Starting phenix.real_space_refine
on Sun Apr  5 10:51:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9llj_63204/04_2026/9llj_63204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9llj_63204/04_2026/9llj_63204.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9llj_63204/04_2026/9llj_63204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9llj_63204/04_2026/9llj_63204.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9llj_63204/04_2026/9llj_63204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9llj_63204/04_2026/9llj_63204.map"
  }
  resolution = 2.61
  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=   0.004 sd=   0.110
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    6373      2.51       5
     N    1653      2.21       5
     O    1738      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9819
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "R"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2154
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 9, 'TRANS': 261}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2591
          Classifications: {'peptide': 340}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 960
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 1843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1843
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "O"
      Number of atoms: 590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 590
          Classifications: {'peptide': 69}
          Link IDs: {'TRANS': 68}
    Chain: "P"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 550
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
    Chain: "Q"
      Number of atoms: 640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 640
          Classifications: {'peptide': 75}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 68}
    Chain: "R"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 47
          Unusual residues: {'LDP': 1, 'PLM': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.21, per 1000 atoms: 0.23
  Number of scatterers: 9819
  At special positions: 0
  Unit cell: (79.98, 100.44, 132.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1738      8.00
     N    1653      7.00
     C    6373      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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: 0.80
  Conformation dependent library (CDL) restraints added in 352.5 milliseconds
  

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2340

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 10 sheets defined
      53.0% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 51 through 56
    Processing helix  chain 'R' and resid 58 through 77
      removed outlier: 4.031A  pdb=" N   PHE R  62 " --> pdb=" O   VAL R  58 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL R  77 " --> pdb=" O   VAL R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 88
      removed outlier: 3.624A  pdb=" N   LYS R  81 " --> pdb=" O   VAL R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 94
      No H-bonds generated for 'chain 'R' and resid 92 through 94'
    Processing helix  chain 'R' and resid 95 through 127
      removed outlier: 3.527A  pdb=" N   SER R 127 " --> pdb=" O   TRP R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 135
    Processing helix  chain 'R' and resid 136 through 154
    Processing helix  chain 'R' and resid 155 through 160
      removed outlier: 3.518A  pdb=" N   VAL R 159 " --> pdb=" O   SER R 155 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 203
    Processing helix  chain 'R' and resid 203 through 234
    Processing helix  chain 'R' and resid 262 through 295
      removed outlier: 3.740A  pdb=" N   PHE R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
    Processing helix  chain 'R' and resid 296 through 298
      No H-bonds generated for 'chain 'R' and resid 296 through 298'
    Processing helix  chain 'R' and resid 309 through 322
    Processing helix  chain 'R' and resid 322 through 332
      removed outlier: 3.596A  pdb=" N   LEU R 326 " --> pdb=" O   ALA R 322 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 346
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 6 through 24
      removed outlier: 3.595A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.862A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.675A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.558A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.774A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
    Processing helix  chain 'O' and resid 2 through 31
      removed outlier: 3.664A  pdb=" N   ILE O  29 " --> pdb=" O   MET O  25 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG O  30 " --> pdb=" O   ARG O  26 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 33 through 69
    Processing helix  chain 'P' and resid 7 through 36
    Processing helix  chain 'P' and resid 42 through 71
    Processing helix  chain 'Q' and resid 9 through 39
    Processing helix  chain 'Q' and resid 46 through 76
      removed outlier: 3.730A  pdb=" N   PHE Q  76 " --> pdb=" O   ILE Q  72 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.685A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.154A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.721A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.570A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.596A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.602A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 8
    Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.199A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 6.421A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)

    602 hydrogen bonds defined for protein.
    1713 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: 1.44

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1531
        1.28 -     1.42: 2657
        1.42 -     1.55: 5760
        1.55 -     1.69: 3
        1.69 -     1.82: 75
  Bond restraints: 10026
  Sorted by residual:
  bond pdb=" C   MET B  61 "
       pdb=" O   MET B  61 "
    ideal  model  delta    sigma   weight residual
    1.234  1.148  0.086 1.22e-02 6.72e+03 4.92e+01
  bond pdb=" C   LEU R 231 "
       pdb=" O   LEU R 231 "
    ideal  model  delta    sigma   weight residual
    1.236  1.170  0.067 1.29e-02 6.01e+03 2.66e+01
  bond pdb=" CA  ALA R 230 "
       pdb=" C   ALA R 230 "
    ideal  model  delta    sigma   weight residual
    1.524  1.464  0.060 1.32e-02 5.74e+03 2.08e+01
  bond pdb=" C   ALA B  60 "
       pdb=" N   MET B  61 "
    ideal  model  delta    sigma   weight residual
    1.331  1.278  0.053 1.29e-02 6.01e+03 1.72e+01
  bond pdb=" C   ALA R 230 "
       pdb=" O   ALA R 230 "
    ideal  model  delta    sigma   weight residual
    1.236  1.189  0.047 1.15e-02 7.56e+03 1.66e+01
  ... (remaining 10021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 13412
        2.09 -     4.19: 141
        4.19 -     6.28: 23
        6.28 -     8.38: 2
        8.38 -    10.47: 2
  Bond angle restraints: 13580
  Sorted by residual:
  angle pdb=" C   LEU R 231 "
        pdb=" N   GLU R 232 "
        pdb=" CA  GLU R 232 "
      ideal   model   delta    sigma   weight residual
     120.28  109.81   10.47 1.34e+00 5.57e-01 6.10e+01
  angle pdb=" N   ALA R 230 "
        pdb=" CA  ALA R 230 "
        pdb=" C   ALA R 230 "
      ideal   model   delta    sigma   weight residual
     111.11  117.20   -6.09 1.20e+00 6.94e-01 2.58e+01
  angle pdb=" O   MET B  61 "
        pdb=" C   MET B  61 "
        pdb=" N   HIS B  62 "
      ideal   model   delta    sigma   weight residual
     123.41  117.60    5.81 1.17e+00 7.31e-01 2.47e+01
  angle pdb=" O   ALA R 229 "
        pdb=" C   ALA R 229 "
        pdb=" N   ALA R 230 "
      ideal   model   delta    sigma   weight residual
     122.15  116.70    5.45 1.14e+00 7.69e-01 2.28e+01
  angle pdb=" CA  MET B  61 "
        pdb=" C   MET B  61 "
        pdb=" N   HIS B  62 "
      ideal   model   delta    sigma   weight residual
     115.98  122.58   -6.60 1.45e+00 4.76e-01 2.07e+01
  ... (remaining 13575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 5412
       17.62 -    35.23: 389
       35.23 -    52.85: 123
       52.85 -    70.46: 25
       70.46 -    88.08: 11
  Dihedral angle restraints: 5960
    sinusoidal: 2365
      harmonic: 3595
  Sorted by residual:
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  PHE R 203 "
           pdb=" C   PHE R 203 "
           pdb=" N   TYR R 204 "
           pdb=" CA  TYR R 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.23  -19.77     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -116.25   30.25     1      1.00e+01 1.00e-02 1.31e+01
  ... (remaining 5957 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1214
       0.045 -    0.090: 290
       0.090 -    0.135: 63
       0.135 -    0.180: 4
       0.180 -    0.225: 3
  Chirality restraints: 1574
  Sorted by residual:
  chirality pdb=" CA  MET B  61 "
            pdb=" N   MET B  61 "
            pdb=" C   MET B  61 "
            pdb=" CB  MET B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  LEU R 231 "
            pdb=" N   LEU R 231 "
            pdb=" C   LEU R 231 "
            pdb=" CB  LEU R 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  ILE R 144 "
            pdb=" CA  ILE R 144 "
            pdb=" CG1 ILE R 144 "
            pdb=" CG2 ILE R 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1571 not shown)

  Planarity restraints: 1679
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  60 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.97e+00
        pdb=" C   ALA B  60 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ALA B  60 "    0.015 2.00e-02 2.50e+03
        pdb=" N   MET B  61 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  52 "   -0.039 5.00e-02 4.00e+02   6.00e-02 5.76e+00
        pdb=" N   PRO C  53 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO C  53 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  53 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B  61 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.56e+00
        pdb=" C   MET B  61 "    0.028 2.00e-02 2.50e+03
        pdb=" O   MET B  61 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   HIS B  62 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1676 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 683
        2.74 -     3.28: 9758
        3.28 -     3.82: 17195
        3.82 -     4.36: 20174
        4.36 -     4.90: 35000
  Nonbonded interactions: 82810
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   ARG A 283 "
            pdb=" ND1 HIS A 357 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   ALA R 101 "
            pdb=" OG  SER R 155 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OE1 GLN B  75 "
            pdb=" O   VAL B 100 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.249 3.040
  ... (remaining 82805 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.780
  Find NCS groups from input model:        0.030
  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:6.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  10029  Z= 0.199
  Angle     :  0.570  10.469  13586  Z= 0.340
  Chirality :  0.041   0.225   1574
  Planarity :  0.004   0.060   1679
  Dihedral  : 14.642  88.078   3611
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.75 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.51 (0.24), residues: 1204
  helix:  2.90 (0.20), residues: 574
  sheet:  0.75 (0.32), residues: 234
  loop :  0.44 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  20 
 TYR   0.009   0.001   TYR R 194 
 PHE   0.019   0.001   PHE R 288 
 TRP   0.022   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10026)
  covalent geometry    : angle       0.57015 (13580)
  SS BOND              : bond        0.00290 (    3)
  SS BOND              : angle       0.99937 (    6)
  hydrogen bonds       : bond        0.13441 (  602)
  hydrogen bonds       : angle       5.39393 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   31 SER cc_start: 0.8675 (m) cc_final: 0.8457 (p)
REVERT: R   57 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8150 (mtmm)
REVERT: R  265 LYS cc_start: 0.7222 (mtmm) cc_final: 0.6961 (mtpp)
REVERT: R  272 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8430 (tttm)
REVERT: B   42 ARG cc_start: 0.7156 (tpm170) cc_final: 0.6860 (tmt170)
REVERT: B  197 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7351 (tpt90)
REVERT: A   28 LYS cc_start: 0.7649 (tttt) cc_final: 0.7068 (mmtm)
REVERT: A   32 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7963 (mttt)
REVERT: A  250 SER cc_start: 0.8475 (p) cc_final: 0.8246 (p)
REVERT: O   38 ARG cc_start: 0.7121 (mtp85) cc_final: 0.6751 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.7053
  time to fit residues: 122.7984
Evaluate side-chains
  143 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.0770
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 117 optimal weight:    3.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.162001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.126596 restraints weight = 9925.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.74
r_work: 0.3194 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.0825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10029  Z= 0.120
  Angle     :  0.489   6.421  13586  Z= 0.266
  Chirality :  0.040   0.149   1574
  Planarity :  0.004   0.050   1679
  Dihedral  :  5.276  48.199   1361
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.19 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.84 (0.24), residues: 1204
  helix:  3.37 (0.20), residues: 577
  sheet:  0.69 (0.32), residues: 229
  loop :  0.38 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  20 
 TYR   0.011   0.001   TYR R 194 
 PHE   0.022   0.002   PHE R 288 
 TRP   0.019   0.002   TRP B 339 
 HIS   0.010   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10026)
  covalent geometry    : angle       0.48797 (13580)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       1.35082 (    6)
  hydrogen bonds       : bond        0.04697 (  602)
  hydrogen bonds       : angle       4.11574 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  265 LYS cc_start: 0.7501 (mtmm) cc_final: 0.7271 (mtpp)
REVERT: R  272 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8463 (tttm)
REVERT: B   42 ARG cc_start: 0.7415 (tpm170) cc_final: 0.6969 (tmt170)
REVERT: B  197 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7742 (tpt90)
REVERT: B  314 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8471 (ttm-80)
REVERT: N   46 GLU cc_start: 0.8236 (tt0) cc_final: 0.7945 (mt-10)
REVERT: A   28 LYS cc_start: 0.8231 (tttt) cc_final: 0.7741 (mmtm)
REVERT: A   32 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8374 (mttt)
REVERT: A  229 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7132 (p0)
REVERT: O   39 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7119 (tmt170)
  outliers start: 23
  outliers final: 8
  residues processed: 156
  average time/residue: 0.6837
  time to fit residues: 113.1329
Evaluate side-chains
  144 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   24 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain P residue   17 LEU
Chi-restraints excluded: chain P residue   25 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 110 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
R 224 GLN
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.161212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.122737 restraints weight = 9766.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.00
r_work: 0.3148 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10029  Z= 0.132
  Angle     :  0.491   6.679  13586  Z= 0.267
  Chirality :  0.040   0.151   1574
  Planarity :  0.004   0.045   1679
  Dihedral  :  5.256  47.269   1361
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.91 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.85 (0.24), residues: 1204
  helix:  3.38 (0.19), residues: 581
  sheet:  0.69 (0.31), residues: 232
  loop :  0.34 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.011   0.002   TYR R 194 
 PHE   0.026   0.002   PHE R 288 
 TRP   0.017   0.002   TRP P  58 
 HIS   0.011   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10026)
  covalent geometry    : angle       0.48987 (13580)
  SS BOND              : bond        0.00202 (    3)
  SS BOND              : angle       1.94445 (    6)
  hydrogen bonds       : bond        0.04625 (  602)
  hydrogen bonds       : angle       4.04236 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   57 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7784 (mmmt)
REVERT: R  265 LYS cc_start: 0.7487 (mtmm) cc_final: 0.7245 (mtpp)
REVERT: R  272 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8497 (tttm)
REVERT: B   44 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7739 (mt0)
REVERT: B   75 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8584 (tp40)
REVERT: B  197 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7718 (tpt90)
REVERT: B  314 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8513 (tmm-80)
REVERT: N   46 GLU cc_start: 0.8214 (tt0) cc_final: 0.7917 (mt-10)
REVERT: A   28 LYS cc_start: 0.8228 (tttt) cc_final: 0.7691 (mmtm)
REVERT: A   32 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8343 (mttt)
REVERT: A  229 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7219 (p0)
REVERT: O   30 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7602 (ptm160)
REVERT: O   39 ARG cc_start: 0.7850 (mtp180) cc_final: 0.7055 (tmt170)
  outliers start: 27
  outliers final: 10
  residues processed: 159
  average time/residue: 0.6586
  time to fit residues: 110.9200
Evaluate side-chains
  149 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   26 ARG
Chi-restraints excluded: chain O residue   30 ARG
Chi-restraints excluded: chain P residue   17 LEU
Chi-restraints excluded: chain P residue   25 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 110 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 105 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0670
   chunk 68 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
R 224 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.162201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.123788 restraints weight = 9898.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.02
r_work: 0.3166 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10029  Z= 0.118
  Angle     :  0.477   8.229  13586  Z= 0.260
  Chirality :  0.040   0.165   1574
  Planarity :  0.004   0.043   1679
  Dihedral  :  5.218  46.944   1361
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.03 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.93 (0.24), residues: 1204
  helix:  3.48 (0.19), residues: 579
  sheet:  0.69 (0.31), residues: 232
  loop :  0.35 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.011   0.001   TYR R 194 
 PHE   0.022   0.002   PHE R 288 
 TRP   0.016   0.002   TRP P  58 
 HIS   0.008   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10026)
  covalent geometry    : angle       0.47645 (13580)
  SS BOND              : bond        0.00316 (    3)
  SS BOND              : angle       1.23585 (    6)
  hydrogen bonds       : bond        0.04362 (  602)
  hydrogen bonds       : angle       3.97424 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  265 LYS cc_start: 0.7490 (mtmm) cc_final: 0.7249 (mtpp)
REVERT: R  272 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8439 (tttm)
REVERT: B   44 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7730 (mt0)
REVERT: B  197 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7679 (tpt90)
REVERT: B  314 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8467 (tmm-80)
REVERT: N   46 GLU cc_start: 0.8159 (tt0) cc_final: 0.7883 (mt-10)
REVERT: A   28 LYS cc_start: 0.8216 (tttt) cc_final: 0.7644 (mmtm)
REVERT: A   32 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8324 (mttt)
REVERT: A  229 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7238 (p0)
REVERT: O   39 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7059 (tmt170)
REVERT: P   13 LEU cc_start: 0.8532 (mt) cc_final: 0.8259 (mt)
  outliers start: 16
  outliers final: 8
  residues processed: 153
  average time/residue: 0.6952
  time to fit residues: 112.5022
Evaluate side-chains
  151 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain P residue   25 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
B 259 GLN
A 239 ASN
A 384 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.156946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.120267 restraints weight = 9868.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.75
r_work: 0.3120 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.084  10029  Z= 0.292
  Angle     :  0.655   7.643  13586  Z= 0.355
  Chirality :  0.047   0.160   1574
  Planarity :  0.005   0.044   1679
  Dihedral  :  6.035  51.664   1361
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 12.07 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.31 (0.24), residues: 1204
  helix:  2.89 (0.19), residues: 575
  sheet:  0.60 (0.31), residues: 226
  loop :  0.10 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  20 
 TYR   0.014   0.002   TYR R 194 
 PHE   0.039   0.003   PHE R 288 
 TRP   0.020   0.003   TRP A 234 
 HIS   0.016   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00701 (10026)
  covalent geometry    : angle       0.65305 (13580)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       2.26901 (    6)
  hydrogen bonds       : bond        0.05965 (  602)
  hydrogen bonds       : angle       4.44629 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  265 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7389 (mtpp)
REVERT: B   44 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7891 (mt0)
REVERT: N   46 GLU cc_start: 0.8210 (tt0) cc_final: 0.7964 (mt-10)
REVERT: A   28 LYS cc_start: 0.8312 (tttt) cc_final: 0.7753 (mmtm)
REVERT: A   32 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8407 (mttt)
REVERT: A  229 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7373 (p0)
REVERT: A  314 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7924 (mp0)
REVERT: A  392 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7900 (mt-10)
REVERT: O   30 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7846 (ptm160)
REVERT: O   39 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7249 (tmt170)
REVERT: P   13 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8413 (mt)
  outliers start: 36
  outliers final: 11
  residues processed: 162
  average time/residue: 0.6824
  time to fit residues: 117.3842
Evaluate side-chains
  153 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   13 SER
Chi-restraints excluded: chain O residue   26 ARG
Chi-restraints excluded: chain O residue   30 ARG
Chi-restraints excluded: chain P residue   13 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
R 224 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.158636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.119548 restraints weight = 9882.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.01
r_work: 0.3114 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10029  Z= 0.159
  Angle     :  0.532   6.949  13586  Z= 0.291
  Chirality :  0.042   0.151   1574
  Planarity :  0.004   0.044   1679
  Dihedral  :  5.754  57.274   1361
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.38 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.51 (0.24), residues: 1204
  helix:  3.07 (0.20), residues: 581
  sheet:  0.69 (0.32), residues: 222
  loop :  0.13 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A  20 
 TYR   0.013   0.002   TYR R 194 
 PHE   0.028   0.002   PHE R 288 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.010   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10026)
  covalent geometry    : angle       0.53040 (13580)
  SS BOND              : bond        0.00094 (    3)
  SS BOND              : angle       2.03913 (    6)
  hydrogen bonds       : bond        0.04912 (  602)
  hydrogen bonds       : angle       4.21017 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  265 LYS cc_start: 0.7553 (mtmm) cc_final: 0.7304 (mtpp)
REVERT: R  272 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8520 (tttm)
REVERT: B   44 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7790 (mt0)
REVERT: B   45 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.6732 (mpp)
REVERT: B   75 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8606 (tp40)
REVERT: B  197 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7692 (tpt90)
REVERT: B  314 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8580 (tmm-80)
REVERT: N    5 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7293 (tm-30)
REVERT: N   46 GLU cc_start: 0.8225 (tt0) cc_final: 0.7871 (mt-10)
REVERT: A   28 LYS cc_start: 0.8271 (tttt) cc_final: 0.7714 (mmtm)
REVERT: A   32 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8370 (mttt)
REVERT: A  229 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7434 (p0)
REVERT: A  314 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7947 (mp0)
REVERT: A  392 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7907 (mt-10)
REVERT: O   30 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7686 (ptm160)
REVERT: O   39 ARG cc_start: 0.7983 (mtp180) cc_final: 0.7149 (tmt170)
REVERT: P   13 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8283 (mt)
  outliers start: 25
  outliers final: 13
  residues processed: 153
  average time/residue: 0.7079
  time to fit residues: 114.9251
Evaluate side-chains
  159 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain R residue  120 ASP
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   26 ARG
Chi-restraints excluded: chain O residue   30 ARG
Chi-restraints excluded: chain P residue   13 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 78 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.158968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.122185 restraints weight = 9763.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.70
r_work: 0.3143 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10029  Z= 0.150
  Angle     :  0.519   7.009  13586  Z= 0.283
  Chirality :  0.041   0.150   1574
  Planarity :  0.004   0.042   1679
  Dihedral  :  5.658  58.625   1361
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.19 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.58 (0.24), residues: 1204
  helix:  3.18 (0.20), residues: 580
  sheet:  0.67 (0.33), residues: 212
  loop :  0.14 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.012   0.002   TYR R 194 
 PHE   0.028   0.002   PHE R 288 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.009   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10026)
  covalent geometry    : angle       0.51747 (13580)
  SS BOND              : bond        0.00065 (    3)
  SS BOND              : angle       1.81424 (    6)
  hydrogen bonds       : bond        0.04764 (  602)
  hydrogen bonds       : angle       4.14624 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  265 LYS cc_start: 0.7557 (mtmm) cc_final: 0.7311 (mtpp)
REVERT: R  272 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8507 (tttm)
REVERT: B   44 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7771 (mt0)
REVERT: B   45 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.6640 (mpp)
REVERT: B  197 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7661 (tpt90)
REVERT: B  314 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8558 (tmm-80)
REVERT: N   46 GLU cc_start: 0.8193 (tt0) cc_final: 0.7903 (mt-10)
REVERT: A   28 LYS cc_start: 0.8300 (tttt) cc_final: 0.7825 (mmtm)
REVERT: A   32 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8374 (mttt)
REVERT: A  314 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8000 (mp0)
REVERT: A  392 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7912 (mt-10)
REVERT: O   30 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7734 (ptm160)
REVERT: O   39 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7225 (tmt170)
REVERT: P   13 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8323 (mt)
  outliers start: 31
  outliers final: 16
  residues processed: 159
  average time/residue: 0.6970
  time to fit residues: 117.6397
Evaluate side-chains
  162 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain R residue  120 ASP
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   30 ARG
Chi-restraints excluded: chain P residue   13 LEU
Chi-restraints excluded: chain P residue   17 LEU
Chi-restraints excluded: chain P residue   25 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    0.1980
   chunk 100 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0770
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 113 ASN
R 222 GLN
R 224 GLN
B 259 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.160509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.124234 restraints weight = 9883.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.70
r_work: 0.3192 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10029  Z= 0.114
  Angle     :  0.479   6.778  13586  Z= 0.261
  Chirality :  0.040   0.148   1574
  Planarity :  0.004   0.041   1679
  Dihedral  :  5.430  53.794   1361
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.75 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.77 (0.24), residues: 1204
  helix:  3.37 (0.19), residues: 580
  sheet:  0.71 (0.33), residues: 210
  loop :  0.21 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  20 
 TYR   0.011   0.001   TYR R 194 
 PHE   0.020   0.001   PHE R 288 
 TRP   0.018   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (10026)
  covalent geometry    : angle       0.47783 (13580)
  SS BOND              : bond        0.00040 (    3)
  SS BOND              : angle       1.43072 (    6)
  hydrogen bonds       : bond        0.04304 (  602)
  hydrogen bonds       : angle       4.02023 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  272 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8422 (tttm)
REVERT: B   44 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7664 (mt0)
REVERT: B   45 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.6337 (mpp)
REVERT: B  197 ARG cc_start: 0.7952 (mmm160) cc_final: 0.7659 (tpt90)
REVERT: N   46 GLU cc_start: 0.8174 (tt0) cc_final: 0.7899 (mt-10)
REVERT: A   28 LYS cc_start: 0.8199 (tttt) cc_final: 0.7733 (mmtm)
REVERT: A   32 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8317 (mttt)
REVERT: A  314 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7986 (mp0)
REVERT: O   30 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6460 (ptm160)
REVERT: O   39 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7188 (tmt170)
  outliers start: 23
  outliers final: 12
  residues processed: 156
  average time/residue: 0.6851
  time to fit residues: 113.5149
Evaluate side-chains
  152 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain R residue  120 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   30 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0570
   chunk 31 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   overall best weight:    0.7898

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
B 259 GLN
N  31 ASN
A 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.160404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.124857 restraints weight = 9873.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.60
r_work: 0.3187 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10029  Z= 0.126
  Angle     :  0.493   7.031  13586  Z= 0.268
  Chirality :  0.041   0.149   1574
  Planarity :  0.004   0.041   1679
  Dihedral  :  5.368  50.063   1361
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.56 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.75 (0.24), residues: 1204
  helix:  3.36 (0.19), residues: 580
  sheet:  0.64 (0.33), residues: 211
  loop :  0.22 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  20 
 TYR   0.011   0.001   TYR R 194 
 PHE   0.024   0.002   PHE R 288 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10026)
  covalent geometry    : angle       0.49236 (13580)
  SS BOND              : bond        0.00028 (    3)
  SS BOND              : angle       1.54235 (    6)
  hydrogen bonds       : bond        0.04409 (  602)
  hydrogen bonds       : angle       4.03035 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  265 LYS cc_start: 0.7535 (mtmm) cc_final: 0.7277 (mtpp)
REVERT: B   44 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7678 (mt0)
REVERT: B   45 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.6368 (mpp)
REVERT: B  197 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7655 (tpt90)
REVERT: B  314 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8680 (tmm-80)
REVERT: N   46 GLU cc_start: 0.8153 (tt0) cc_final: 0.7878 (mt-10)
REVERT: A   28 LYS cc_start: 0.8223 (tttt) cc_final: 0.7750 (mmtm)
REVERT: A   32 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8325 (mttt)
REVERT: A  314 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7948 (mp0)
REVERT: A  392 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7909 (mt-10)
REVERT: O   30 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7683 (ptm160)
REVERT: O   39 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7195 (tmt170)
  outliers start: 25
  outliers final: 12
  residues processed: 158
  average time/residue: 0.6920
  time to fit residues: 116.0678
Evaluate side-chains
  158 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain R residue  120 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   30 ARG
Chi-restraints excluded: chain P residue   17 LEU
Chi-restraints excluded: chain P residue   25 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 111 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.161150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.124396 restraints weight = 9780.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.75
r_work: 0.3165 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10029  Z= 0.125
  Angle     :  0.506   9.845  13586  Z= 0.271
  Chirality :  0.040   0.149   1574
  Planarity :  0.004   0.057   1679
  Dihedral  :  5.319  46.582   1361
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.03 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.74 (0.24), residues: 1204
  helix:  3.33 (0.19), residues: 581
  sheet:  0.63 (0.33), residues: 208
  loop :  0.24 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A  20 
 TYR   0.011   0.001   TYR R 194 
 PHE   0.023   0.002   PHE R 288 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10026)
  covalent geometry    : angle       0.50553 (13580)
  SS BOND              : bond        0.00049 (    3)
  SS BOND              : angle       1.46781 (    6)
  hydrogen bonds       : bond        0.04377 (  602)
  hydrogen bonds       : angle       4.01877 ( 1713)

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

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

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2408 Ramachandran restraints generated.
    1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  272 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8470 (tttm)
REVERT: B   44 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7654 (mt0)
REVERT: B   45 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.6319 (mpp)
REVERT: B  197 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7677 (tpt90)
REVERT: B  314 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8631 (tmm-80)
REVERT: N   46 GLU cc_start: 0.8163 (tt0) cc_final: 0.7912 (mt-10)
REVERT: A   28 LYS cc_start: 0.8243 (tttt) cc_final: 0.7764 (mmtm)
REVERT: A   32 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8347 (mttt)
REVERT: A  314 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7983 (mp0)
REVERT: A  392 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7956 (mp0)
REVERT: O   30 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7599 (ptm160)
REVERT: O   39 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7199 (tmt170)
  outliers start: 22
  outliers final: 14
  residues processed: 155
  average time/residue: 0.7148
  time to fit residues: 117.4001
Evaluate side-chains
  159 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain R residue  120 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   30 ARG
Chi-restraints excluded: chain O residue   41 LEU
Chi-restraints excluded: chain P residue   17 LEU
Chi-restraints excluded: chain P residue   25 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0980
   chunk 40 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0370
   chunk 97 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
R 222 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.162064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.124730 restraints weight = 9944.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.89
r_work: 0.3198 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10029  Z= 0.105
  Angle     :  0.477   7.513  13586  Z= 0.256
  Chirality :  0.040   0.148   1574
  Planarity :  0.004   0.058   1679
  Dihedral  :  5.089  44.429   1361
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.50 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.90 (0.24), residues: 1204
  helix:  3.49 (0.19), residues: 577
  sheet:  0.70 (0.33), residues: 205
  loop :  0.32 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A  20 
 TYR   0.010   0.001   TYR R 204 
 PHE   0.017   0.001   PHE R 288 
 TRP   0.018   0.002   TRP B 339 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (10026)
  covalent geometry    : angle       0.47644 (13580)
  SS BOND              : bond        0.00062 (    3)
  SS BOND              : angle       1.24853 (    6)
  hydrogen bonds       : bond        0.04008 (  602)
  hydrogen bonds       : angle       3.91293 ( 1713)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3997.88 seconds
wall clock time: 68 minutes 44.24 seconds (4124.24 seconds total)