Starting phenix.real_space_refine
on Tue Mar  3 19:18:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tko_10515/03_2026/6tko_10515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tko_10515/03_2026/6tko_10515.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tko_10515/03_2026/6tko_10515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tko_10515/03_2026/6tko_10515.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tko_10515/03_2026/6tko_10515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tko_10515/03_2026/6tko_10515.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      36      5.16       5
     C    5177      2.51       5
     N    1358      2.21       5
     O    1508      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8085
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2241
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 10, 'TRANS': 282}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 38
    Chain: "B"
      Number of atoms: 2684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2684
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 318}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "H"
      Number of atoms: 1529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1529
          Classifications: {'peptide': 204}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 191}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "L"
      Number of atoms: 1606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1606
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'H98': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.92, per 1000 atoms: 0.24
  Number of scatterers: 8085
  At special positions: 0
  Unit cell: (126.5, 106.7, 104.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P       6     15.00
     O    1508      8.00
     N    1358      7.00
     C    5177      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  44 " - pdb=" SG  CYS A 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 114 " - pdb=" SG  CYS A 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " 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: 0.78
  Conformation dependent library (CDL) restraints added in 296.1 milliseconds
  

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1996

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 16 sheets defined
      27.9% alpha, 32.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 69
      removed outlier: 3.957A  pdb=" N   VAL A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 105
      removed outlier: 3.535A  pdb=" N   LEU A  78 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   PHE A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A  80 " --> pdb=" O   THR A  76 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   VAL A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 110 through 144
      removed outlier: 3.938A  pdb=" N   GLU A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 153
      removed outlier: 4.221A  pdb=" N   SER A 151 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 180
      removed outlier: 4.237A  pdb=" N   LEU A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 186 through 195
    Processing helix  chain 'A' and resid 204 through 216
    Processing helix  chain 'A' and resid 216 through 242
    Processing helix  chain 'A' and resid 281 through 316
      removed outlier: 3.708A  pdb=" N   PHE A 299 " --> pdb=" O   ILE A 295 " (cutoff:3.500A)
      Proline residue:  A 305  - end of helix
      removed outlier: 3.696A  pdb=" N   VAL A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 315 " --> pdb=" O   ILE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 344
      removed outlier: 3.904A  pdb=" N   ASN A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER A 336 " --> pdb=" O   GLY A 332 " (cutoff:3.500A)
      Proline residue:  A 340  - end of helix
    Processing helix  chain 'A' and resid 346 through 358
    Processing helix  chain 'B' and resid 98 through 109
    Processing helix  chain 'B' and resid 280 through 284
      removed outlier: 4.087A  pdb=" N   GLU B 283 " --> pdb=" O   ASN B 280 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.542A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 122 through 129
    Processing helix  chain 'L' and resid 184 through 190
      removed outlier: 3.685A  pdb=" N   GLU L 188 " --> pdb=" O   LYS L 184 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   HIS L 190 " --> pdb=" O   ASP L 186 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1361 through 1364
      removed outlier: 3.670A  pdb=" N   ALA A1361 " --> pdb=" O   LYS B  10 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.967A  pdb=" N   LEU B 166 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B 146 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.718A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   VAL B  53 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   GLN B  85 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   VAL B  55 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   ASN B  83 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   CYS B  59 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.967A  pdb=" N   LEU B 166 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B 146 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.718A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   CYS B 140 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 187
      removed outlier: 3.635A  pdb=" N   ALA B 201 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR B 186 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 187
      removed outlier: 3.635A  pdb=" N   ALA B 201 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR B 186 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 207 through 208
      removed outlier: 3.870A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 8.700A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LYS B 230 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ALA B 254 " --> pdb=" O   VAL B 235 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   GLN B 237 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ALA B 239 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   LYS B 250 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ILE B 241 " --> pdb=" O   GLN B 248 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   GLN B 248 " --> pdb=" O   ILE B 241 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.811A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 8.858A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA H  95 " --> pdb=" O   VAL H 119 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   TYR H  97 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.605A  pdb=" N   ASP H 154 " --> pdb=" O   TYR H 186 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL H 191 " --> pdb=" O   HIS H 174 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.605A  pdb=" N   ASP H 154 " --> pdb=" O   TYR H 186 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 161 through 164
    Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 14
      removed outlier: 3.602A  pdb=" N   GLU L 106 " --> pdb=" O   LEU L  12 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA L  14 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.730A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 115 through 119
      removed outlier: 3.512A  pdb=" N   ASN L 139 " --> pdb=" O   TYR L 174 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   SER L 175 " --> pdb=" O   THR L 165 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156
      removed outlier: 4.589A  pdb=" N   TRP L 149 " --> pdb=" O   GLN L 156 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.13

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2531
        1.34 -     1.46: 1273
        1.46 -     1.57: 4417
        1.57 -     1.69: 6
        1.69 -     1.81: 44
  Bond restraints: 8271
  Sorted by residual:
  bond pdb=" OG1 TPO A1360 "
       pdb=" P   TPO A1360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" OG1 TPO A1359 "
       pdb=" P   TPO A1359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" O2P SEP A1363 "
       pdb=" P   SEP A1363 "
    ideal  model  delta    sigma   weight residual
    1.610  1.509  0.101 2.00e-02 2.50e+03 2.55e+01
  bond pdb=" O3P SEP A1363 "
       pdb=" P   SEP A1363 "
    ideal  model  delta    sigma   weight residual
    1.610  1.509  0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" O3P SEP A1362 "
       pdb=" P   SEP A1362 "
    ideal  model  delta    sigma   weight residual
    1.610  1.509  0.101 2.00e-02 2.50e+03 2.53e+01
  ... (remaining 8266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 11191
        2.34 -     4.69: 71
        4.69 -     7.03: 10
        7.03 -     9.37: 3
        9.37 -    11.71: 4
  Bond angle restraints: 11279
  Sorted by residual:
  angle pdb=" CB  SEP A1364 "
        pdb=" OG  SEP A1364 "
        pdb=" P   SEP A1364 "
      ideal   model   delta    sigma   weight residual
     110.00  121.71  -11.71 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" CB  SEP A1363 "
        pdb=" OG  SEP A1363 "
        pdb=" P   SEP A1363 "
      ideal   model   delta    sigma   weight residual
     110.00  120.85  -10.85 3.00e+00 1.11e-01 1.31e+01
  angle pdb=" CB  SEP A1357 "
        pdb=" OG  SEP A1357 "
        pdb=" P   SEP A1357 "
      ideal   model   delta    sigma   weight residual
     110.00  120.57  -10.57 3.00e+00 1.11e-01 1.24e+01
  angle pdb=" CB  SEP A1362 "
        pdb=" OG  SEP A1362 "
        pdb=" P   SEP A1362 "
      ideal   model   delta    sigma   weight residual
     110.00  120.51  -10.51 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" OG1 TPO A1359 "
        pdb=" P   TPO A1359 "
        pdb=" O1P TPO A1359 "
      ideal   model   delta    sigma   weight residual
     100.43  109.13   -8.70 3.00e+00 1.11e-01 8.41e+00
  ... (remaining 11274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 4589
       17.44 -    34.89: 286
       34.89 -    52.33: 51
       52.33 -    69.77: 8
       69.77 -    87.22: 14
  Dihedral angle restraints: 4948
    sinusoidal: 1863
      harmonic: 3085
  Sorted by residual:
  dihedral pdb=" CB  CYS A  44 "
           pdb=" SG  CYS A  44 "
           pdb=" SG  CYS A 103 "
           pdb=" CB  CYS A 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.03   56.97     1      1.00e+01 1.00e-02 4.37e+01
  dihedral pdb=" CA  ASP B  78 "
           pdb=" CB  ASP B  78 "
           pdb=" CG  ASP B  78 "
           pdb=" OD1 ASP B  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.26   52.26     1      2.00e+01 2.50e-03 9.31e+00
  dihedral pdb=" CA  ARG A 345 "
           pdb=" CB  ARG A 345 "
           pdb=" CG  ARG A 345 "
           pdb=" CD  ARG A 345 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.63   53.63     3      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 4945 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1136
       0.055 -    0.109: 143
       0.109 -    0.164: 28
       0.164 -    0.218: 0
       0.218 -    0.273: 1
  Chirality restraints: 1308
  Sorted by residual:
  chirality pdb=" C12 H98 A2001 "
            pdb=" C11 H98 A2001 "
            pdb=" C13 H98 A2001 "
            pdb=" O4  H98 A2001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.43   -2.70    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" C2  H98 A2001 "
            pdb=" C1  H98 A2001 "
            pdb=" C3  H98 A2001 "
            pdb=" N1  H98 A2001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.71   -0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CA  ILE B 318 "
            pdb=" N   ILE B 318 "
            pdb=" C   ILE B 318 "
            pdb=" CB  ILE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 1305 not shown)

  Planarity restraints: 1413
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 275 "    0.014 5.00e-02 4.00e+02   2.10e-02 7.03e-01
        pdb=" N   PRO B 276 "   -0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO B 276 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO B 276 "    0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 218 "    0.012 5.00e-02 4.00e+02   1.82e-02 5.28e-01
        pdb=" N   PRO A 219 "   -0.031 5.00e-02 4.00e+02
        pdb=" CA  PRO A 219 "    0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO A 219 "    0.010 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 158 "    0.012 5.00e-02 4.00e+02   1.79e-02 5.15e-01
        pdb=" N   PRO H 159 "   -0.031 5.00e-02 4.00e+02
        pdb=" CA  PRO H 159 "    0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO H 159 "    0.010 5.00e-02 4.00e+02
  ... (remaining 1410 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 88
        2.64 -     3.21: 7440
        3.21 -     3.77: 12363
        3.77 -     4.34: 17084
        4.34 -     4.90: 28443
  Nonbonded interactions: 65418
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  13 "
            pdb=" OD1 ASN B  15 "
     model   vdw
     2.079 3.040
  nonbonded pdb=" OG  SER H  36 "
            pdb=" OG  SER H 102 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" O   HIS L 190 "
            pdb=" NH1 ARG L 212 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" OH  TYR A 193 "
            pdb=" O   VAL A 202 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   PHE B 277 "
            pdb=" ND2 ASN B 281 "
     model   vdw
     2.285 3.120
  ... (remaining 65413 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=0.65 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:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.750
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   8278  Z= 0.243
  Angle     :  0.509  11.713  11293  Z= 0.242
  Chirality :  0.040   0.273   1308
  Planarity :  0.002   0.021   1413
  Dihedral  : 12.600  87.216   2931
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  7.58 %
    Favored  : 92.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    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: -2.07 (0.24), residues: 1023
  helix: -0.38 (0.29), residues: 255
  sheet: -1.90 (0.25), residues: 333
  loop : -1.36 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 165 
 TYR   0.004   0.000   TYR L  92 
 PHE   0.004   0.000   PHE A 147 
 TRP   0.002   0.000   TRP A 330 
 HIS   0.001   0.000   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 8271)
  covalent geometry    : angle       0.50922 (11279)
  SS BOND              : bond        0.00042 (    7)
  SS BOND              : angle       0.18720 (   14)
  hydrogen bonds       : bond        0.20574 (  392)
  hydrogen bonds       : angle       7.75909 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 303
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASN cc_start: 0.7881 (m-40) cc_final: 0.7569 (m-40)
REVERT: A  121 ASP cc_start: 0.8282 (t0) cc_final: 0.8066 (t0)
REVERT: A  154 THR cc_start: 0.8467 (m) cc_final: 0.8072 (p)
REVERT: A  182 TRP cc_start: 0.7354 (p-90) cc_final: 0.6972 (p-90)
REVERT: A  192 CYS cc_start: 0.4226 (t) cc_final: 0.3700 (t)
REVERT: A  204 ASN cc_start: 0.7277 (p0) cc_final: 0.6898 (p0)
REVERT: A  217 TYR cc_start: 0.7651 (m-80) cc_final: 0.7390 (m-80)
REVERT: A  221 LEU cc_start: 0.8424 (tp) cc_final: 0.8158 (tt)
REVERT: A  235 LYS cc_start: 0.7549 (mttt) cc_final: 0.7322 (mtpp)
REVERT: A  325 PHE cc_start: 0.8508 (t80) cc_final: 0.8230 (t80)
REVERT: A  339 ASN cc_start: 0.8419 (m-40) cc_final: 0.8104 (m110)
REVERT: B   29 ASP cc_start: 0.7763 (t0) cc_final: 0.7501 (t0)
REVERT: H  111 ASP cc_start: 0.7495 (m-30) cc_final: 0.6562 (m-30)
REVERT: L    3 ILE cc_start: 0.7294 (mt) cc_final: 0.7026 (mp)
REVERT: L   80 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7661 (mp10)
REVERT: L   91 GLN cc_start: 0.8215 (pp30) cc_final: 0.7818 (pp30)
REVERT: L  178 SER cc_start: 0.8134 (t) cc_final: 0.7860 (t)
REVERT: L  195 CYS cc_start: 0.4880 (m) cc_final: 0.4225 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 305
  average time/residue: 0.0932
  time to fit residues: 38.2183
Evaluate side-chains
  195 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  85 GLN
B 162 ASN
H  31 ASN
L 148 GLN
L 167 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.173866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.129837 restraints weight = 11530.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.71
r_work: 0.3513 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8278  Z= 0.179
  Angle     :  0.609   9.994  11293  Z= 0.308
  Chirality :  0.043   0.177   1308
  Planarity :  0.004   0.048   1413
  Dihedral  :  7.085  84.025   1164
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.42 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.25), residues: 1023
  helix:  1.34 (0.31), residues: 256
  sheet: -1.19 (0.27), residues: 329
  loop : -0.72 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  19 
 TYR   0.016   0.002   TYR L 141 
 PHE   0.022   0.002   PHE H 156 
 TRP   0.008   0.001   TRP A 181 
 HIS   0.002   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8271)
  covalent geometry    : angle       0.60842 (11279)
  SS BOND              : bond        0.00501 (    7)
  SS BOND              : angle       1.19337 (   14)
  hydrogen bonds       : bond        0.03780 (  392)
  hydrogen bonds       : angle       5.59067 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 213
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8827 (tpp) cc_final: 0.8476 (mmm)
REVERT: A  154 THR cc_start: 0.8318 (m) cc_final: 0.7871 (p)
REVERT: A  192 CYS cc_start: 0.4431 (t) cc_final: 0.4179 (t)
REVERT: A  221 LEU cc_start: 0.8439 (tp) cc_final: 0.8157 (tt)
REVERT: A  235 LYS cc_start: 0.7764 (mttt) cc_final: 0.7382 (mtpp)
REVERT: A  325 PHE cc_start: 0.8540 (t80) cc_final: 0.8331 (t80)
REVERT: A  339 ASN cc_start: 0.8546 (m-40) cc_final: 0.8199 (m110)
REVERT: B  346 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7471 (mt-10)
REVERT: H   68 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8132 (ttpp)
REVERT: H   83 TYR cc_start: 0.8142 (m-80) cc_final: 0.7819 (m-80)
REVERT: H  120 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8649 (m)
REVERT: H  220 LYS cc_start: 0.8794 (pptt) cc_final: 0.8450 (pptt)
REVERT: L   71 ASP cc_start: 0.8241 (m-30) cc_final: 0.8022 (m-30)
REVERT: L   91 GLN cc_start: 0.8684 (pp30) cc_final: 0.8303 (pp30)
REVERT: L  109 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7597 (ptm160)
REVERT: L  146 LYS cc_start: 0.8772 (tptm) cc_final: 0.8543 (tttm)
REVERT: L  150 LYS cc_start: 0.8334 (mttt) cc_final: 0.7931 (mmmt)
REVERT: L  164 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7424 (p)
REVERT: L  178 SER cc_start: 0.8147 (t) cc_final: 0.7787 (t)
  outliers start: 28
  outliers final: 17
  residues processed: 229
  average time/residue: 0.0876
  time to fit residues: 27.2583
Evaluate side-chains
  201 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 182
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  245 ASN
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue  126 LEU
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  164 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0870
   chunk 92 optimal weight:    0.3980
   chunk 63 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0570
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.4076

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
B  30 HIS
B 101 GLN
B 172 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.173576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.129407 restraints weight = 11351.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.68
r_work: 0.3499 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8278  Z= 0.142
  Angle     :  0.587   8.334  11293  Z= 0.292
  Chirality :  0.043   0.179   1308
  Planarity :  0.004   0.033   1413
  Dihedral  :  6.925  83.431   1163
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.39 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.26), residues: 1023
  helix:  1.65 (0.31), residues: 259
  sheet: -0.89 (0.29), residues: 312
  loop : -0.60 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 236 
 TYR   0.015   0.002   TYR H 186 
 PHE   0.024   0.002   PHE H 156 
 TRP   0.008   0.001   TRP A 181 
 HIS   0.005   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8271)
  covalent geometry    : angle       0.58443 (11279)
  SS BOND              : bond        0.00474 (    7)
  SS BOND              : angle       1.51891 (   14)
  hydrogen bonds       : bond        0.03399 (  392)
  hydrogen bonds       : angle       5.36575 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8908 (tpp) cc_final: 0.8528 (mmm)
REVERT: A  154 THR cc_start: 0.8441 (m) cc_final: 0.8094 (m)
REVERT: A  235 LYS cc_start: 0.7760 (mttt) cc_final: 0.7351 (mtpp)
REVERT: A  323 TRP cc_start: 0.8344 (p-90) cc_final: 0.7860 (t60)
REVERT: A  339 ASN cc_start: 0.8493 (m-40) cc_final: 0.8193 (m-40)
REVERT: B  346 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7416 (mt-10)
REVERT: H   68 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8194 (ttpp)
REVERT: H   83 TYR cc_start: 0.8143 (m-80) cc_final: 0.7901 (m-80)
REVERT: H  119 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.6818 (t)
REVERT: L   91 GLN cc_start: 0.8647 (pp30) cc_final: 0.8349 (pp30)
REVERT: L  109 ARG cc_start: 0.7871 (ptm160) cc_final: 0.7595 (ptm160)
REVERT: L  133 VAL cc_start: 0.8312 (t) cc_final: 0.7999 (m)
REVERT: L  146 LYS cc_start: 0.8763 (tptm) cc_final: 0.8554 (tttm)
REVERT: L  150 LYS cc_start: 0.8274 (mttt) cc_final: 0.7787 (mmmt)
REVERT: L  177 SER cc_start: 0.8603 (m) cc_final: 0.8090 (m)
REVERT: L  196 GLU cc_start: 0.7835 (tt0) cc_final: 0.7290 (pt0)
  outliers start: 23
  outliers final: 14
  residues processed: 220
  average time/residue: 0.0784
  time to fit residues: 24.1251
Evaluate side-chains
  196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  245 ASN
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue  126 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0870
   overall best weight:    1.4166

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 GLN
B 172 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.164340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.117537 restraints weight = 11414.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.63
r_work: 0.3394 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3417
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3417
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.102   8278  Z= 0.275
  Angle     :  0.667   9.764  11293  Z= 0.339
  Chirality :  0.045   0.156   1308
  Planarity :  0.005   0.085   1413
  Dihedral  :  6.987  80.108   1163
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.30 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.26), residues: 1023
  helix:  1.54 (0.31), residues: 259
  sheet: -1.01 (0.28), residues: 333
  loop : -0.38 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 236 
 TYR   0.019   0.002   TYR B 173 
 PHE   0.030   0.002   PHE H  71 
 TRP   0.011   0.002   TRP A 109 
 HIS   0.007   0.002   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00646 ( 8271)
  covalent geometry    : angle       0.66456 (11279)
  SS BOND              : bond        0.00367 (    7)
  SS BOND              : angle       1.84874 (   14)
  hydrogen bonds       : bond        0.03770 (  392)
  hydrogen bonds       : angle       5.64485 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 LYS cc_start: 0.7804 (mttt) cc_final: 0.7463 (mtpp)
REVERT: A  291 THR cc_start: 0.8053 (m) cc_final: 0.7818 (p)
REVERT: A  323 TRP cc_start: 0.8372 (p-90) cc_final: 0.7925 (t60)
REVERT: A  339 ASN cc_start: 0.8385 (m-40) cc_final: 0.8059 (m-40)
REVERT: B   85 GLN cc_start: 0.8466 (tp40) cc_final: 0.8145 (tp40)
REVERT: B  238 TYR cc_start: 0.8039 (m-80) cc_final: 0.7327 (m-80)
REVERT: H   68 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8351 (ttpp)
REVERT: H  127 LYS cc_start: 0.8723 (tttt) cc_final: 0.8497 (mptt)
REVERT: L   25 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7368 (mmm-85)
REVERT: L   91 GLN cc_start: 0.8984 (pp30) cc_final: 0.8389 (pp30)
REVERT: L  109 ARG cc_start: 0.8123 (ptm160) cc_final: 0.7860 (ptm160)
REVERT: L  150 LYS cc_start: 0.8264 (mttt) cc_final: 0.7811 (mmmt)
REVERT: L  170 LYS cc_start: 0.8350 (tmmt) cc_final: 0.8116 (tmmt)
REVERT: L  177 SER cc_start: 0.8653 (m) cc_final: 0.8391 (p)
REVERT: L  196 GLU cc_start: 0.7941 (tt0) cc_final: 0.7427 (pt0)
  outliers start: 28
  outliers final: 21
  residues processed: 209
  average time/residue: 0.0699
  time to fit residues: 20.6923
Evaluate side-chains
  193 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  114 CYS
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  245 ASN
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue  126 LEU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  179 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 87 optimal weight:    0.0870
   chunk 89 optimal weight:    0.9990
   chunk 44 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.168661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122586 restraints weight = 11289.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.65
r_work: 0.3471 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8278  Z= 0.140
  Angle     :  0.605   8.707  11293  Z= 0.300
  Chirality :  0.043   0.213   1308
  Planarity :  0.004   0.076   1413
  Dihedral  :  6.729  82.686   1163
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.77 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.26), residues: 1023
  helix:  1.68 (0.31), residues: 258
  sheet: -0.89 (0.29), residues: 322
  loop : -0.49 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 165 
 TYR   0.023   0.002   TYR B 113 
 PHE   0.025   0.002   PHE H 132 
 TRP   0.016   0.001   TRP A 182 
 HIS   0.007   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8271)
  covalent geometry    : angle       0.60248 (11279)
  SS BOND              : bond        0.00208 (    7)
  SS BOND              : angle       1.71443 (   14)
  hydrogen bonds       : bond        0.03222 (  392)
  hydrogen bonds       : angle       5.41018 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 191
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8998 (tpp) cc_final: 0.8432 (mmm)
REVERT: A  154 THR cc_start: 0.8579 (m) cc_final: 0.8271 (p)
REVERT: A  235 LYS cc_start: 0.7755 (mttt) cc_final: 0.7427 (mtpp)
REVERT: A  323 TRP cc_start: 0.8257 (p-90) cc_final: 0.7834 (t60)
REVERT: A  339 ASN cc_start: 0.8431 (m-40) cc_final: 0.8151 (m-40)
REVERT: B  238 TYR cc_start: 0.7741 (m-80) cc_final: 0.7104 (m-80)
REVERT: H   68 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8440 (ttpp)
REVERT: H  119 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7244 (t)
REVERT: H  155 TYR cc_start: 0.8220 (p90) cc_final: 0.7613 (p90)
REVERT: L   91 GLN cc_start: 0.8691 (pp30) cc_final: 0.8353 (pp30)
REVERT: L  109 ARG cc_start: 0.7951 (ptm160) cc_final: 0.7660 (ptm160)
REVERT: L  150 LYS cc_start: 0.8160 (mttt) cc_final: 0.7491 (mmmt)
REVERT: L  170 LYS cc_start: 0.8264 (tmmt) cc_final: 0.8023 (tmmt)
REVERT: L  177 SER cc_start: 0.8813 (m) cc_final: 0.8333 (m)
REVERT: L  196 GLU cc_start: 0.7902 (tt0) cc_final: 0.7491 (pt0)
  outliers start: 25
  outliers final: 19
  residues processed: 203
  average time/residue: 0.0715
  time to fit residues: 20.9693
Evaluate side-chains
  197 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 177
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  114 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  245 ASN
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain L residue  126 LEU
Chi-restraints excluded: chain L residue  164 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 101 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 47 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 95 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.163517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.116624 restraints weight = 11249.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.61
r_work: 0.3391 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   8278  Z= 0.224
  Angle     :  0.638   8.607  11293  Z= 0.318
  Chirality :  0.044   0.192   1308
  Planarity :  0.004   0.063   1413
  Dihedral  :  6.778  80.868   1163
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.05 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.26), residues: 1023
  helix:  1.64 (0.31), residues: 261
  sheet: -1.04 (0.27), residues: 345
  loop : -0.36 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  19 
 TYR   0.020   0.002   TYR L 141 
 PHE   0.025   0.002   PHE H 132 
 TRP   0.014   0.001   TRP A 182 
 HIS   0.007   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 8271)
  covalent geometry    : angle       0.63574 (11279)
  SS BOND              : bond        0.00358 (    7)
  SS BOND              : angle       1.79459 (   14)
  hydrogen bonds       : bond        0.03465 (  392)
  hydrogen bonds       : angle       5.52708 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 181
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  235 LYS cc_start: 0.7797 (mttt) cc_final: 0.7451 (mtpp)
REVERT: A  239 ARG cc_start: 0.7037 (mtp180) cc_final: 0.6682 (ptm160)
REVERT: A  323 TRP cc_start: 0.8278 (p-90) cc_final: 0.7840 (t60)
REVERT: A  339 ASN cc_start: 0.8607 (m-40) cc_final: 0.8356 (m-40)
REVERT: B   58 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8527 (t)
REVERT: B  238 TYR cc_start: 0.7959 (m-80) cc_final: 0.7383 (m-80)
REVERT: H   68 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8379 (ttpp)
REVERT: H   85 GLN cc_start: 0.8203 (tp40) cc_final: 0.7776 (tp40)
REVERT: H  119 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7888 (m)
REVERT: H  127 LYS cc_start: 0.8693 (tttt) cc_final: 0.8457 (mptt)
REVERT: H  155 TYR cc_start: 0.8429 (p90) cc_final: 0.7711 (p90)
REVERT: L   91 GLN cc_start: 0.8775 (pp30) cc_final: 0.8277 (pp30)
REVERT: L  109 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7618 (ptm160)
REVERT: L  150 LYS cc_start: 0.8188 (mttt) cc_final: 0.7723 (mmmt)
REVERT: L  177 SER cc_start: 0.8836 (m) cc_final: 0.8426 (p)
REVERT: L  196 GLU cc_start: 0.7951 (tt0) cc_final: 0.7495 (pt0)
  outliers start: 26
  outliers final: 23
  residues processed: 196
  average time/residue: 0.0688
  time to fit residues: 18.9798
Evaluate side-chains
  205 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  134 LEU
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain L residue  126 LEU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  186 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 86 optimal weight:    0.4980
   chunk 82 optimal weight:    0.0370
   chunk 98 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0020
   chunk 64 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.4466

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 181 GLN
L  90 GLN
** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.165929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.121131 restraints weight = 11340.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.56
r_work: 0.3453 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3479
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8278  Z= 0.143
  Angle     :  0.611   8.545  11293  Z= 0.301
  Chirality :  0.043   0.206   1308
  Planarity :  0.004   0.060   1413
  Dihedral  :  6.661  82.263   1163
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.29 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.26), residues: 1023
  helix:  1.63 (0.32), residues: 264
  sheet: -0.99 (0.28), residues: 332
  loop : -0.41 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 285 
 TYR   0.021   0.002   TYR L 141 
 PHE   0.028   0.002   PHE H 132 
 TRP   0.025   0.001   TRP A 182 
 HIS   0.007   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8271)
  covalent geometry    : angle       0.60876 (11279)
  SS BOND              : bond        0.00169 (    7)
  SS BOND              : angle       1.53867 (   14)
  hydrogen bonds       : bond        0.03171 (  392)
  hydrogen bonds       : angle       5.38066 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 188
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8374 (mm-40)
REVERT: A  153 MET cc_start: 0.8946 (tpp) cc_final: 0.8589 (mmm)
REVERT: A  184 ASP cc_start: 0.6878 (t70) cc_final: 0.6455 (m-30)
REVERT: A  193 TYR cc_start: 0.7718 (m-80) cc_final: 0.7492 (m-80)
REVERT: A  235 LYS cc_start: 0.7765 (mttt) cc_final: 0.7436 (mtpp)
REVERT: A  239 ARG cc_start: 0.7018 (mtp180) cc_final: 0.6729 (ptm160)
REVERT: A  323 TRP cc_start: 0.8246 (p-90) cc_final: 0.7837 (t60)
REVERT: A  339 ASN cc_start: 0.8505 (m-40) cc_final: 0.8227 (m-40)
REVERT: B   58 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8534 (t)
REVERT: B  238 TYR cc_start: 0.7785 (m-80) cc_final: 0.7059 (m-80)
REVERT: H   68 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8451 (ttpp)
REVERT: H   85 GLN cc_start: 0.8093 (tp40) cc_final: 0.7769 (tp40)
REVERT: H  155 TYR cc_start: 0.8342 (p90) cc_final: 0.7637 (p90)
REVERT: L   91 GLN cc_start: 0.8690 (pp30) cc_final: 0.8326 (pp30)
REVERT: L  150 LYS cc_start: 0.8169 (mttt) cc_final: 0.7688 (mmmt)
REVERT: L  177 SER cc_start: 0.8816 (m) cc_final: 0.8355 (m)
REVERT: L  196 GLU cc_start: 0.7866 (tt0) cc_final: 0.7384 (pt0)
  outliers start: 27
  outliers final: 22
  residues processed: 205
  average time/residue: 0.0739
  time to fit residues: 21.2311
Evaluate side-chains
  199 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  114 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue  134 LEU
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain L residue  126 LEU
Chi-restraints excluded: chain L residue  164 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0770
   chunk 54 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0470
   chunk 57 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0050
   chunk 45 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.2650

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.167429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.122657 restraints weight = 11246.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.56
r_work: 0.3475 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8278  Z= 0.130
  Angle     :  0.619   8.395  11293  Z= 0.306
  Chirality :  0.043   0.200   1308
  Planarity :  0.004   0.052   1413
  Dihedral  :  6.628  82.627   1163
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.92 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.26), residues: 1023
  helix:  1.57 (0.32), residues: 264
  sheet: -0.91 (0.29), residues: 317
  loop : -0.40 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 285 
 TYR   0.019   0.002   TYR H 186 
 PHE   0.028   0.002   PHE H 132 
 TRP   0.028   0.002   TRP A 182 
 HIS   0.007   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8271)
  covalent geometry    : angle       0.61766 (11279)
  SS BOND              : bond        0.00182 (    7)
  SS BOND              : angle       1.48298 (   14)
  hydrogen bonds       : bond        0.03159 (  392)
  hydrogen bonds       : angle       5.43361 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8915 (tpp) cc_final: 0.8527 (mmm)
REVERT: A  181 TRP cc_start: 0.7949 (m-90) cc_final: 0.7730 (m-90)
REVERT: A  235 LYS cc_start: 0.7802 (mttt) cc_final: 0.7444 (mtpp)
REVERT: A  239 ARG cc_start: 0.7008 (mtp180) cc_final: 0.6708 (ptm160)
REVERT: A  323 TRP cc_start: 0.8264 (p-90) cc_final: 0.7859 (t60)
REVERT: A  328 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8360 (t80)
REVERT: A  339 ASN cc_start: 0.8491 (m-40) cc_final: 0.8228 (m-40)
REVERT: B   58 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8503 (t)
REVERT: B  154 LEU cc_start: 0.8891 (mm) cc_final: 0.8553 (mm)
REVERT: B  238 TYR cc_start: 0.7709 (m-80) cc_final: 0.6963 (m-80)
REVERT: H   68 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8449 (ttpp)
REVERT: H   79 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7886 (pttt)
REVERT: H   85 GLN cc_start: 0.8056 (tp40) cc_final: 0.7726 (tp40)
REVERT: H  155 TYR cc_start: 0.8251 (p90) cc_final: 0.7613 (p90)
REVERT: L  109 ARG cc_start: 0.7911 (ptm160) cc_final: 0.7446 (ptm160)
REVERT: L  170 LYS cc_start: 0.8252 (tmmt) cc_final: 0.7988 (tmmt)
REVERT: L  177 SER cc_start: 0.8804 (m) cc_final: 0.8349 (m)
REVERT: L  196 GLU cc_start: 0.7902 (tt0) cc_final: 0.7205 (pt0)
  outliers start: 23
  outliers final: 18
  residues processed: 203
  average time/residue: 0.0695
  time to fit residues: 20.3766
Evaluate side-chains
  200 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  114 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue  126 LEU
Chi-restraints excluded: chain L residue  164 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 81 optimal weight:    0.3980
   chunk 76 optimal weight:    7.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.166514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.119956 restraints weight = 11220.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.63
r_work: 0.3440 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3461
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3461
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8278  Z= 0.162
  Angle     :  0.629   8.548  11293  Z= 0.311
  Chirality :  0.044   0.261   1308
  Planarity :  0.005   0.088   1413
  Dihedral  :  6.589  81.276   1163
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 24.50 %
    Favored  : 72.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.26), residues: 1023
  helix:  1.49 (0.32), residues: 264
  sheet: -0.96 (0.28), residues: 331
  loop : -0.26 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 285 
 TYR   0.026   0.002   TYR L 141 
 PHE   0.026   0.002   PHE H 132 
 TRP   0.031   0.002   TRP A 182 
 HIS   0.011   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8271)
  covalent geometry    : angle       0.62713 (11279)
  SS BOND              : bond        0.00290 (    7)
  SS BOND              : angle       1.50648 (   14)
  hydrogen bonds       : bond        0.03275 (  392)
  hydrogen bonds       : angle       5.45958 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 178
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8917 (tpp) cc_final: 0.8510 (mmm)
REVERT: A  235 LYS cc_start: 0.7817 (mttt) cc_final: 0.7510 (mtpp)
REVERT: A  239 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6675 (ptm160)
REVERT: A  323 TRP cc_start: 0.8251 (p-90) cc_final: 0.7809 (t60)
REVERT: A  328 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8408 (t80)
REVERT: A  339 ASN cc_start: 0.8469 (m-40) cc_final: 0.8203 (m110)
REVERT: B   58 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8499 (t)
REVERT: B  238 TYR cc_start: 0.7844 (m-80) cc_final: 0.7103 (m-80)
REVERT: B  285 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7644 (mmm-85)
REVERT: H   68 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8451 (ttpp)
REVERT: H   79 LYS cc_start: 0.8405 (mtmm) cc_final: 0.7929 (pttt)
REVERT: H   85 GLN cc_start: 0.8106 (tp40) cc_final: 0.7763 (tp40)
REVERT: H  115 GLN cc_start: 0.8270 (tp40) cc_final: 0.7958 (tp40)
REVERT: H  155 TYR cc_start: 0.8164 (p90) cc_final: 0.7632 (p90)
REVERT: L  109 ARG cc_start: 0.7975 (ptm160) cc_final: 0.7571 (ptm160)
REVERT: L  150 LYS cc_start: 0.8279 (mttt) cc_final: 0.7756 (mmmt)
REVERT: L  170 LYS cc_start: 0.8179 (tmmt) cc_final: 0.7971 (tmmt)
REVERT: L  177 SER cc_start: 0.8834 (m) cc_final: 0.8555 (p)
REVERT: L  196 GLU cc_start: 0.7961 (tt0) cc_final: 0.7430 (pt0)
  outliers start: 22
  outliers final: 20
  residues processed: 190
  average time/residue: 0.0686
  time to fit residues: 18.4449
Evaluate side-chains
  196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  114 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain L residue  126 LEU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  176 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.164406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.117486 restraints weight = 11246.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.63
r_work: 0.3365 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3382
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.4760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8278  Z= 0.194
  Angle     :  0.651   8.807  11293  Z= 0.323
  Chirality :  0.045   0.236   1308
  Planarity :  0.005   0.086   1413
  Dihedral  :  6.598  81.493   1163
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.80 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.26), residues: 1023
  helix:  1.46 (0.32), residues: 263
  sheet: -1.05 (0.28), residues: 333
  loop : -0.29 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 285 
 TYR   0.034   0.002   TYR L 141 
 PHE   0.020   0.002   PHE A 216 
 TRP   0.034   0.002   TRP A 182 
 HIS   0.012   0.002   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 8271)
  covalent geometry    : angle       0.64855 (11279)
  SS BOND              : bond        0.00281 (    7)
  SS BOND              : angle       1.62596 (   14)
  hydrogen bonds       : bond        0.03346 (  392)
  hydrogen bonds       : angle       5.52573 ( 1143)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8898 (tpp) cc_final: 0.8203 (mmm)
REVERT: A  203 THR cc_start: 0.8048 (p) cc_final: 0.7684 (t)
REVERT: A  235 LYS cc_start: 0.7833 (mttt) cc_final: 0.7497 (mtpp)
REVERT: A  239 ARG cc_start: 0.7062 (mtp180) cc_final: 0.6736 (ptm160)
REVERT: A  323 TRP cc_start: 0.8126 (p-90) cc_final: 0.7740 (t60)
REVERT: A  328 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8444 (t80)
REVERT: A  339 ASN cc_start: 0.8445 (m-40) cc_final: 0.8190 (m110)
REVERT: B   58 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8542 (t)
REVERT: B  238 TYR cc_start: 0.7913 (m-80) cc_final: 0.7192 (m-80)
REVERT: H    9 GLU cc_start: 0.7405 (pm20) cc_final: 0.7157 (pm20)
REVERT: H   68 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8490 (ttpp)
REVERT: H   79 LYS cc_start: 0.8493 (mtmm) cc_final: 0.7981 (pttt)
REVERT: H   85 GLN cc_start: 0.8098 (tp40) cc_final: 0.7766 (tp40)
REVERT: H  127 LYS cc_start: 0.8131 (mptt) cc_final: 0.7923 (mmtt)
REVERT: H  155 TYR cc_start: 0.8316 (p90) cc_final: 0.7709 (p90)
REVERT: L  109 ARG cc_start: 0.7892 (ptm160) cc_final: 0.7606 (ptm160)
REVERT: L  150 LYS cc_start: 0.8261 (mttt) cc_final: 0.7738 (mmmt)
REVERT: L  177 SER cc_start: 0.8842 (m) cc_final: 0.8560 (p)
REVERT: L  196 GLU cc_start: 0.7986 (tt0) cc_final: 0.7477 (pt0)
  outliers start: 24
  outliers final: 19
  residues processed: 189
  average time/residue: 0.0764
  time to fit residues: 19.9650
Evaluate side-chains
  196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  114 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue  134 LEU
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain L residue  164 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 76 optimal weight:    8.9990
   chunk 63 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0470
   chunk 100 optimal weight:    0.5980
   chunk 96 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0970
   chunk 74 optimal weight:    0.6980
   chunk 98 optimal weight:    0.4980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 ASN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 174 HIS
** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.166877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.121420 restraints weight = 11206.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.59
r_work: 0.3421 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8278  Z= 0.137
  Angle     :  0.637   8.583  11293  Z= 0.315
  Chirality :  0.044   0.246   1308
  Planarity :  0.005   0.084   1413
  Dihedral  :  6.477  80.194   1163
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 25.32 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.26), residues: 1023
  helix:  1.47 (0.32), residues: 264
  sheet: -0.98 (0.28), residues: 331
  loop : -0.20 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 165 
 TYR   0.030   0.002   TYR L 141 
 PHE   0.023   0.002   PHE H 132 
 TRP   0.039   0.002   TRP A 181 
 HIS   0.009   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8271)
  covalent geometry    : angle       0.63540 (11279)
  SS BOND              : bond        0.00191 (    7)
  SS BOND              : angle       1.33518 (   14)
  hydrogen bonds       : bond        0.03247 (  392)
  hydrogen bonds       : angle       5.36469 ( 1143)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2227.79 seconds
wall clock time: 38 minutes 52.22 seconds (2332.22 seconds total)