.060   1258
  Dihedral  : 26.064 177.680   1916
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 14.35 %
    Favored  : 81.96 %
  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 are not related in a simple way.
  whole: -1.76 (0.27), residues: 822
  helix: -0.34 (0.25), residues: 328
  sheet: -1.14 (0.34), residues: 222
  loop : -2.00 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 107 
 TYR   0.025   0.002   TYR C  99 
 PHE   0.014   0.002   PHE A 121 
 TRP   0.030   0.002   TRP D 132 
 HIS   0.007   0.002   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00509 /  0.24 ( 8966)
  covalent geometry    : angle       0.71134 /  0.41 (12516)
  hydrogen bonds       : bond        0.05095 /  3.45 (  436)
  hydrogen bonds       : angle       5.51002 /  3.93 ( 1138)
  metal coordination   : bond        0.02403 /  1.23 (    8)
  metal coordination   : angle       4.79061 /  4.34 (    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
  149 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8018 (ttm-80)
REVERT: A   69 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7358 (tt0)
REVERT: A  144 ASN cc_start: 0.9094 (t0) cc_final: 0.8738 (t0)
REVERT: A  230 SER cc_start: 0.7775 (m) cc_final: 0.7264 (t)
REVERT: B   96 GLU cc_start: 0.7467 (mp0) cc_final: 0.7195 (mp0)
REVERT: B  101 LEU cc_start: 0.8956 (mt) cc_final: 0.8678 (tp)
REVERT: B  102 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8839 (mm)
REVERT: C   85 GLU cc_start: 0.7867 (tp30) cc_final: 0.7638 (mm-30)
REVERT: C  144 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8780 (t0)
REVERT: C  230 SER cc_start: 0.7730 (m) cc_final: 0.7218 (t)
REVERT: D   96 GLU cc_start: 0.7508 (mp0) cc_final: 0.7212 (mp0)
REVERT: D  101 LEU cc_start: 0.8892 (mt) cc_final: 0.8576 (tt)
  outliers start: 26
  outliers final: 18
  residues processed: 139
  average time/residue: 0.0982
  time to fit residues: 18.6256
Evaluate side-chains
  128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
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  184 ASN
Chi-restraints excluded: chain A residue  195 SER
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   13 GLU
Chi-restraints excluded: chain C residue   79 VAL
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  102 LEU
Chi-restraints excluded: chain D residue  104 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:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 144 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 ASN
D 168 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.117196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.098920 restraints weight = 21416.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.101067 restraints weight = 12748.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.102544 restraints weight = 9244.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.103333 restraints weight = 7536.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.104029 restraints weight = 6689.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8974  Z= 0.169
  Angle     :  0.657   8.290  12520  Z= 0.374
  Chirality :  0.047   0.270   1388
  Planarity :  0.004   0.039   1258
  Dihedral  : 26.131 178.455   1916
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.62 %
    Favored  : 80.82 %
  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 are not related in a simple way.
  whole: -1.20 (0.28), residues: 822
  helix:  0.09 (0.26), residues: 332
  sheet: -0.44 (0.35), residues: 210
  loop : -2.07 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 269 
 TYR   0.020   0.002   TYR C  99 
 PHE   0.012   0.002   PHE A 181 
 TRP   0.023   0.001   TRP D 132 
 HIS   0.005   0.001   HIS A  12 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.17 ( 8966)
  covalent geometry    : angle       0.65055 /  0.37 (12516)
  hydrogen bonds       : bond        0.04468 /  3.02 (  436)
  hydrogen bonds       : angle       5.20277 /  3.72 ( 1138)
  metal coordination   : bond        0.00717 /  0.35 (    8)
  metal coordination   : angle       5.05751 /  4.42 (    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
  148 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7903 (ttm-80)
REVERT: A  194 TYR cc_start: 0.7742 (m-80) cc_final: 0.7453 (m-80)
REVERT: A  195 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.6261 (t)
REVERT: A  230 SER cc_start: 0.7648 (m) cc_final: 0.7189 (t)
REVERT: B  102 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8907 (mm)
REVERT: C  144 ASN cc_start: 0.8908 (t0) cc_final: 0.8342 (t0)
REVERT: C  178 MET cc_start: 0.8546 (mtp) cc_final: 0.7774 (mtt)
REVERT: C  230 SER cc_start: 0.7611 (m) cc_final: 0.7154 (t)
REVERT: D   65 CYS cc_start: 0.7197 (p) cc_final: 0.6626 (t)
REVERT: D   96 GLU cc_start: 0.7205 (mp0) cc_final: 0.6979 (mp0)
  outliers start: 25
  outliers final: 16
  residues processed: 139
  average time/residue: 0.0837
  time to fit residues: 16.7266
Evaluate side-chains
  125 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  195 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  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   79 VAL
Chi-restraints excluded: chain C residue   87 GLU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 ASN
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 183 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.118142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.099727 restraints weight = 21682.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.101949 restraints weight = 13209.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.103425 restraints weight = 9618.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.104392 restraints weight = 7886.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.104992 restraints weight = 6906.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8974  Z= 0.144
  Angle     :  0.634   8.181  12520  Z= 0.365
  Chirality :  0.047   0.271   1388
  Planarity :  0.004   0.031   1258
  Dihedral  : 26.187 178.873   1916
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.47 %
    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 are not related in a simple way.
  whole: -0.93 (0.28), residues: 822
  helix:  0.20 (0.26), residues: 344
  sheet: -0.15 (0.35), residues: 210
  loop : -1.96 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 224 
 TYR   0.020   0.002   TYR C  99 
 PHE   0.030   0.002   PHE D 100 
 TRP   0.020   0.001   TRP B 132 
 HIS   0.008   0.001   HIS D 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.14 ( 8966)
  covalent geometry    : angle       0.62823 /  0.36 (12516)
  hydrogen bonds       : bond        0.04177 /  2.81 (  436)
  hydrogen bonds       : angle       5.03111 /  3.58 ( 1138)
  metal coordination   : bond        0.00632 /  0.38 (    8)
  metal coordination   : angle       5.00042 /  4.37 (    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
  137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.9010 (t0) cc_final: 0.8799 (t0)
REVERT: B  102 LEU cc_start: 0.9297 (mm) cc_final: 0.8957 (mt)
REVERT: C  144 ASN cc_start: 0.8940 (t0) cc_final: 0.8467 (t0)
REVERT: C  178 MET cc_start: 0.8590 (mtp) cc_final: 0.7797 (mtt)
REVERT: C  246 GLU cc_start: 0.6185 (tm-30) cc_final: 0.5776 (tm-30)
REVERT: D   65 CYS cc_start: 0.7146 (p) cc_final: 0.6714 (t)
REVERT: D   96 GLU cc_start: 0.7215 (mp0) cc_final: 0.6882 (mp0)
REVERT: D  166 ARG cc_start: 0.5975 (tpt90) cc_final: 0.4894 (mmm160)
  outliers start: 19
  outliers final: 16
  residues processed: 128
  average time/residue: 0.0692
  time to fit residues: 13.1508
Evaluate side-chains
  123 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
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  259 VAL
Chi-restraints excluded: chain C residue   87 GLU
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  104 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  172 LEU
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:    9.9990
   chunk 43 optimal weight:   20.0000
   chunk 78 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0870
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    2.2166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 114 HIS
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 184 ASN ** 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 = 0.3750 r_free = 0.3750 target = 0.115287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.096831 restraints weight = 21765.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.098919 restraints weight = 13302.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.100342 restraints weight = 9762.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.101048 restraints weight = 8037.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.101674 restraints weight = 7197.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8974  Z= 0.197
  Angle     :  0.667   7.282  12520  Z= 0.380
  Chirality :  0.048   0.272   1388
  Planarity :  0.004   0.032   1258
  Dihedral  : 26.506 177.587   1916
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 17.05 %
    Favored  : 79.12 %
  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 are not related in a simple way.
  whole: -0.85 (0.28), residues: 822
  helix:  0.38 (0.26), residues: 334
  sheet: -0.10 (0.35), residues: 214
  loop : -2.05 (0.34), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 224 
 TYR   0.022   0.002   TYR C  99 
 PHE   0.032   0.002   PHE B 121 
 TRP   0.016   0.002   TRP B 132 
 HIS   0.006   0.001   HIS C 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.20 ( 8966)
  covalent geometry    : angle       0.66468 /  0.38 (12516)
  hydrogen bonds       : bond        0.04522 /  3.08 (  436)
  hydrogen bonds       : angle       5.06533 /  3.59 ( 1138)
  metal coordination   : bond        0.01581 /  0.82 (    8)
  metal coordination   : angle       3.01122 /  2.75 (    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
  142 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.8995 (t0) cc_final: 0.8723 (t0)
REVERT: A  178 MET cc_start: 0.8703 (mtt) cc_final: 0.7183 (mtt)
REVERT: A  230 SER cc_start: 0.7580 (m) cc_final: 0.7078 (t)
REVERT: B   74 LEU cc_start: 0.8649 (mp) cc_final: 0.8391 (tp)
REVERT: B  102 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9098 (mt)
REVERT: B  132 TRP cc_start: 0.8713 (t60) cc_final: 0.8100 (t60)
REVERT: C  144 ASN cc_start: 0.8966 (t0) cc_final: 0.8558 (t0)
REVERT: C  178 MET cc_start: 0.8645 (mtp) cc_final: 0.8034 (mtt)
REVERT: C  230 SER cc_start: 0.7577 (m) cc_final: 0.7055 (t)
REVERT: D   65 CYS cc_start: 0.7282 (p) cc_final: 0.7038 (t)
REVERT: D   96 GLU cc_start: 0.7079 (mp0) cc_final: 0.6770 (mp0)
  outliers start: 27
  outliers final: 24
  residues processed: 130
  average time/residue: 0.0777
  time to fit residues: 14.7824
Evaluate side-chains
  135 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  195 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   87 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
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  104 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  154 MET
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:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 67 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 168 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.116246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.097845 restraints weight = 21962.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.099957 restraints weight = 13278.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.101379 restraints weight = 9727.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.102128 restraints weight = 7982.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.102822 restraints weight = 7135.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.4751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8974  Z= 0.149
  Angle     :  0.620   7.477  12520  Z= 0.355
  Chirality :  0.046   0.274   1388
  Planarity :  0.004   0.033   1258
  Dihedral  : 26.549 178.632   1916
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.75 %
    Favored  : 77.98 %
  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 are not related in a simple way.
  whole: -0.65 (0.28), residues: 822
  helix:  0.43 (0.26), residues: 348
  sheet:  0.12 (0.34), residues: 224
  loop : -2.09 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 224 
 TYR   0.015   0.002   TYR C  99 
 PHE   0.013   0.001   PHE C 181 
 TRP   0.018   0.001   TRP D 132 
 HIS   0.006   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.15 ( 8966)
  covalent geometry    : angle       0.61449 /  0.35 (12516)
  hydrogen bonds       : bond        0.04138 /  2.80 (  436)
  hydrogen bonds       : angle       4.83004 /  3.43 ( 1138)
  metal coordination   : bond        0.00456 /  0.24 (    8)
  metal coordination   : angle       4.46253 /  3.96 (    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
  143 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.8924 (t0) cc_final: 0.8605 (t0)
REVERT: A  178 MET cc_start: 0.8754 (mtt) cc_final: 0.6761 (mtt)
REVERT: A  230 SER cc_start: 0.7477 (m) cc_final: 0.6982 (t)
REVERT: A  269 ARG cc_start: 0.4819 (tmt170) cc_final: 0.4587 (tpt170)
REVERT: B   74 LEU cc_start: 0.8694 (mp) cc_final: 0.8334 (tt)
REVERT: B  102 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9042 (mt)
REVERT: B  132 TRP cc_start: 0.8705 (t60) cc_final: 0.7625 (t60)
REVERT: C  144 ASN cc_start: 0.8910 (t0) cc_final: 0.8480 (t0)
REVERT: C  178 MET cc_start: 0.8605 (mtp) cc_final: 0.7973 (mtt)
REVERT: C  230 SER cc_start: 0.7464 (m) cc_final: 0.6966 (t)
REVERT: D   96 GLU cc_start: 0.7079 (mp0) cc_final: 0.6571 (mp0)
REVERT: D  229 ASP cc_start: 0.7524 (m-30) cc_final: 0.7305 (m-30)
REVERT: D  263 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7603 (mtm110)
  outliers start: 23
  outliers final: 17
  residues processed: 133
  average time/residue: 0.0678
  time to fit residues: 13.6827
Evaluate side-chains
  126 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  195 SER
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   89 ILE
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   87 GLU
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  164 GLN
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:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0470
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.8086

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 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 = 0.3752 r_free = 0.3752 target = 0.115175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.096584 restraints weight = 21700.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.098670 restraints weight = 13268.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.100084 restraints weight = 9777.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.100873 restraints weight = 8066.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.101518 restraints weight = 7190.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.4949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8974  Z= 0.170
  Angle     :  0.634   9.211  12520  Z= 0.358
  Chirality :  0.045   0.270   1388
  Planarity :  0.004   0.033   1258
  Dihedral  : 26.726 177.956   1916
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.75 %
    Favored  : 77.70 %
  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 are not related in a simple way.
  whole: -0.54 (0.28), residues: 822
  helix:  0.51 (0.26), residues: 348
  sheet:  0.20 (0.36), residues: 214
  loop : -1.97 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 224 
 TYR   0.013   0.002   TYR C  99 
 PHE   0.012   0.002   PHE D 121 
 TRP   0.016   0.001   TRP D 132 
 HIS   0.005   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.17 ( 8966)
  covalent geometry    : angle       0.62486 /  0.36 (12516)
  hydrogen bonds       : bond        0.04243 /  2.91 (  436)
  hydrogen bonds       : angle       4.80860 /  3.42 ( 1138)
  metal coordination   : bond        0.02150 /  1.04 (    8)
  metal coordination   : angle       5.96708 /  4.04 (    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
  141 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.8963 (t0) cc_final: 0.8619 (t0)
REVERT: A  178 MET cc_start: 0.8819 (mtt) cc_final: 0.8160 (mtt)
REVERT: A  230 SER cc_start: 0.7231 (m) cc_final: 0.6772 (t)
REVERT: B   74 LEU cc_start: 0.8724 (mp) cc_final: 0.8318 (tt)
REVERT: B  100 PHE cc_start: 0.8420 (t80) cc_final: 0.8146 (t80)
REVERT: B  102 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9052 (mt)
REVERT: C  144 ASN cc_start: 0.8895 (t0) cc_final: 0.8478 (t0)
REVERT: C  178 MET cc_start: 0.8562 (mtp) cc_final: 0.7941 (mtt)
REVERT: C  230 SER cc_start: 0.7211 (m) cc_final: 0.6752 (t)
REVERT: D   96 GLU cc_start: 0.7141 (mp0) cc_final: 0.6812 (mp0)
REVERT: D  229 ASP cc_start: 0.7560 (m-30) cc_final: 0.7358 (m-30)
  outliers start: 25
  outliers final: 18
  residues processed: 129
  average time/residue: 0.0800
  time to fit residues: 15.1207
Evaluate side-chains
  127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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   89 ILE
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  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  164 GLN
Chi-restraints excluded: chain D residue  172 LEU
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:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0980
   chunk 36 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0030
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 120 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 120 ASN ** 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 = 0.3787 r_free = 0.3787 target = 0.117696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.099436 restraints weight = 21605.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.101596 restraints weight = 13037.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.103009 restraints weight = 9521.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.103709 restraints weight = 7821.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.104426 restraints weight = 7003.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8974  Z= 0.126
  Angle     :  0.627  11.826  12520  Z= 0.349
  Chirality :  0.046   0.286   1388
  Planarity :  0.004   0.033   1258
  Dihedral  : 26.604 178.531   1916
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.45 %
    Favored  : 77.13 %
  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 are not related in a simple way.
  whole: -0.28 (0.28), residues: 822
  helix:  0.69 (0.26), residues: 350
  sheet:  0.32 (0.35), residues: 224
  loop : -1.86 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 224 
 TYR   0.014   0.002   TYR A  99 
 PHE   0.018   0.002   PHE D 121 
 TRP   0.019   0.001   TRP D 132 
 HIS   0.004   0.001   HIS C  12 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.13 ( 8966)
  covalent geometry    : angle       0.61315 /  0.35 (12516)
  hydrogen bonds       : bond        0.03983 /  2.71 (  436)
  hydrogen bonds       : angle       4.67436 /  3.32 ( 1138)
  metal coordination   : bond        0.00995 /  0.46 (    8)
  metal coordination   : angle       7.35022 /  5.16 (    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
  137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.8997 (t0) cc_final: 0.8591 (t0)
REVERT: A  178 MET cc_start: 0.8789 (mtt) cc_final: 0.6926 (mtt)
REVERT: A  230 SER cc_start: 0.7388 (m) cc_final: 0.6904 (t)
REVERT: B   74 LEU cc_start: 0.8726 (mp) cc_final: 0.8405 (tp)
REVERT: B   87 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: B  100 PHE cc_start: 0.8436 (t80) cc_final: 0.8230 (t80)
REVERT: B  102 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9115 (mt)
REVERT: B  132 TRP cc_start: 0.8729 (t60) cc_final: 0.7761 (t60)
REVERT: C   18 ASN cc_start: 0.7696 (p0) cc_final: 0.7464 (p0)
REVERT: C  144 ASN cc_start: 0.8856 (t0) cc_final: 0.8398 (t0)
REVERT: C  178 MET cc_start: 0.8547 (mtp) cc_final: 0.7904 (mtt)
REVERT: C  230 SER cc_start: 0.7394 (m) cc_final: 0.6892 (t)
REVERT: D   74 LEU cc_start: 0.8391 (tp) cc_final: 0.8184 (mp)
  outliers start: 17
  outliers final: 14
  residues processed: 132
  average time/residue: 0.0802
  time to fit residues: 15.2632
Evaluate side-chains
  124 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   89 ILE
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 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  164 GLN
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:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 222 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.114523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.096051 restraints weight = 21733.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.098112 restraints weight = 13345.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.099545 restraints weight = 9814.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.100424 restraints weight = 8067.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.100919 restraints weight = 7151.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8974  Z= 0.187
  Angle     :  0.653   6.821  12520  Z= 0.365
  Chirality :  0.046   0.265   1388
  Planarity :  0.004   0.034   1258
  Dihedral  : 26.791 177.222   1916
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.03 %
    Favored  : 77.13 %
  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 are not related in a simple way.
  whole: -0.36 (0.28), residues: 822
  helix:  0.68 (0.26), residues: 348
  sheet:  0.22 (0.36), residues: 214
  loop : -1.86 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  20 
 TYR   0.016   0.002   TYR A  99 
 PHE   0.010   0.001   PHE C 121 
 TRP   0.015   0.002   TRP B 132 
 HIS   0.005   0.001   HIS C  12 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.19 ( 8966)
  covalent geometry    : angle       0.64780 /  0.36 (12516)
  hydrogen bonds       : bond        0.04323 /  2.98 (  436)
  hydrogen bonds       : angle       4.75385 /  3.37 ( 1138)
  metal coordination   : bond        0.01516 /  0.83 (    8)
  metal coordination   : angle       4.45163 /  3.13 (    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
  130 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.8987 (t0) cc_final: 0.8660 (t0)
REVERT: A  178 MET cc_start: 0.8837 (mtt) cc_final: 0.8175 (mtt)
REVERT: A  230 SER cc_start: 0.7120 (m) cc_final: 0.6671 (t)
REVERT: B   74 LEU cc_start: 0.8771 (mp) cc_final: 0.8415 (tp)
REVERT: B   83 TYR cc_start: 0.7636 (t80) cc_final: 0.6979 (t80)
REVERT: C  144 ASN cc_start: 0.8865 (t0) cc_final: 0.8443 (t0)
REVERT: C  178 MET cc_start: 0.8525 (mtp) cc_final: 0.8058 (mtt)
REVERT: C  230 SER cc_start: 0.7109 (m) cc_final: 0.6659 (t)
REVERT: D   83 TYR cc_start: 0.7481 (t80) cc_final: 0.7047 (t80)
  outliers start: 20
  outliers final: 17
  residues processed: 123
  average time/residue: 0.0737
  time to fit residues: 13.2790
Evaluate side-chains
  121 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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  195 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   89 ILE
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  124 THR
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  164 GLN
Chi-restraints excluded: chain D residue  172 LEU
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:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 84 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 65 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 120 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 = 0.3763 r_free = 0.3763 target = 0.116138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.097736 restraints weight = 21781.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.099881 restraints weight = 13257.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.101309 restraints weight = 9686.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.102224 restraints weight = 7957.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.102723 restraints weight = 7041.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8974  Z= 0.135
  Angle     :  0.629   9.128  12520  Z= 0.351
  Chirality :  0.046   0.270   1388
  Planarity :  0.004   0.035   1258
  Dihedral  : 26.697 177.836   1916
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.60 %
    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 are not related in a simple way.
  whole: -0.17 (0.28), residues: 822
  helix:  0.84 (0.26), residues: 350
  sheet:  0.24 (0.35), residues: 214
  loop : -1.69 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 224 
 TYR   0.014   0.001   TYR A  99 
 PHE   0.010   0.001   PHE C 100 
 TRP   0.018   0.001   TRP B 132 
 HIS   0.004   0.001   HIS A  12 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 ( 8966)
  covalent geometry    : angle       0.62168 /  0.35 (12516)
  hydrogen bonds       : bond        0.03990 /  2.72 (  436)
  hydrogen bonds       : angle       4.64961 /  3.29 ( 1138)
  metal coordination   : bond        0.00739 /  0.46 (    8)
  metal coordination   : angle       5.29523 /  4.21 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1277.03 seconds
wall clock time: 22 minutes 46.05 seconds (1366.05 seconds total)