Starting phenix.real_space_refine
on Wed Aug  5 03:00:14 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8hik_34819/08_2026/8hik_34819.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hik_34819/08_2026/8hik_34819.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hik_34819/08_2026/8hik_34819.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hik_34819/08_2026/8hik_34819.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8hik_34819/08_2026/8hik_34819.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8hik_34819/08_2026/8hik_34819.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hik_34819/08_2026/8hik_34819.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hik_34819/08_2026/8hik_34819.cif"
  }
  resolution = 3.72
  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=   0.000 sd=   0.016
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     C    5296      2.51       5
     N    1376      2.21       5
     O    1537      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8238
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 3969
          Classifications: {'peptide': 498}
          Link IDs: {'PTRANS': 17, 'TRANS': 480}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1686
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
    Chain: "N"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1632
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'TPP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.02, per 1000 atoms: 0.25
  Number of scatterers: 8238
  At special positions: 0
  Unit cell: (66.34, 99.51, 148.73, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       2     15.00
     O    1537      8.00
     N    1376      7.00
     C    5296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 154 " - pdb=" SG  CYS H 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 447.4 milliseconds
  

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1972

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      39.7% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid -80 through -64
      removed outlier: 3.672A  pdb=" N   LYS A -64 " --> pdb=" O   LYS A -68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -57 through -43
      removed outlier: 3.598A  pdb=" N   ALA A -43 " --> pdb=" O   ALA A -47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -38 through -33
      removed outlier: 4.020A  pdb=" N   ASP A -33 " --> pdb=" O   PRO A -37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -25 through -3
      removed outlier: 3.702A  pdb=" N   LEU A  -5 " --> pdb=" O   ASP A  -9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 3.694A  pdb=" N   ALA A   6 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 23
    Processing helix  chain 'A' and resid 27 through 39
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 66
    Processing helix  chain 'A' and resid 68 through 81
    Processing helix  chain 'A' and resid 82 through 90
      removed outlier: 4.114A  pdb=" N   LEU A  86 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 112
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.884A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 144
      removed outlier: 4.115A  pdb=" N   SER A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 176
    Processing helix  chain 'A' and resid 181 through 202
    Processing helix  chain 'A' and resid 251 through 259
    Processing helix  chain 'A' and resid 260 through 262
      No H-bonds generated for 'chain 'A' and resid 260 through 262'
    Processing helix  chain 'A' and resid 264 through 296
      removed outlier: 3.936A  pdb=" N   TYR A 287 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP A 296 " --> pdb=" O   TRP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 323
    Processing helix  chain 'A' and resid 335 through 355
    Processing helix  chain 'A' and resid 361 through 375
    Processing helix  chain 'A' and resid 379 through 389
      removed outlier: 3.718A  pdb=" N   ILE A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 418
    Processing helix  chain 'A' and resid 427 through 451
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.532A  pdb=" N   ASP H  93 " --> pdb=" O   ARG H  90 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 90 through 94'
    Processing helix  chain 'H' and resid 107 through 112
      removed outlier: 3.631A  pdb=" N   LYS H 112 " --> pdb=" O   GLU H 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.097A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 188
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15
      removed outlier: 3.588A  pdb=" N   VAL H  15 " --> pdb=" O   THR H 124 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.145A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.145A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 164 through 167
      removed outlier: 4.332A  pdb=" N   TYR H 208 " --> pdb=" O   VAL H 225 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.735A  pdb=" N   SER N   7 " --> pdb=" O   SER N  21 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.833A  pdb=" N   THR N 118 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR N 115 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 115 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   MET N  34 " --> pdb=" O   VAL N  50 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   VAL N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.833A  pdb=" N   THR N 118 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR N 115 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 115 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   TYR N 110 " --> pdb=" O   ILE N  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AB1, first strand: chain 'L' and resid 13 through 14
    Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.941A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN L  91 " --> pdb=" O   THR L  99 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.941A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120
      removed outlier: 5.961A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 147 through 148

    446 hydrogen bonds defined for protein.
    1248 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.13

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2562
        1.34 -     1.46: 2030
        1.46 -     1.58: 3807
        1.58 -     1.70: 3
        1.70 -     1.81: 38
  Bond restraints: 8440
  Sorted by residual:
  bond pdb=" C5  TPP A 601 "
       pdb=" S1  TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.727  1.510  0.217 1.00e-02 1.00e+04 4.69e+02
  bond pdb=" C2  TPP A 601 "
       pdb=" S1  TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.675  1.544  0.131 1.00e-02 1.00e+04 1.71e+02
  bond pdb=" C4' TPP A 601 "
       pdb=" N4' TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.454 -0.117 1.10e-02 8.26e+03 1.13e+02
  bond pdb=" C2  TPP A 601 "
       pdb=" N3  TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.318  1.424 -0.106 1.30e-02 5.92e+03 6.66e+01
  bond pdb=" O3A TPP A 601 "
       pdb=" PB  TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.587  1.662 -0.075 1.10e-02 8.26e+03 4.66e+01
  ... (remaining 8435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 11372
        3.25 -     6.49: 91
        6.49 -     9.74: 18
        9.74 -    12.98: 2
       12.98 -    16.23: 1
  Bond angle restraints: 11484
  Sorted by residual:
  angle pdb=" PA  TPP A 601 "
        pdb=" O3A TPP A 601 "
        pdb=" PB  TPP A 601 "
      ideal   model   delta    sigma   weight residual
     139.87  123.64   16.23 1.00e+00 1.00e+00 2.63e+02
  angle pdb=" C2  TPP A 601 "
        pdb=" S1  TPP A 601 "
        pdb=" C5  TPP A 601 "
      ideal   model   delta    sigma   weight residual
      91.33  104.13  -12.80 1.00e+00 1.00e+00 1.64e+02
  angle pdb=" C7  TPP A 601 "
        pdb=" O7  TPP A 601 "
        pdb=" PA  TPP A 601 "
      ideal   model   delta    sigma   weight residual
     124.29  118.57    5.72 1.00e+00 1.00e+00 3.27e+01
  angle pdb=" N1' TPP A 601 "
        pdb=" C2' TPP A 601 "
        pdb=" N3' TPP A 601 "
      ideal   model   delta    sigma   weight residual
     125.71  119.88    5.83 1.07e+00 8.80e-01 2.99e+01
  angle pdb=" N3  TPP A 601 "
        pdb=" C2  TPP A 601 "
        pdb=" S1  TPP A 601 "
      ideal   model   delta    sigma   weight residual
     112.34  107.32    5.02 1.00e+00 1.00e+00 2.52e+01
  ... (remaining 11479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 4807
       16.52 -    33.03: 110
       33.03 -    49.54: 34
       49.54 -    66.06: 1
       66.06 -    82.57: 11
  Dihedral angle restraints: 4963
    sinusoidal: 1886
      harmonic: 3077
  Sorted by residual:
  dihedral pdb=" CB  CYS H 154 "
           pdb=" SG  CYS H 154 "
           pdb=" SG  CYS H 210 "
           pdb=" CB  CYS H 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.57  -82.57     1      1.00e+01 1.00e-02 8.36e+01
  dihedral pdb=" CB  CYS L 136 "
           pdb=" SG  CYS L 136 "
           pdb=" SG  CYS L 196 "
           pdb=" CB  CYS L 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -120.31   34.31     1      1.00e+01 1.00e-02 1.67e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.67   20.33     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 4960 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 957
       0.049 -    0.097: 267
       0.097 -    0.146: 64
       0.146 -    0.195: 7
       0.195 -    0.243: 1
  Chirality restraints: 1296
  Sorted by residual:
  chirality pdb=" CA  THR A  69 "
            pdb=" N   THR A  69 "
            pdb=" C   THR A  69 "
            pdb=" CB  THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  THR A  69 "
            pdb=" CA  THR A  69 "
            pdb=" OG1 THR A  69 "
            pdb=" CG2 THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.13e-01
  chirality pdb=" CA  TYR N 104 "
            pdb=" N   TYR N 104 "
            pdb=" C   TYR N 104 "
            pdb=" CB  TYR N 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.80e-01
  ... (remaining 1293 not shown)

  Planarity restraints: 1437
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 102 "   -0.016 2.00e-02 2.50e+03   1.51e-02 5.66e+00
        pdb=" CG  TRP H 102 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 102 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 102 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 102 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 102 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 102 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 102 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 102 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 102 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP H 105 "    0.038 5.00e-02 4.00e+02   5.76e-02 5.31e+00
        pdb=" N   PRO H 106 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO H 106 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H 106 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 108 "   -0.035 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO H 109 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO H 109 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO H 109 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1434 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2236
        2.81 -     3.33: 7133
        3.33 -     3.85: 13492
        3.85 -     4.38: 15090
        4.38 -     4.90: 26545
  Nonbonded interactions: 64496
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 168 "
            pdb=" O   GLY A 307 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG  SER L  64 "
            pdb=" OG1 THR L  75 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   GLU A -26 "
            pdb=" OH  TYR A  22 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" NE  ARG A -49 "
            pdb=" O   LEU L  93 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O   TRP H 111 "
            pdb=" OH  TYR L  92 "
     model   vdw
     2.345 3.040
  ... (remaining 64491 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.210
  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:         0.040
  Set scattering table:                    0.030
  Process input model:                     8.960
  Find NCS groups from input model:        0.040
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6273
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      :  0.005   0.217   8445  Z= 0.385
  Angle     :  0.821  16.228  11494  Z= 0.473
  Chirality :  0.047   0.243   1296
  Planarity :  0.006   0.058   1437
  Dihedral  :  9.444  75.327   2976
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -3.54 (0.21), residues: 1045
  helix: -1.96 (0.20), residues: 380
  sheet: -1.92 (0.29), residues: 241
  loop : -2.84 (0.25), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  62 
 TYR   0.023   0.002   TYR H  53 
 PHE   0.029   0.002   PHE A 103 
 TRP   0.041   0.002   TRP H 102 
 HIS   0.006   0.002   HIS H  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00515 /  0.39 ( 8440)
  covalent geometry    : angle       0.82034 /  0.47 (11484)
  SS BOND              : bond        0.00134 /  0.08 (    5)
  SS BOND              : angle       1.34217 /  0.86 (   10)
  hydrogen bonds       : bond        0.11935 /  7.62 (  420)
  hydrogen bonds       : angle       6.64327 /  4.41 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.7460 (tttt) cc_final: 0.7258 (mtmm)
REVERT: A  -50 MET cc_start: 0.6246 (mmm) cc_final: 0.5921 (mmm)
REVERT: A  -22 PHE cc_start: 0.7319 (t80) cc_final: 0.6815 (t80)
REVERT: A   27 HIS cc_start: 0.5170 (m90) cc_final: 0.4851 (m-70)
REVERT: A   73 SER cc_start: 0.6585 (m) cc_final: 0.6353 (t)
REVERT: A  140 ILE cc_start: 0.7951 (mt) cc_final: 0.7742 (tp)
REVERT: A  281 TYR cc_start: 0.6510 (t80) cc_final: 0.6203 (t80)
REVERT: A  304 VAL cc_start: 0.7185 (t) cc_final: 0.5917 (m)
REVERT: A  386 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7062 (tm-30)
REVERT: A  387 ILE cc_start: 0.7155 (mt) cc_final: 0.6955 (mt)
REVERT: H   86 MET cc_start: 0.6378 (mtm) cc_final: 0.6146 (mtm)
REVERT: H   99 CYS cc_start: 0.5632 (t) cc_final: 0.5367 (t)
REVERT: H  112 LYS cc_start: 0.7716 (mttt) cc_final: 0.7507 (ttmm)
REVERT: H  119 GLN cc_start: 0.6958 (mt0) cc_final: 0.6698 (mt0)
REVERT: H  135 VAL cc_start: 0.7872 (t) cc_final: 0.7591 (m)
REVERT: H  136 PHE cc_start: 0.7526 (m-80) cc_final: 0.7085 (m-80)
REVERT: N   34 MET cc_start: 0.6441 (mtp) cc_final: 0.6214 (mtp)
REVERT: L   32 SER cc_start: 0.7747 (t) cc_final: 0.7452 (p)
REVERT: L   37 TYR cc_start: 0.8262 (m-10) cc_final: 0.7689 (m-80)
REVERT: L   43 LYS cc_start: 0.8431 (mttt) cc_final: 0.8095 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.0709
  time to fit residues: 21.6278
Evaluate side-chains
  184 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0070
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A -77 ASN
A -42 GLN
A  27 HIS
A 120 GLN
A 358 HIS
H 178 HIS
** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  28 GLN
L  39 GLN
L  90 GLN
L 162 GLN
** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 191 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.170418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.151691 restraints weight = 13135.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.155496 restraints weight = 7261.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.157999 restraints weight = 4574.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.159689 restraints weight = 3212.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.160824 restraints weight = 2449.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6504
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092   8445  Z= 0.217
  Angle     :  0.648  10.014  11494  Z= 0.337
  Chirality :  0.043   0.170   1296
  Planarity :  0.005   0.052   1437
  Dihedral  :  5.243  43.862   1159
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  9.85 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -2.19 (0.24), residues: 1045
  helix: -0.38 (0.25), residues: 388
  sheet: -1.48 (0.31), residues: 240
  loop : -2.39 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A -49 
 TYR   0.030   0.002   TYR A 126 
 PHE   0.018   0.002   PHE L 211 
 TRP   0.035   0.003   TRP H 102 
 HIS   0.005   0.001   HIS H  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.22 ( 8440)
  covalent geometry    : angle       0.64287 /  0.33 (11484)
  SS BOND              : bond        0.00719 /  0.36 (    5)
  SS BOND              : angle       2.91382 /  1.71 (   10)
  hydrogen bonds       : bond        0.04003 /  2.63 (  420)
  hydrogen bonds       : angle       5.51520 /  3.73 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 221
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.7674 (tttt) cc_final: 0.7313 (mtmm)
REVERT: A  -50 MET cc_start: 0.6424 (mmm) cc_final: 0.5992 (mmm)
REVERT: A   27 HIS cc_start: 0.5905 (m-70) cc_final: 0.5648 (m-70)
REVERT: A   73 SER cc_start: 0.7496 (m) cc_final: 0.7163 (t)
REVERT: A   99 GLN cc_start: 0.7890 (tt0) cc_final: 0.7449 (tt0)
REVERT: A  281 TYR cc_start: 0.6721 (t80) cc_final: 0.6374 (t80)
REVERT: A  294 GLU cc_start: 0.6928 (tt0) cc_final: 0.6662 (tt0)
REVERT: A  386 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7112 (tm-30)
REVERT: A  387 ILE cc_start: 0.7141 (mt) cc_final: 0.6836 (mt)
REVERT: H    7 LEU cc_start: 0.7527 (mm) cc_final: 0.7319 (mt)
REVERT: H   46 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8160 (mmmm)
REVERT: H   63 TYR cc_start: 0.7695 (m-10) cc_final: 0.7176 (m-10)
REVERT: H   86 MET cc_start: 0.6684 (mtm) cc_final: 0.6463 (mtm)
REVERT: H  110 TRP cc_start: 0.7961 (t60) cc_final: 0.7068 (t60)
REVERT: H  135 VAL cc_start: 0.7908 (t) cc_final: 0.7569 (m)
REVERT: H  136 PHE cc_start: 0.7550 (m-80) cc_final: 0.7233 (m-80)
REVERT: H  197 THR cc_start: 0.7173 (p) cc_final: 0.6972 (p)
REVERT: N   59 PHE cc_start: 0.7030 (m-80) cc_final: 0.6791 (m-80)
REVERT: L   36 TRP cc_start: 0.8123 (m100) cc_final: 0.7782 (m100)
REVERT: L   37 TYR cc_start: 0.8336 (m-10) cc_final: 0.8034 (m-80)
REVERT: L   43 LYS cc_start: 0.8619 (mttt) cc_final: 0.8326 (mmmm)
REVERT: L   47 LEU cc_start: 0.8590 (tp) cc_final: 0.8318 (tt)
REVERT: L   74 LEU cc_start: 0.8144 (tt) cc_final: 0.7939 (tp)
REVERT: L   87 TYR cc_start: 0.8413 (m-80) cc_final: 0.7947 (m-10)
REVERT: L  117 VAL cc_start: 0.8265 (t) cc_final: 0.7953 (p)
REVERT: L  141 PHE cc_start: 0.8627 (p90) cc_final: 0.8419 (p90)
REVERT: L  166 THR cc_start: 0.8448 (t) cc_final: 0.7946 (m)
REVERT: L  177 LEU cc_start: 0.8129 (tt) cc_final: 0.7928 (tt)
  outliers start: 20
  outliers final: 10
  residues processed: 228
  average time/residue: 0.0754
  time to fit residues: 24.3058
Evaluate side-chains
  208 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 198
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0670
   chunk 52 optimal weight:    0.2980
   overall best weight:    0.4918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A -77 ASN
A -20 HIS
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 GLN
L  28 GLN
L 160 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.168493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.149997 restraints weight = 13075.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.153676 restraints weight = 7289.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.156063 restraints weight = 4616.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.157718 restraints weight = 3267.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.158726 restraints weight = 2507.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   8445  Z= 0.173
  Angle     :  0.609   7.574  11494  Z= 0.310
  Chirality :  0.042   0.154   1296
  Planarity :  0.004   0.048   1437
  Dihedral  :  5.005  38.245   1159
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 10.64 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -1.59 (0.26), residues: 1045
  helix:  0.21 (0.26), residues: 387
  sheet: -1.22 (0.31), residues: 243
  loop : -2.12 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A -49 
 TYR   0.024   0.002   TYR A 126 
 PHE   0.017   0.001   PHE A 212 
 TRP   0.025   0.002   TRP H 102 
 HIS   0.003   0.001   HIS H  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00373 /  0.17 ( 8440)
  covalent geometry    : angle       0.60785 /  0.31 (11484)
  SS BOND              : bond        0.00570 /  0.29 (    5)
  SS BOND              : angle       1.59392 /  1.01 (   10)
  hydrogen bonds       : bond        0.03808 /  2.50 (  420)
  hydrogen bonds       : angle       5.17453 /  3.50 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 209
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -56 LYS cc_start: 0.8159 (tttt) cc_final: 0.7946 (ttpt)
REVERT: A   73 SER cc_start: 0.7768 (m) cc_final: 0.7358 (t)
REVERT: A   99 GLN cc_start: 0.7558 (tt0) cc_final: 0.7058 (tt0)
REVERT: A  294 GLU cc_start: 0.6861 (tt0) cc_final: 0.6572 (tt0)
REVERT: A  373 ARG cc_start: 0.6022 (mmm-85) cc_final: 0.5760 (mmm-85)
REVERT: A  386 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6983 (tm-30)
REVERT: A  387 ILE cc_start: 0.7096 (mt) cc_final: 0.6884 (mt)
REVERT: H  135 VAL cc_start: 0.7893 (t) cc_final: 0.7532 (m)
REVERT: H  136 PHE cc_start: 0.7709 (m-80) cc_final: 0.7448 (m-80)
REVERT: H  197 THR cc_start: 0.7080 (p) cc_final: 0.6873 (p)
REVERT: N   39 GLN cc_start: 0.5923 (mp10) cc_final: 0.4010 (mp10)
REVERT: L   36 TRP cc_start: 0.8094 (m100) cc_final: 0.7812 (m100)
REVERT: L   43 LYS cc_start: 0.8665 (mttt) cc_final: 0.8385 (mtpp)
REVERT: L   48 LEU cc_start: 0.8011 (tp) cc_final: 0.7679 (tp)
REVERT: L   74 LEU cc_start: 0.8170 (tt) cc_final: 0.7924 (tp)
REVERT: L  104 THR cc_start: 0.7898 (p) cc_final: 0.7626 (p)
  outliers start: 24
  outliers final: 19
  residues processed: 218
  average time/residue: 0.0746
  time to fit residues: 23.2750
Evaluate side-chains
  216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 197
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.0980
   chunk 59 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.8828 > 50:)
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 49 optimal weight:    0.1980
   chunk 91 optimal weight:    0.1980
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.3380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 169 ASN
L 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.168659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.150379 restraints weight = 13315.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.154141 restraints weight = 7248.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.156592 restraints weight = 4509.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.158167 restraints weight = 3139.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.159302 restraints weight = 2395.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8445  Z= 0.137
  Angle     :  0.575   7.285  11494  Z= 0.289
  Chirality :  0.040   0.136   1296
  Planarity :  0.004   0.049   1437
  Dihedral  :  4.706  34.801   1159
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.23 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -1.21 (0.26), residues: 1045
  helix:  0.54 (0.27), residues: 385
  sheet: -0.94 (0.32), residues: 234
  loop : -1.94 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A -49 
 TYR   0.023   0.002   TYR A 126 
 PHE   0.012   0.001   PHE H 180 
 TRP   0.016   0.001   TRP H 102 
 HIS   0.003   0.001   HIS A 355 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 ( 8440)
  covalent geometry    : angle       0.57435 /  0.29 (11484)
  SS BOND              : bond        0.00342 /  0.20 (    5)
  SS BOND              : angle       0.99235 /  0.83 (   10)
  hydrogen bonds       : bond        0.03511 /  2.31 (  420)
  hydrogen bonds       : angle       4.97635 /  3.35 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -56 LYS cc_start: 0.8259 (tttt) cc_final: 0.8022 (ttpt)
REVERT: A  -49 ARG cc_start: 0.7712 (tpt-90) cc_final: 0.7449 (ttm-80)
REVERT: A  -25 MET cc_start: 0.6481 (tpp) cc_final: 0.6195 (mmm)
REVERT: A  -22 PHE cc_start: 0.7542 (t80) cc_final: 0.7339 (t80)
REVERT: A   28 LEU cc_start: 0.7877 (mm) cc_final: 0.7505 (mp)
REVERT: A   73 SER cc_start: 0.7868 (m) cc_final: 0.7449 (t)
REVERT: A   86 LEU cc_start: 0.7504 (tt) cc_final: 0.7270 (tp)
REVERT: A   99 GLN cc_start: 0.7640 (tt0) cc_final: 0.7077 (tt0)
REVERT: A  264 ARG cc_start: 0.3899 (mtm110) cc_final: 0.3570 (mtp-110)
REVERT: A  294 GLU cc_start: 0.6876 (tt0) cc_final: 0.6675 (tt0)
REVERT: A  386 GLN cc_start: 0.7452 (mm-40) cc_final: 0.6973 (tm-30)
REVERT: A  387 ILE cc_start: 0.7090 (mt) cc_final: 0.6869 (mt)
REVERT: H   20 SER cc_start: 0.7987 (m) cc_final: 0.7581 (p)
REVERT: H   37 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7690 (mt)
REVERT: H  135 VAL cc_start: 0.7848 (t) cc_final: 0.7492 (m)
REVERT: H  136 PHE cc_start: 0.7694 (m-80) cc_final: 0.7470 (m-80)
REVERT: N   95 TYR cc_start: 0.6022 (m-10) cc_final: 0.5774 (m-10)
REVERT: L   32 SER cc_start: 0.8169 (t) cc_final: 0.7753 (p)
REVERT: L   36 TRP cc_start: 0.8163 (m100) cc_final: 0.7774 (m100)
REVERT: L   37 TYR cc_start: 0.8268 (m-80) cc_final: 0.7983 (m-80)
REVERT: L   43 LYS cc_start: 0.8665 (mttt) cc_final: 0.8340 (mtpp)
REVERT: L   48 LEU cc_start: 0.8011 (tp) cc_final: 0.7562 (tp)
REVERT: L   87 TYR cc_start: 0.8456 (m-80) cc_final: 0.7996 (m-10)
REVERT: L   88 TYR cc_start: 0.8356 (m-80) cc_final: 0.7653 (m-80)
  outliers start: 25
  outliers final: 16
  residues processed: 212
  average time/residue: 0.0768
  time to fit residues: 22.8688
Evaluate side-chains
  212 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 195
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain H residue   33 VAL
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   5 GLN
A  27 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.164176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.145314 restraints weight = 13128.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.149129 restraints weight = 7046.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.151700 restraints weight = 4382.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.153380 restraints weight = 3041.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.154545 restraints weight = 2306.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   8445  Z= 0.213
  Angle     :  0.644   8.802  11494  Z= 0.329
  Chirality :  0.043   0.136   1296
  Planarity :  0.004   0.052   1437
  Dihedral  :  4.926  23.497   1159
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.90 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -1.27 (0.26), residues: 1045
  helix:  0.51 (0.26), residues: 385
  sheet: -1.06 (0.32), residues: 245
  loop : -1.95 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A -49 
 TYR   0.029   0.002   TYR A 126 
 PHE   0.015   0.002   PHE L 211 
 TRP   0.016   0.002   TRP H 117 
 HIS   0.004   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.21 ( 8440)
  covalent geometry    : angle       0.64353 /  0.33 (11484)
  SS BOND              : bond        0.00737 /  0.40 (    5)
  SS BOND              : angle       1.05540 /  0.99 (   10)
  hydrogen bonds       : bond        0.04046 /  2.66 (  420)
  hydrogen bonds       : angle       5.28910 /  3.57 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 207
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -76 TRP cc_start: 0.6223 (t-100) cc_final: 0.5925 (t-100)
REVERT: A  -56 LYS cc_start: 0.8313 (tttt) cc_final: 0.8054 (ttpt)
REVERT: A  -50 MET cc_start: 0.6455 (mmm) cc_final: 0.6067 (tmm)
REVERT: A  -49 ARG cc_start: 0.7879 (tpt-90) cc_final: 0.7596 (tpp80)
REVERT: A   73 SER cc_start: 0.8175 (m) cc_final: 0.7800 (t)
REVERT: A  128 VAL cc_start: 0.8175 (m) cc_final: 0.7780 (p)
REVERT: A  264 ARG cc_start: 0.4234 (mtm110) cc_final: 0.3867 (mtm110)
REVERT: A  294 GLU cc_start: 0.6872 (tt0) cc_final: 0.6612 (tt0)
REVERT: A  300 ASN cc_start: 0.5982 (t0) cc_final: 0.5774 (t0)
REVERT: A  386 GLN cc_start: 0.7356 (mm-40) cc_final: 0.6953 (tt0)
REVERT: A  387 ILE cc_start: 0.7118 (mt) cc_final: 0.6882 (mt)
REVERT: H   20 SER cc_start: 0.8156 (m) cc_final: 0.7752 (p)
REVERT: H   37 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7706 (mt)
REVERT: H   63 TYR cc_start: 0.7772 (m-10) cc_final: 0.7415 (m-10)
REVERT: H  135 VAL cc_start: 0.7871 (t) cc_final: 0.7660 (m)
REVERT: N   95 TYR cc_start: 0.5996 (m-10) cc_final: 0.5717 (m-10)
REVERT: L   32 SER cc_start: 0.8214 (t) cc_final: 0.7861 (p)
REVERT: L   38 GLN cc_start: 0.8379 (tt0) cc_final: 0.7914 (tt0)
REVERT: L   48 LEU cc_start: 0.7962 (tp) cc_final: 0.7566 (tp)
REVERT: L   72 PHE cc_start: 0.8405 (m-80) cc_final: 0.8201 (m-80)
REVERT: L   91 GLN cc_start: 0.7354 (pp30) cc_final: 0.7131 (pp30)
REVERT: L   92 TYR cc_start: 0.8251 (p90) cc_final: 0.7685 (p90)
REVERT: L  166 THR cc_start: 0.8613 (t) cc_final: 0.8208 (m)
  outliers start: 24
  outliers final: 20
  residues processed: 219
  average time/residue: 0.0775
  time to fit residues: 23.5792
Evaluate side-chains
  216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 195
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   26 ARG
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain H residue  200 SER
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0370
   chunk 48 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 13 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.160460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.141752 restraints weight = 13264.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.145558 restraints weight = 7242.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148077 restraints weight = 4514.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.149727 restraints weight = 3135.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.150855 restraints weight = 2376.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          0.4975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   8445  Z= 0.185
  Angle     :  0.645  11.520  11494  Z= 0.321
  Chirality :  0.042   0.130   1296
  Planarity :  0.004   0.057   1437
  Dihedral  :  4.819  21.168   1159
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.25 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -1.16 (0.26), residues: 1045
  helix:  0.57 (0.26), residues: 387
  sheet: -0.83 (0.33), residues: 235
  loop : -1.97 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A -49 
 TYR   0.025   0.002   TYR A 126 
 PHE   0.027   0.001   PHE H 136 
 TRP   0.013   0.002   TRP H 168 
 HIS   0.004   0.001   HIS A 355 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.19 ( 8440)
  covalent geometry    : angle       0.64467 /  0.32 (11484)
  SS BOND              : bond        0.00389 /  0.21 (    5)
  SS BOND              : angle       1.02122 /  0.87 (   10)
  hydrogen bonds       : bond        0.03912 /  2.56 (  420)
  hydrogen bonds       : angle       5.14268 /  3.48 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -56 LYS cc_start: 0.8399 (tttt) cc_final: 0.8174 (ttpt)
REVERT: A  -49 ARG cc_start: 0.7894 (tpt-90) cc_final: 0.7248 (ttt180)
REVERT: A   73 SER cc_start: 0.8015 (m) cc_final: 0.7651 (t)
REVERT: A   99 GLN cc_start: 0.7617 (tt0) cc_final: 0.7052 (tt0)
REVERT: A  122 MET cc_start: 0.7172 (tmm) cc_final: 0.6002 (tmm)
REVERT: A  128 VAL cc_start: 0.8152 (m) cc_final: 0.7767 (p)
REVERT: A  294 GLU cc_start: 0.6870 (tt0) cc_final: 0.6608 (tt0)
REVERT: A  300 ASN cc_start: 0.6019 (t0) cc_final: 0.5814 (t0)
REVERT: A  386 GLN cc_start: 0.7327 (mm-40) cc_final: 0.6924 (tt0)
REVERT: A  387 ILE cc_start: 0.7123 (mt) cc_final: 0.6878 (mt)
REVERT: H   20 SER cc_start: 0.8164 (m) cc_final: 0.7780 (p)
REVERT: H   63 TYR cc_start: 0.7789 (m-10) cc_final: 0.7433 (m-10)
REVERT: H  110 TRP cc_start: 0.8329 (t60) cc_final: 0.7162 (t60)
REVERT: L    7 GLN cc_start: 0.7180 (tt0) cc_final: 0.6609 (tt0)
REVERT: L   32 SER cc_start: 0.8215 (t) cc_final: 0.7793 (p)
REVERT: L   36 TRP cc_start: 0.8233 (m100) cc_final: 0.7813 (m100)
REVERT: L   39 GLN cc_start: 0.8238 (tt0) cc_final: 0.7985 (tt0)
REVERT: L   92 TYR cc_start: 0.8357 (p90) cc_final: 0.7853 (p90)
REVERT: L  142 TYR cc_start: 0.7585 (t80) cc_final: 0.7051 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 209
  average time/residue: 0.0784
  time to fit residues: 22.7808
Evaluate side-chains
  211 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 194
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -26 GLU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    0.4980
   chunk 66 optimal weight:    0.1980
   chunk 80 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 103 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0970
   chunk 100 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0470
   chunk 7 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.1874

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  39 GLN
L 160 ASN
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.163260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.144423 restraints weight = 13518.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148195 restraints weight = 7353.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.150608 restraints weight = 4604.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.152396 restraints weight = 3227.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.153381 restraints weight = 2438.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6590
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8445  Z= 0.116
  Angle     :  0.603  10.361  11494  Z= 0.296
  Chirality :  0.040   0.133   1296
  Planarity :  0.004   0.047   1437
  Dihedral  :  4.532  21.735   1159
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.47 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.78 (0.26), residues: 1045
  helix:  0.92 (0.27), residues: 386
  sheet: -0.68 (0.33), residues: 242
  loop : -1.77 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  42 
 TYR   0.020   0.002   TYR H  53 
 PHE   0.022   0.001   PHE H 136 
 TRP   0.015   0.001   TRP H 168 
 HIS   0.004   0.001   HIS A 355 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 8440)
  covalent geometry    : angle       0.60274 /  0.30 (11484)
  SS BOND              : bond        0.00286 /  0.14 (    5)
  SS BOND              : angle       0.83809 /  0.64 (   10)
  hydrogen bonds       : bond        0.03579 /  2.34 (  420)
  hydrogen bonds       : angle       4.74697 /  3.22 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 189
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -56 LYS cc_start: 0.8348 (tttt) cc_final: 0.8121 (ttpt)
REVERT: A  -50 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6132 (tmm)
REVERT: A  -49 ARG cc_start: 0.7768 (tpt-90) cc_final: 0.7306 (tpp80)
REVERT: A   73 SER cc_start: 0.8001 (m) cc_final: 0.7603 (t)
REVERT: A   99 GLN cc_start: 0.7658 (tt0) cc_final: 0.7004 (tt0)
REVERT: A  128 VAL cc_start: 0.8110 (m) cc_final: 0.7781 (p)
REVERT: A  366 TYR cc_start: 0.6534 (m-80) cc_final: 0.6043 (m-80)
REVERT: A  373 ARG cc_start: 0.6424 (mmm-85) cc_final: 0.6173 (ttm-80)
REVERT: A  386 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7024 (tt0)
REVERT: A  387 ILE cc_start: 0.7090 (mt) cc_final: 0.6863 (mt)
REVERT: H   20 SER cc_start: 0.8029 (m) cc_final: 0.7630 (p)
REVERT: H  110 TRP cc_start: 0.8225 (t60) cc_final: 0.7019 (t60)
REVERT: H  155 LEU cc_start: 0.7563 (tp) cc_final: 0.7358 (tt)
REVERT: L   32 SER cc_start: 0.8112 (t) cc_final: 0.7714 (p)
REVERT: L   92 TYR cc_start: 0.8301 (p90) cc_final: 0.7925 (p90)
REVERT: L  142 TYR cc_start: 0.7544 (t80) cc_final: 0.6990 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 199
  average time/residue: 0.0786
  time to fit residues: 21.6455
Evaluate side-chains
  215 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0870
   chunk 4 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 102 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 91 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 289 HIS
** H  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.159998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.141329 restraints weight = 13362.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.145099 restraints weight = 7326.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.147615 restraints weight = 4586.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.149316 restraints weight = 3192.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.150225 restraints weight = 2419.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.5120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8445  Z= 0.166
  Angle     :  0.624  10.411  11494  Z= 0.312
  Chirality :  0.041   0.131   1296
  Planarity :  0.004   0.047   1437
  Dihedral  :  4.644  21.884   1159
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.03 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.80 (0.26), residues: 1045
  helix:  0.85 (0.26), residues: 388
  sheet: -0.71 (0.33), residues: 244
  loop : -1.73 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  52 
 TYR   0.027   0.002   TYR H  53 
 PHE   0.020   0.001   PHE H 136 
 TRP   0.023   0.002   TRP H 168 
 HIS   0.004   0.001   HIS A 355 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.17 ( 8440)
  covalent geometry    : angle       0.62332 /  0.31 (11484)
  SS BOND              : bond        0.00260 /  0.14 (    5)
  SS BOND              : angle       0.90344 /  0.75 (   10)
  hydrogen bonds       : bond        0.03804 /  2.50 (  420)
  hydrogen bonds       : angle       4.94321 /  3.35 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -56 LYS cc_start: 0.8359 (tttt) cc_final: 0.8125 (ttpt)
REVERT: A  -50 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6167 (tmm)
REVERT: A  -49 ARG cc_start: 0.7862 (tpt-90) cc_final: 0.7622 (tpp80)
REVERT: A   73 SER cc_start: 0.8052 (m) cc_final: 0.7667 (t)
REVERT: A   99 GLN cc_start: 0.7652 (tt0) cc_final: 0.7086 (tt0)
REVERT: A  128 VAL cc_start: 0.8142 (m) cc_final: 0.7781 (p)
REVERT: A  300 ASN cc_start: 0.5980 (t0) cc_final: 0.5769 (t0)
REVERT: A  366 TYR cc_start: 0.6819 (m-80) cc_final: 0.6295 (m-80)
REVERT: A  386 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6938 (tt0)
REVERT: A  387 ILE cc_start: 0.7112 (mt) cc_final: 0.6868 (mt)
REVERT: H   20 SER cc_start: 0.8152 (m) cc_final: 0.7755 (p)
REVERT: H   63 TYR cc_start: 0.7762 (m-10) cc_final: 0.7536 (m-10)
REVERT: H  110 TRP cc_start: 0.8344 (t60) cc_final: 0.7086 (t60)
REVERT: H  206 GLN cc_start: 0.6944 (tt0) cc_final: 0.6701 (tt0)
REVERT: L   32 SER cc_start: 0.8174 (t) cc_final: 0.7788 (p)
REVERT: L   74 LEU cc_start: 0.8213 (tt) cc_final: 0.7981 (tp)
REVERT: L   92 TYR cc_start: 0.8353 (p90) cc_final: 0.7980 (p90)
REVERT: L  142 TYR cc_start: 0.7562 (t80) cc_final: 0.7085 (t80)
REVERT: L  166 THR cc_start: 0.8564 (t) cc_final: 0.8122 (m)
  outliers start: 25
  outliers final: 20
  residues processed: 214
  average time/residue: 0.0723
  time to fit residues: 21.4508
Evaluate side-chains
  220 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain H residue  200 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 68 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.158758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.140205 restraints weight = 13150.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.144011 restraints weight = 7191.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.146540 restraints weight = 4488.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.148084 restraints weight = 3134.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.149292 restraints weight = 2413.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.5625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   8445  Z= 0.225
  Angle     :  0.699  10.016  11494  Z= 0.351
  Chirality :  0.044   0.213   1296
  Planarity :  0.005   0.047   1437
  Dihedral  :  5.061  23.992   1159
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.04 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -1.04 (0.26), residues: 1045
  helix:  0.56 (0.26), residues: 387
  sheet: -0.82 (0.33), residues: 240
  loop : -1.74 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  52 
 TYR   0.033   0.002   TYR H  53 
 PHE   0.021   0.002   PHE H 136 
 TRP   0.022   0.002   TRP H 168 
 HIS   0.004   0.001   HIS A 355 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00484 /  0.22 ( 8440)
  covalent geometry    : angle       0.69865 /  0.35 (11484)
  SS BOND              : bond        0.00259 /  0.14 (    5)
  SS BOND              : angle       0.95645 /  0.82 (   10)
  hydrogen bonds       : bond        0.04200 /  2.77 (  420)
  hydrogen bonds       : angle       5.29249 /  3.59 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A  -56 LYS cc_start: 0.8306 (tttt) cc_final: 0.8083 (ttpt)
REVERT: A  -50 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6029 (tmm)
REVERT: A  -49 ARG cc_start: 0.7872 (tpt-90) cc_final: 0.7497 (ttm-80)
REVERT: A    3 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6843 (mm-30)
REVERT: A   46 SER cc_start: 0.8094 (m) cc_final: 0.7484 (t)
REVERT: A   73 SER cc_start: 0.8118 (m) cc_final: 0.7792 (t)
REVERT: A   99 GLN cc_start: 0.7679 (tt0) cc_final: 0.7152 (tt0)
REVERT: A  128 VAL cc_start: 0.8214 (m) cc_final: 0.7789 (p)
REVERT: A  294 GLU cc_start: 0.6976 (tt0) cc_final: 0.6714 (tt0)
REVERT: A  300 ASN cc_start: 0.5967 (t0) cc_final: 0.5759 (t0)
REVERT: A  386 GLN cc_start: 0.7305 (mm-40) cc_final: 0.6817 (tm-30)
REVERT: A  387 ILE cc_start: 0.7142 (mt) cc_final: 0.6919 (mt)
REVERT: H   63 TYR cc_start: 0.7805 (m-10) cc_final: 0.7565 (m-10)
REVERT: L   32 SER cc_start: 0.8259 (t) cc_final: 0.7830 (p)
REVERT: L   74 LEU cc_start: 0.8166 (tt) cc_final: 0.7944 (tp)
REVERT: L   92 TYR cc_start: 0.8393 (p90) cc_final: 0.8014 (p90)
REVERT: L   94 TYR cc_start: 0.7857 (t80) cc_final: 0.7641 (t80)
REVERT: L  142 TYR cc_start: 0.7579 (t80) cc_final: 0.7084 (t80)
REVERT: L  166 THR cc_start: 0.8587 (t) cc_final: 0.8169 (m)
  outliers start: 26
  outliers final: 22
  residues processed: 219
  average time/residue: 0.0696
  time to fit residues: 21.2072
Evaluate side-chains
  227 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 204
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain H residue  207 THR
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 101 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 60 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.159893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.141290 restraints weight = 13142.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.145115 restraints weight = 7172.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.147590 restraints weight = 4464.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.149271 restraints weight = 3111.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.150400 restraints weight = 2360.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.5727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   8445  Z= 0.202
  Angle     :  0.706  11.940  11494  Z= 0.347
  Chirality :  0.043   0.181   1296
  Planarity :  0.004   0.048   1437
  Dihedral  :  5.025  25.058   1159
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.26 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -1.06 (0.26), residues: 1045
  helix:  0.52 (0.26), residues: 386
  sheet: -0.87 (0.33), residues: 246
  loop : -1.71 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A -21 
 TYR   0.034   0.002   TYR H  53 
 PHE   0.024   0.002   PHE H 136 
 TRP   0.018   0.002   TRP H 168 
 HIS   0.004   0.001   HIS A 355 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.20 ( 8440)
  covalent geometry    : angle       0.70605 /  0.35 (11484)
  SS BOND              : bond        0.00261 /  0.15 (    5)
  SS BOND              : angle       0.95327 /  0.87 (   10)
  hydrogen bonds       : bond        0.04085 /  2.68 (  420)
  hydrogen bonds       : angle       5.19727 /  3.52 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A  -73 LEU cc_start: 0.7934 (tp) cc_final: 0.7656 (tp)
REVERT: A  -56 LYS cc_start: 0.8367 (tttt) cc_final: 0.8159 (ttpt)
REVERT: A  -50 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5858 (tmm)
REVERT: A  -49 ARG cc_start: 0.7833 (tpt-90) cc_final: 0.7350 (ttm170)
REVERT: A    3 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6756 (mm-30)
REVERT: A   73 SER cc_start: 0.7955 (m) cc_final: 0.7639 (t)
REVERT: A   99 GLN cc_start: 0.7643 (tt0) cc_final: 0.7110 (tt0)
REVERT: A  128 VAL cc_start: 0.8247 (m) cc_final: 0.7823 (p)
REVERT: A  264 ARG cc_start: 0.4078 (mtm110) cc_final: 0.3781 (mtm110)
REVERT: A  294 GLU cc_start: 0.6906 (tt0) cc_final: 0.6667 (tt0)
REVERT: A  300 ASN cc_start: 0.5988 (t0) cc_final: 0.5775 (t0)
REVERT: A  366 TYR cc_start: 0.7151 (m-80) cc_final: 0.6840 (m-80)
REVERT: A  386 GLN cc_start: 0.7297 (mm-40) cc_final: 0.6804 (tm-30)
REVERT: A  387 ILE cc_start: 0.7136 (mt) cc_final: 0.6899 (mt)
REVERT: H    7 LEU cc_start: 0.7499 (mm) cc_final: 0.6972 (mt)
REVERT: H   20 SER cc_start: 0.8209 (m) cc_final: 0.7824 (p)
REVERT: H   37 LEU cc_start: 0.7921 (mm) cc_final: 0.7602 (mt)
REVERT: L   32 SER cc_start: 0.8166 (t) cc_final: 0.7796 (p)
REVERT: L   92 TYR cc_start: 0.8387 (p90) cc_final: 0.8025 (p90)
REVERT: L   94 TYR cc_start: 0.7878 (t80) cc_final: 0.7632 (t80)
REVERT: L  142 TYR cc_start: 0.7559 (t80) cc_final: 0.7061 (t80)
REVERT: L  166 THR cc_start: 0.8565 (t) cc_final: 0.8153 (m)
  outliers start: 21
  outliers final: 18
  residues processed: 224
  average time/residue: 0.0776
  time to fit residues: 24.0623
Evaluate side-chains
  227 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 208
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain H residue  196 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0670
   chunk 12 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.3718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  42 GLN
** H  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  39 GLN
L 160 ASN
** L 201 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 = 0.4062 r_free = 0.4062 target = 0.161641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.142904 restraints weight = 13231.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.146711 restraints weight = 7229.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.149233 restraints weight = 4536.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.150871 restraints weight = 3159.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.152010 restraints weight = 2405.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.5689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8445  Z= 0.151
  Angle     :  0.670  10.075  11494  Z= 0.325
  Chirality :  0.042   0.172   1296
  Planarity :  0.004   0.046   1437
  Dihedral  :  4.882  30.183   1159
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.83 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.83 (0.26), residues: 1045
  helix:  0.70 (0.26), residues: 387
  sheet: -0.82 (0.33), residues: 252
  loop : -1.53 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A -21 
 TYR   0.031   0.002   TYR A 149 
 PHE   0.022   0.001   PHE H 136 
 TRP   0.026   0.001   TRP H 168 
 HIS   0.004   0.001   HIS A 355 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 8440)
  covalent geometry    : angle       0.66953 /  0.33 (11484)
  SS BOND              : bond        0.00120 /  0.06 (    5)
  SS BOND              : angle       1.03941 /  0.80 (   10)
  hydrogen bonds       : bond        0.03847 /  2.51 (  420)
  hydrogen bonds       : angle       4.98630 /  3.37 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1336.67 seconds
wall clock time: 23 minutes 47.66 seconds (1427.66 seconds total)