Starting phenix.real_space_refine
on Wed Feb 12 19:44:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tko_10515/02_2025/6tko_10515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tko_10515/02_2025/6tko_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tko_10515/02_2025/6tko_10515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tko_10515/02_2025/6tko_10515.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tko_10515/02_2025/6tko_10515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tko_10515/02_2025/6tko_10515.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'TPO:plan-1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 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, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          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: {'GLU:plan': 2, 'ASP:plan': 1}
          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: 4.93, per 1000 atoms: 0.61
  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: 2.12
  Conformation dependent library (CDL) restraints added in 939.9 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: 1.03
  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: 2.61

  Time building geometry restraints manager: 2.45 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:             0.580
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.600
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.580
-------------------------------------------------------------------------------
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   8271  Z= 0.314
  Angle     :  0.509  11.713  11279  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 : 2.87
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.002   0.000   TRP A 330 
 HIS   0.001   0.000   HIS B  30 
 PHE   0.004   0.000   PHE A 147 
 TYR   0.004   0.000   TYR L  92 
 ARG   0.001   0.000   ARG B 165 

*********************** 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  : 0.963 
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: 0.2196
  time to fit residues: 88.6704
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  : 0.867 
-------------------------------------------------------------------------------
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 87 optimal weight:    0.3980
   chunk 78 optimal weight:   10.0000
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4193 r_free = 0.4193 target = 0.174074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.130745 restraints weight = 11333.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.65
r_work: 0.3518 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3544 r_free = 0.3544    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 = 0.3543 r_free = 0.3543    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3543
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8271  Z= 0.253
  Angle     :  0.603  10.103  11279  Z= 0.304
  Chirality :  0.043   0.183   1308
  Planarity :  0.005   0.048   1413
  Dihedral  :  7.081  83.375   1164
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.54 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.25), residues: 1023
  helix:  1.33 (0.31), residues: 257
  sheet: -1.17 (0.27), residues: 329
  loop : -0.72 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 181 
 HIS   0.003   0.001   HIS H 174 
 PHE   0.021   0.002   PHE H 156 
 TYR   0.016   0.002   TYR L 141 
 ARG   0.005   0.001   ARG B 285 

*********************** 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
  239 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8812 (tpp) cc_final: 0.8469 (mmm)
REVERT: A  154 THR cc_start: 0.8311 (m) cc_final: 0.7853 (p)
REVERT: A  192 CYS cc_start: 0.4419 (t) cc_final: 0.4143 (t)
REVERT: A  221 LEU cc_start: 0.8439 (tp) cc_final: 0.8158 (tt)
REVERT: A  235 LYS cc_start: 0.7768 (mttt) cc_final: 0.7383 (mtpp)
REVERT: A  339 ASN cc_start: 0.8594 (m-40) cc_final: 0.8314 (m110)
REVERT: B  346 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7461 (mt-10)
REVERT: H   68 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8145 (ttpp)
REVERT: H   83 TYR cc_start: 0.8125 (m-80) cc_final: 0.7810 (m-80)
REVERT: H  120 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8565 (m)
REVERT: H  220 LYS cc_start: 0.8799 (pptt) cc_final: 0.8316 (pptt)
REVERT: L   71 ASP cc_start: 0.8218 (m-30) cc_final: 0.8012 (m-30)
REVERT: L   91 GLN cc_start: 0.8678 (pp30) cc_final: 0.8302 (pp30)
REVERT: L  109 ARG cc_start: 0.7848 (ptm160) cc_final: 0.7596 (ptm160)
REVERT: L  146 LYS cc_start: 0.8768 (tptm) cc_final: 0.8546 (tttm)
REVERT: L  150 LYS cc_start: 0.8333 (mttt) cc_final: 0.7934 (mmmt)
REVERT: L  178 SER cc_start: 0.8209 (t) cc_final: 0.7851 (t)
  outliers start: 28
  outliers final: 17
  residues processed: 227
  average time/residue: 0.2026
  time to fit residues: 62.0004
Evaluate side-chains
  201 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
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   59 VAL
Chi-restraints excluded: chain L residue  126 LEU
Chi-restraints excluded: chain L residue  135 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 82 optimal weight:    0.4980
   chunk 5 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0470
   chunk 64 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.3878

-------------------------------------------------------------------------------
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 172 GLN
** L  90 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 = 0.4195 r_free = 0.4195 target = 0.173632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.129725 restraints weight = 11457.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.67
r_work: 0.3504 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    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 = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
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   0.057   8271  Z= 0.213
  Angle     :  0.586   7.996  11279  Z= 0.293
  Chirality :  0.042   0.173   1308
  Planarity :  0.004   0.034   1413
  Dihedral  :  6.921  83.462   1163
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.15 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.25), residues: 1023
  helix:  1.63 (0.31), residues: 259
  sheet: -0.96 (0.28), residues: 318
  loop : -0.56 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 181 
 HIS   0.005   0.001   HIS L 190 
 PHE   0.025   0.002   PHE H 156 
 TYR   0.015   0.002   TYR L 141 
 ARG   0.006   0.000   ARG B 236 

*********************** 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
  224 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 202
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8912 (tpp) cc_final: 0.8525 (mmm)
REVERT: A  154 THR cc_start: 0.8438 (m) cc_final: 0.8094 (m)
REVERT: A  184 ASP cc_start: 0.7064 (t0) cc_final: 0.6839 (t70)
REVERT: A  235 LYS cc_start: 0.7767 (mttt) cc_final: 0.7352 (mtpp)
REVERT: A  323 TRP cc_start: 0.8344 (p-90) cc_final: 0.7876 (t60)
REVERT: A  325 PHE cc_start: 0.8300 (t80) cc_final: 0.8068 (t80)
REVERT: A  339 ASN cc_start: 0.8506 (m-40) cc_final: 0.8195 (m-40)
REVERT: H   68 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8196 (ttpp)
REVERT: H   83 TYR cc_start: 0.8159 (m-80) cc_final: 0.7891 (m-80)
REVERT: H  119 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.6701 (t)
REVERT: L   25 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7636 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8092 (m-30) cc_final: 0.7823 (m-30)
REVERT: L   91 GLN cc_start: 0.8645 (pp30) cc_final: 0.8349 (pp30)
REVERT: L  109 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7580 (ptm160)
REVERT: L  133 VAL cc_start: 0.8313 (t) cc_final: 0.7998 (m)
REVERT: L  146 LYS cc_start: 0.8763 (tptm) cc_final: 0.8551 (tttm)
REVERT: L  150 LYS cc_start: 0.8251 (mttt) cc_final: 0.7755 (mmmt)
REVERT: L  177 SER cc_start: 0.8539 (m) cc_final: 0.8028 (m)
REVERT: L  196 GLU cc_start: 0.7903 (tt0) cc_final: 0.7360 (pt0)
  outliers start: 22
  outliers final: 15
  residues processed: 218
  average time/residue: 0.1937
  time to fit residues: 57.9605
Evaluate side-chains
  196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
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  114 CYS
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  108 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  126 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    0.1980
   chunk 13 optimal weight:    0.2980
   chunk 55 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 102 optimal weight:    4.9990
   chunk 94 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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
L  39 GLN
** L  90 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 = 0.4154 r_free = 0.4154 target = 0.169573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.125491 restraints weight = 11240.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.59
r_work: 0.3456 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8271  Z= 0.247
  Angle     :  0.588  10.495  11279  Z= 0.293
  Chirality :  0.042   0.155   1308
  Planarity :  0.004   0.081   1413
  Dihedral  :  6.819  82.601   1163
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.02 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.26), residues: 1023
  helix:  1.69 (0.31), residues: 259
  sheet: -0.82 (0.28), residues: 319
  loop : -0.43 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 182 
 HIS   0.007   0.001   HIS L 190 
 PHE   0.022   0.002   PHE H 132 
 TYR   0.016   0.002   TYR B 113 
 ARG   0.004   0.000   ARG A 139 

*********************** 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
  210 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 186
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8969 (tpp) cc_final: 0.8455 (mmm)
REVERT: A  154 THR cc_start: 0.8488 (m) cc_final: 0.8101 (m)
REVERT: A  235 LYS cc_start: 0.7756 (mttt) cc_final: 0.7449 (mtpp)
REVERT: A  323 TRP cc_start: 0.8337 (p-90) cc_final: 0.7939 (t60)
REVERT: A  339 ASN cc_start: 0.8467 (m-40) cc_final: 0.8179 (m-40)
REVERT: B   85 GLN cc_start: 0.8358 (tp40) cc_final: 0.8080 (tp40)
REVERT: B  138 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8317 (mttp)
REVERT: B  204 ASP cc_start: 0.6597 (p0) cc_final: 0.6356 (p0)
REVERT: H   83 TYR cc_start: 0.8159 (m-80) cc_final: 0.7934 (m-80)
REVERT: H  119 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.6892 (t)
REVERT: H  120 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8354 (m)
REVERT: L   25 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7697 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8076 (m-30) cc_final: 0.7800 (m-30)
REVERT: L   91 GLN cc_start: 0.8744 (pp30) cc_final: 0.8354 (pp30)
REVERT: L  146 LYS cc_start: 0.8755 (tptm) cc_final: 0.8547 (tttm)
REVERT: L  150 LYS cc_start: 0.8244 (mttt) cc_final: 0.7784 (mmmt)
REVERT: L  170 LYS cc_start: 0.8306 (tmmt) cc_final: 0.8086 (tmmt)
REVERT: L  177 SER cc_start: 0.8539 (m) cc_final: 0.8069 (m)
REVERT: L  196 GLU cc_start: 0.7962 (tt0) cc_final: 0.7401 (pt0)
  outliers start: 24
  outliers final: 19
  residues processed: 204
  average time/residue: 0.1939
  time to fit residues: 54.5910
Evaluate side-chains
  194 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 173
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  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  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 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   59 VAL
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain L residue  126 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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**
B 210 HIS
L  38 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 = 0.4130 r_free = 0.4130 target = 0.167842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.122807 restraints weight = 11110.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.58
r_work: 0.3418 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3501
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8271  Z= 0.264
  Angle     :  0.590   9.073  11279  Z= 0.294
  Chirality :  0.043   0.161   1308
  Planarity :  0.004   0.074   1413
  Dihedral  :  6.739  82.314   1163
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.84 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.26), residues: 1023
  helix:  1.63 (0.31), residues: 262
  sheet: -0.88 (0.28), residues: 330
  loop : -0.25 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 182 
 HIS   0.007   0.001   HIS L 190 
 PHE   0.025   0.002   PHE H 132 
 TYR   0.018   0.002   TYR L 141 
 ARG   0.003   0.000   ARG A 139 

*********************** 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
  215 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8996 (tpp) cc_final: 0.8558 (mmm)
REVERT: A  154 THR cc_start: 0.8493 (m) cc_final: 0.8117 (m)
REVERT: A  235 LYS cc_start: 0.7799 (mttt) cc_final: 0.7474 (mtpp)
REVERT: A  323 TRP cc_start: 0.8274 (p-90) cc_final: 0.7858 (t60)
REVERT: A  339 ASN cc_start: 0.8429 (m-40) cc_final: 0.8116 (m-40)
REVERT: H   83 TYR cc_start: 0.8205 (m-80) cc_final: 0.7985 (m-80)
REVERT: H   85 GLN cc_start: 0.8085 (tp40) cc_final: 0.7780 (tp40)
REVERT: H  119 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7153 (t)
REVERT: H  155 TYR cc_start: 0.8047 (p90) cc_final: 0.7662 (p90)
REVERT: L   25 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7836 (mtp-110)
REVERT: L   91 GLN cc_start: 0.8764 (pp30) cc_final: 0.8352 (pp30)
REVERT: L  109 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7485 (ptm160)
REVERT: L  150 LYS cc_start: 0.8302 (mttt) cc_final: 0.7614 (mmmt)
REVERT: L  170 LYS cc_start: 0.8341 (tmmt) cc_final: 0.8068 (tmmt)
REVERT: L  177 SER cc_start: 0.8682 (m) cc_final: 0.8218 (m)
REVERT: L  196 GLU cc_start: 0.7919 (tt0) cc_final: 0.7425 (pt0)
  outliers start: 26
  outliers final: 17
  residues processed: 207
  average time/residue: 0.1918
  time to fit residues: 54.7515
Evaluate side-chains
  192 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
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   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  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   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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:    0.0030
   chunk 76 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0980
   chunk 73 optimal weight:    0.1980
   overall best weight:    0.2390

-------------------------------------------------------------------------------
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  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 = 0.4164 r_free = 0.4164 target = 0.171276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.126475 restraints weight = 11212.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.64
r_work: 0.3470 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    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 = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8271  Z= 0.175
  Angle     :  0.582   9.660  11279  Z= 0.285
  Chirality :  0.043   0.200   1308
  Planarity :  0.004   0.059   1413
  Dihedral  :  6.622  83.739   1163
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.00 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.26), residues: 1023
  helix:  1.64 (0.31), residues: 264
  sheet: -0.79 (0.29), residues: 320
  loop : -0.35 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 182 
 HIS   0.007   0.001   HIS L 190 
 PHE   0.026   0.002   PHE H 132 
 TYR   0.030   0.002   TYR A 193 
 ARG   0.003   0.000   ARG L  19 

*********************** 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
  212 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.9106 (tpp) cc_final: 0.8533 (mmm)
REVERT: A  154 THR cc_start: 0.8457 (m) cc_final: 0.8076 (m)
REVERT: A  184 ASP cc_start: 0.7074 (t0) cc_final: 0.6701 (t70)
REVERT: A  235 LYS cc_start: 0.7749 (mttt) cc_final: 0.7424 (mtpp)
REVERT: A  323 TRP cc_start: 0.8281 (p-90) cc_final: 0.7937 (t60)
REVERT: A  339 ASN cc_start: 0.8360 (m-40) cc_final: 0.8073 (m-40)
REVERT: B   58 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8275 (t)
REVERT: B   78 ASP cc_start: 0.8207 (m-30) cc_final: 0.7762 (m-30)
REVERT: H   68 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8282 (ttpp)
REVERT: H   83 TYR cc_start: 0.8184 (m-80) cc_final: 0.7838 (m-80)
REVERT: H   85 GLN cc_start: 0.7992 (tp40) cc_final: 0.7685 (tp40)
REVERT: H  119 VAL cc_start: 0.7741 (OUTLIER) cc_final: 0.6845 (t)
REVERT: H  155 TYR cc_start: 0.7944 (p90) cc_final: 0.7567 (p90)
REVERT: L   91 GLN cc_start: 0.8589 (pp30) cc_final: 0.8345 (pp30)
REVERT: L  109 ARG cc_start: 0.7719 (ptm160) cc_final: 0.7310 (ptm160)
REVERT: L  150 LYS cc_start: 0.8281 (mttt) cc_final: 0.7796 (mmmt)
REVERT: L  170 LYS cc_start: 0.8326 (tmmt) cc_final: 0.8067 (tmmt)
REVERT: L  177 SER cc_start: 0.8718 (m) cc_final: 0.8353 (m)
REVERT: L  196 GLU cc_start: 0.7839 (tt0) cc_final: 0.7464 (pt0)
  outliers start: 20
  outliers final: 15
  residues processed: 206
  average time/residue: 0.1723
  time to fit residues: 50.3624
Evaluate side-chains
  195 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
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  114 CYS
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   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain H residue   28 SER
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  126 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0040
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.6192

-------------------------------------------------------------------------------
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  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 148 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.169318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.130692 restraints weight = 11337.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 3.32
r_work: 0.3385 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    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 = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3466
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8271  Z= 0.234
  Angle     :  0.604  10.204  11279  Z= 0.296
  Chirality :  0.043   0.211   1308
  Planarity :  0.004   0.082   1413
  Dihedral  :  6.584  82.531   1163
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 22.75 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1023
  helix:  1.70 (0.32), residues: 264
  sheet: -0.75 (0.29), residues: 320
  loop : -0.31 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 181 
 HIS   0.009   0.001   HIS L 190 
 PHE   0.026   0.002   PHE H 132 
 TYR   0.038   0.002   TYR H 186 
 ARG   0.004   0.000   ARG A 139 

*********************** 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
  209 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 192
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.9177 (tpp) cc_final: 0.8924 (tpp)
REVERT: A  181 TRP cc_start: 0.7833 (m-90) cc_final: 0.7590 (m-90)
REVERT: A  235 LYS cc_start: 0.7788 (mttt) cc_final: 0.7497 (mtpp)
REVERT: A  239 ARG cc_start: 0.6810 (mtp180) cc_final: 0.6556 (ptm160)
REVERT: A  323 TRP cc_start: 0.8290 (p-90) cc_final: 0.7939 (t60)
REVERT: A  339 ASN cc_start: 0.8542 (m-40) cc_final: 0.8200 (m-40)
REVERT: B   58 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8250 (t)
REVERT: B   78 ASP cc_start: 0.8274 (m-30) cc_final: 0.7815 (m-30)
REVERT: H   68 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8400 (ttpp)
REVERT: H  119 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7046 (t)
REVERT: L   91 GLN cc_start: 0.8731 (pp30) cc_final: 0.8326 (pp30)
REVERT: L  109 ARG cc_start: 0.7747 (ptm160) cc_final: 0.7212 (ptm160)
REVERT: L  150 LYS cc_start: 0.8272 (mttt) cc_final: 0.7768 (mmmt)
REVERT: L  170 LYS cc_start: 0.8358 (tmmt) cc_final: 0.8086 (tmmt)
REVERT: L  177 SER cc_start: 0.8765 (m) cc_final: 0.8202 (m)
REVERT: L  196 GLU cc_start: 0.7919 (tt0) cc_final: 0.7507 (pt0)
  outliers start: 17
  outliers final: 14
  residues processed: 204
  average time/residue: 0.1828
  time to fit residues: 51.9579
Evaluate side-chains
  193 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
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   53 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  245 ASN
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  126 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0070
   chunk 34 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 310 ASN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 181 GLN
** L  90 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 = 0.4126 r_free = 0.4126 target = 0.167546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.122274 restraints weight = 11266.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.62
r_work: 0.3414 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3494
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    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 = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.4359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8271  Z= 0.238
  Angle     :  0.611   8.618  11279  Z= 0.304
  Chirality :  0.043   0.220   1308
  Planarity :  0.005   0.085   1413
  Dihedral  :  6.587  82.001   1163
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 22.87 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.26), residues: 1023
  helix:  1.63 (0.32), residues: 264
  sheet: -0.70 (0.30), residues: 320
  loop : -0.32 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 181 
 HIS   0.011   0.001   HIS L 190 
 PHE   0.029   0.002   PHE H 132 
 TYR   0.024   0.002   TYR H 186 
 ARG   0.004   0.000   ARG B 285 

*********************** 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
  205 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TRP cc_start: 0.6066 (t-100) cc_final: 0.5843 (t-100)
REVERT: A  181 TRP cc_start: 0.7898 (m-90) cc_final: 0.7638 (m-90)
REVERT: A  235 LYS cc_start: 0.7787 (mttt) cc_final: 0.7495 (mtpp)
REVERT: A  239 ARG cc_start: 0.6887 (mtp180) cc_final: 0.6599 (ptm160)
REVERT: A  323 TRP cc_start: 0.8208 (p-90) cc_final: 0.7874 (t60)
REVERT: A  328 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8204 (t80)
REVERT: A  339 ASN cc_start: 0.8593 (m-40) cc_final: 0.8322 (m-40)
REVERT: B   58 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8265 (t)
REVERT: B   78 ASP cc_start: 0.8211 (m-30) cc_final: 0.7820 (m-30)
REVERT: H   79 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7837 (pttt)
REVERT: H   83 TYR cc_start: 0.7959 (m-80) cc_final: 0.7555 (m-80)
REVERT: H  119 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7416 (m)
REVERT: L   91 GLN cc_start: 0.8767 (pp30) cc_final: 0.8308 (pp30)
REVERT: L  109 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7232 (ptm160)
REVERT: L  150 LYS cc_start: 0.8260 (mttt) cc_final: 0.7739 (mmmt)
REVERT: L  170 LYS cc_start: 0.8318 (tmmt) cc_final: 0.8100 (tmmt)
REVERT: L  177 SER cc_start: 0.8764 (m) cc_final: 0.8325 (m)
REVERT: L  196 GLU cc_start: 0.7927 (tt0) cc_final: 0.7493 (pt0)
  outliers start: 23
  outliers final: 20
  residues processed: 195
  average time/residue: 0.1832
  time to fit residues: 50.0217
Evaluate side-chains
  202 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 179
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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  171 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  328 PHE
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   84 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  245 ASN
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0170
   chunk 2 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.6618

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.168121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.121506 restraints weight = 11481.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.68
r_work: 0.3461 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3487 r_free = 0.3487    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 = 0.3487 r_free = 0.3487    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8271  Z= 0.247
  Angle     :  0.634  10.980  11279  Z= 0.311
  Chirality :  0.043   0.220   1308
  Planarity :  0.004   0.081   1413
  Dihedral  :  6.555  81.441   1163
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.34 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.26), residues: 1023
  helix:  1.65 (0.32), residues: 264
  sheet: -0.70 (0.29), residues: 332
  loop : -0.23 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 181 
 HIS   0.011   0.001   HIS L 190 
 PHE   0.025   0.002   PHE H 132 
 TYR   0.022   0.002   TYR L 141 
 ARG   0.007   0.000   ARG B 285 

*********************** 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
  196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TRP cc_start: 0.6124 (t-100) cc_final: 0.5877 (t-100)
REVERT: A  153 MET cc_start: 0.8873 (tpp) cc_final: 0.8484 (mmm)
REVERT: A  181 TRP cc_start: 0.7881 (m-90) cc_final: 0.7646 (m-90)
REVERT: A  235 LYS cc_start: 0.7789 (mttt) cc_final: 0.7490 (mtpp)
REVERT: A  239 ARG cc_start: 0.6867 (mtp180) cc_final: 0.6557 (ptm160)
REVERT: A  323 TRP cc_start: 0.8089 (p-90) cc_final: 0.7758 (t60)
REVERT: A  328 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8461 (t80)
REVERT: A  339 ASN cc_start: 0.8529 (m-40) cc_final: 0.8224 (m110)
REVERT: B   78 ASP cc_start: 0.8134 (m-30) cc_final: 0.7860 (m-30)
REVERT: H   79 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7731 (pttt)
REVERT: H   83 TYR cc_start: 0.8039 (m-80) cc_final: 0.7587 (m-80)
REVERT: L  109 ARG cc_start: 0.7878 (ptm160) cc_final: 0.7474 (ptm160)
REVERT: L  150 LYS cc_start: 0.8257 (mttt) cc_final: 0.7778 (mmmt)
REVERT: L  170 LYS cc_start: 0.8301 (tmmt) cc_final: 0.8092 (tmmt)
REVERT: L  177 SER cc_start: 0.8874 (m) cc_final: 0.8537 (p)
REVERT: L  196 GLU cc_start: 0.7951 (tt0) cc_final: 0.7425 (pt0)
  outliers start: 23
  outliers final: 21
  residues processed: 188
  average time/residue: 0.1815
  time to fit residues: 47.5671
Evaluate side-chains
  193 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
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  114 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  328 PHE
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   84 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  245 ASN
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   97 VAL
Chi-restraints excluded: chain L residue  126 LEU
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 20 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0040
   chunk 6 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.8796

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.166225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.119417 restraints weight = 11260.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.65
r_work: 0.3428 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.4629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8271  Z= 0.291
  Angle     :  0.657  11.177  11279  Z= 0.323
  Chirality :  0.044   0.232   1308
  Planarity :  0.005   0.081   1413
  Dihedral  :  6.566  80.013   1163
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.34 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.26), residues: 1023
  helix:  1.53 (0.32), residues: 264
  sheet: -0.83 (0.28), residues: 348
  loop : -0.16 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 182 
 HIS   0.011   0.001   HIS L 190 
 PHE   0.025   0.002   PHE H 132 
 TYR   0.022   0.002   TYR L 141 
 ARG   0.008   0.001   ARG H  90 

********************** 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
  203 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TRP cc_start: 0.6128 (t-100) cc_final: 0.5823 (t-100)
REVERT: A  153 MET cc_start: 0.8940 (tpp) cc_final: 0.8463 (mmm)
REVERT: A  181 TRP cc_start: 0.7926 (m-90) cc_final: 0.7683 (m-90)
REVERT: A  235 LYS cc_start: 0.7777 (mttt) cc_final: 0.7472 (mtpp)
REVERT: A  239 ARG cc_start: 0.7029 (mtp180) cc_final: 0.6714 (ptm160)
REVERT: A  323 TRP cc_start: 0.8109 (p-90) cc_final: 0.7773 (t60)
REVERT: A  328 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8320 (t80)
REVERT: A  339 ASN cc_start: 0.8541 (m-40) cc_final: 0.8261 (m110)
REVERT: B   78 ASP cc_start: 0.8198 (m-30) cc_final: 0.7910 (m-30)
REVERT: B  285 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7707 (mtp85)
REVERT: H   79 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7907 (pttt)
REVERT: H   83 TYR cc_start: 0.8189 (m-80) cc_final: 0.7785 (m-80)
REVERT: L  109 ARG cc_start: 0.7856 (ptm160) cc_final: 0.7380 (ptm160)
REVERT: L  150 LYS cc_start: 0.8253 (mttt) cc_final: 0.7726 (mmmt)
REVERT: L  177 SER cc_start: 0.8902 (m) cc_final: 0.8641 (p)
REVERT: L  196 GLU cc_start: 0.7909 (tt0) cc_final: 0.7402 (pt0)
  outliers start: 23
  outliers final: 21
  residues processed: 194
  average time/residue: 0.1889
  time to fit residues: 50.4176
Evaluate side-chains
  194 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
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  192 CYS
Chi-restraints excluded: chain A residue  328 PHE
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   84 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  245 ASN
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   97 VAL
Chi-restraints excluded: chain L residue  126 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0030
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.3596

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.161698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.114827 restraints weight = 11280.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.59
r_work: 0.3323 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.4897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.097   8271  Z= 0.401
  Angle     :  0.714  10.812  11279  Z= 0.355
  Chirality :  0.046   0.250   1308
  Planarity :  0.005   0.084   1413
  Dihedral  :  6.622  84.686   1163
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 23.45 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.26), residues: 1023
  helix:  1.47 (0.32), residues: 264
  sheet: -0.98 (0.28), residues: 343
  loop : -0.32 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 182 
 HIS   0.010   0.002   HIS L 190 
 PHE   0.024   0.002   PHE H 132 
 TYR   0.028   0.002   TYR B 113 
 ARG   0.007   0.001   ARG H  90 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4709.68 seconds
wall clock time: 84 minutes 5.01 seconds (5045.01 seconds total)