Starting phenix.real_space_refine
on Wed Mar 12 20:35:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tko_10515/03_2025/6tko_10515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tko_10515/03_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_10515/03_2025/6tko_10515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tko_10515/03_2025/6tko_10515.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tko_10515/03_2025/6tko_10515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tko_10515/03_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-5624/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: 4.86, per 1000 atoms: 0.60
  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: 2.14
  Conformation dependent library (CDL) restraints added in 906.6 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: 1.01
  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: 2.28

  Time building geometry restraints manager: 2.48 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 88
        2.64 -     3.21: 7440
        3.21 -     3.77: 12363
        3.77 -     4.34: 17084
        4.34 -     4.90: 28443
  Nonbonded interactions: 65418
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  13 "
            pdb=" OD1 ASN B  15 "
     model   vdw
     2.079 3.040
  nonbonded pdb=" OG  SER H  36 "
            pdb=" OG  SER H 102 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" O   HIS L 190 "
            pdb=" NH1 ARG L 212 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" OH  TYR A 193 "
            pdb=" O   VAL A 202 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   PHE B 277 "
            pdb=" ND2 ASN B 281 "
     model   vdw
     2.285 3.120
  ... (remaining 65413 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.65 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.100
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.410
-------------------------------------------------------------------------------
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  : 0.937 
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: 0.2101
  time to fit residues: 85.2161
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  : 0.832 
-------------------------------------------------------------------------------
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 = 46)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.130705 restraints weight = 11333.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.66
r_work: 0.3518 rms_B_bonded: 3.32 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 = 0.3544 r_free = 0.3544    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3544
-------------------------------------------------------------------------------
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  : 0.907 
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: 0.8814 (tpp) cc_final: 0.8472 (mmm)
REVERT: A  154 THR cc_start: 0.8311 (m) cc_final: 0.7856 (p)
REVERT: A  192 CYS cc_start: 0.4428 (t) cc_final: 0.4150 (t)
REVERT: A  221 LEU cc_start: 0.8439 (tp) cc_final: 0.8157 (tt)
REVERT: A  235 LYS cc_start: 0.7768 (mttt) cc_final: 0.7384 (mtpp)
REVERT: A  339 ASN cc_start: 0.8595 (m-40) cc_final: 0.8313 (m110)
REVERT: B  346 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7462 (mt-10)
REVERT: H   68 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8146 (ttpp)
REVERT: H   83 TYR cc_start: 0.8126 (m-80) cc_final: 0.7811 (m-80)
REVERT: H  120 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8567 (m)
REVERT: H  220 LYS cc_start: 0.8800 (pptt) cc_final: 0.8315 (pptt)
REVERT: L   71 ASP cc_start: 0.8224 (m-30) cc_final: 0.8018 (m-30)
REVERT: L   91 GLN cc_start: 0.8682 (pp30) cc_final: 0.8303 (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: 0.8545 (tttm)
REVERT: L  150 LYS cc_start: 0.8334 (mttt) cc_final: 0.7932 (mmmt)
REVERT: L  178 SER cc_start: 0.8206 (t) cc_final: 0.7849 (t)
  outliers start: 28
  outliers final: 17
  residues processed: 227
  average time/residue: 0.1988
  time to fit residues: 61.1688
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  : 0.901 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 31 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0470
   chunk 64 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.3478

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.173997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.130021 restraints weight = 11465.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 2.68
r_work: 0.3510 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8271  Z= 0.201
  Angle     :  0.585   8.115  11279  Z= 0.292
  Chirality :  0.042   0.174   1308
  Planarity :  0.004   0.034   1413
  Dihedral  :  6.913  83.533   1163
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.27 %
    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: -0.26 (0.26), residues: 1023
  helix:  1.64 (0.31), residues: 259
  sheet: -0.94 (0.28), residues: 318
  loop : -0.55 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 181 
 HIS   0.005   0.001   HIS L 190 
 PHE   0.024   0.002   PHE H 156 
 TYR   0.015   0.001   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
  221 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8917 (tpp) cc_final: 0.8529 (mmm)
REVERT: A  154 THR cc_start: 0.8440 (m) cc_final: 0.8092 (m)
REVERT: A  184 ASP cc_start: 0.7086 (t0) cc_final: 0.6883 (t70)
REVERT: A  226 VAL cc_start: 0.7925 (p) cc_final: 0.7707 (p)
REVERT: A  235 LYS cc_start: 0.7766 (mttt) cc_final: 0.7352 (mtpp)
REVERT: A  323 TRP cc_start: 0.8343 (p-90) cc_final: 0.7880 (t60)
REVERT: A  339 ASN cc_start: 0.8500 (m-40) cc_final: 0.8187 (m-40)
REVERT: H   68 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8193 (ttpp)
REVERT: H   83 TYR cc_start: 0.8144 (m-80) cc_final: 0.7882 (m-80)
REVERT: H  119 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.6663 (t)
REVERT: L   25 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7646 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8093 (m-30) cc_final: 0.7837 (m-30)
REVERT: L   91 GLN cc_start: 0.8626 (pp30) cc_final: 0.8350 (pp30)
REVERT: L  109 ARG cc_start: 0.7860 (ptm160) cc_final: 0.7592 (ptm160)
REVERT: L  133 VAL cc_start: 0.8307 (t) cc_final: 0.7992 (m)
REVERT: L  146 LYS cc_start: 0.8763 (tptm) cc_final: 0.8550 (tttm)
REVERT: L  150 LYS cc_start: 0.8264 (mttt) cc_final: 0.7776 (mmmt)
REVERT: L  170 LYS cc_start: 0.8352 (tmmt) cc_final: 0.8120 (tmmt)
REVERT: L  177 SER cc_start: 0.8534 (m) cc_final: 0.8024 (m)
REVERT: L  196 GLU cc_start: 0.7899 (tt0) cc_final: 0.7347 (pt0)
  outliers start: 21
  outliers final: 13
  residues processed: 215
  average time/residue: 0.1979
  time to fit residues: 58.8234
Evaluate side-chains
  198 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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  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   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:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 89 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0970
   chunk 55 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 94 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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
** L  90 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 = 0.4165 r_free = 0.4165 target = 0.170741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.126040 restraints weight = 11308.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.64
r_work: 0.3475 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3533
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3533 r_free = 0.3533    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 = 0.3533 r_free = 0.3533    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8271  Z= 0.241
  Angle     :  0.588  10.525  11279  Z= 0.292
  Chirality :  0.043   0.231   1308
  Planarity :  0.004   0.084   1413
  Dihedral  :  6.818  82.594   1163
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.49 %
    Favored  : 77.95 %
  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:  1.67 (0.31), residues: 259
  sheet: -0.83 (0.29), residues: 321
  loop : -0.40 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 182 
 HIS   0.007   0.001   HIS L 190 
 PHE   0.022   0.002   PHE H 132 
 TYR   0.017   0.002   TYR B 113 
 ARG   0.004   0.000   ARG B 236 

*********************** 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
  211 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8976 (tpp) cc_final: 0.8456 (mmm)
REVERT: A  154 THR cc_start: 0.8479 (m) cc_final: 0.8101 (m)
REVERT: A  235 LYS cc_start: 0.7752 (mttt) cc_final: 0.7450 (mtpp)
REVERT: A  323 TRP cc_start: 0.8328 (p-90) cc_final: 0.7978 (t60)
REVERT: A  339 ASN cc_start: 0.8475 (m-40) cc_final: 0.8181 (m-40)
REVERT: B   85 GLN cc_start: 0.8445 (tp40) cc_final: 0.8185 (tp40)
REVERT: B  138 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8309 (mttp)
REVERT: B  204 ASP cc_start: 0.6595 (p0) cc_final: 0.6357 (p0)
REVERT: H   83 TYR cc_start: 0.8159 (m-80) cc_final: 0.7931 (m-80)
REVERT: H  119 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.6862 (t)
REVERT: L   25 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7683 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8042 (m-30) cc_final: 0.7769 (m-30)
REVERT: L   91 GLN cc_start: 0.8750 (pp30) cc_final: 0.8347 (pp30)
REVERT: L  109 ARG cc_start: 0.7902 (ptm160) cc_final: 0.7645 (ptm160)
REVERT: L  150 LYS cc_start: 0.8247 (mttt) cc_final: 0.7781 (mmmt)
REVERT: L  170 LYS cc_start: 0.8335 (tmmt) cc_final: 0.8054 (tmmt)
REVERT: L  177 SER cc_start: 0.8558 (m) cc_final: 0.8083 (m)
REVERT: L  196 GLU cc_start: 0.7856 (tt0) cc_final: 0.7409 (pt0)
  outliers start: 22
  outliers final: 19
  residues processed: 205
  average time/residue: 0.1823
  time to fit residues: 52.0097
Evaluate side-chains
  196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 176
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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 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:    0.9980
   chunk 10 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 95 optimal weight:    6.9990
   chunk 43 optimal weight:    0.1980
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0050
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
L  39 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 = 0.4154 r_free = 0.4154 target = 0.169785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.132919 restraints weight = 11075.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 3.20
r_work: 0.3427 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3506 r_free = 0.3506    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 = 0.3506 r_free = 0.3506    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8271  Z= 0.206
  Angle     :  0.574   9.330  11279  Z= 0.284
  Chirality :  0.042   0.220   1308
  Planarity :  0.004   0.073   1413
  Dihedral  :  6.701  83.046   1163
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.02 %
    Favored  : 77.95 %
  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: -0.81 (0.29), residues: 320
  loop : -0.33 (0.28), residues: 441

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   0.025   0.002   PHE H 132 
 TYR   0.020   0.001   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
  219 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 193
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.9001 (tpp) cc_final: 0.8639 (mmm)
REVERT: A  154 THR cc_start: 0.8496 (m) cc_final: 0.8129 (m)
REVERT: A  235 LYS cc_start: 0.7786 (mttt) cc_final: 0.7465 (mtpp)
REVERT: A  323 TRP cc_start: 0.8295 (p-90) cc_final: 0.7979 (t60)
REVERT: A  339 ASN cc_start: 0.8458 (m-40) cc_final: 0.8130 (m-40)
REVERT: B   85 GLN cc_start: 0.8517 (tp40) cc_final: 0.8147 (tp40)
REVERT: H   83 TYR cc_start: 0.8166 (m-80) cc_final: 0.7925 (m-80)
REVERT: H   85 GLN cc_start: 0.8050 (tp40) cc_final: 0.7735 (tp40)
REVERT: H  119 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7005 (t)
REVERT: H  155 TYR cc_start: 0.7958 (p90) cc_final: 0.7585 (p90)
REVERT: L   25 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7760 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8066 (m-30) cc_final: 0.7802 (m-30)
REVERT: L   91 GLN cc_start: 0.8686 (pp30) cc_final: 0.8345 (pp30)
REVERT: L  150 LYS cc_start: 0.8369 (mttt) cc_final: 0.7822 (mmmt)
REVERT: L  170 LYS cc_start: 0.8318 (tmmt) cc_final: 0.7996 (tmmt)
REVERT: L  177 SER cc_start: 0.8586 (m) cc_final: 0.8128 (m)
REVERT: L  196 GLU cc_start: 0.7929 (tt0) cc_final: 0.7572 (pt0)
  outliers start: 26
  outliers final: 19
  residues processed: 211
  average time/residue: 0.1805
  time to fit residues: 52.9080
Evaluate side-chains
  198 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
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  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   84 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  169 GLU
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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:    0.0770
   chunk 76 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0870
   chunk 39 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0010
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0670
   overall best weight:    0.1660

-------------------------------------------------------------------------------
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  85 GLN
** B 210 HIS ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.173781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.136606 restraints weight = 11226.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 3.32
r_work: 0.3471 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8271  Z= 0.166
  Angle     :  0.566   9.809  11279  Z= 0.279
  Chirality :  0.042   0.219   1308
  Planarity :  0.004   0.055   1413
  Dihedral  :  6.590  83.926   1163
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.07 %
    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:  0.03 (0.26), residues: 1023
  helix:  1.69 (0.31), residues: 264
  sheet: -0.69 (0.29), residues: 320
  loop : -0.33 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 182 
 HIS   0.006   0.001   HIS L 190 
 PHE   0.026   0.001   PHE H 132 
 TYR   0.028   0.002   TYR A 193 
 ARG   0.004   0.000   ARG A 183 

*********************** 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
  215 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 ASP cc_start: 0.6166 (OUTLIER) cc_final: 0.5577 (m-30)
REVERT: A  193 TYR cc_start: 0.7589 (m-10) cc_final: 0.7196 (m-80)
REVERT: A  235 LYS cc_start: 0.7770 (mttt) cc_final: 0.7451 (mtpp)
REVERT: A  323 TRP cc_start: 0.8285 (p-90) cc_final: 0.7995 (t60)
REVERT: A  339 ASN cc_start: 0.8408 (m-40) cc_final: 0.8097 (m-40)
REVERT: B   22 LEU cc_start: 0.8460 (mp) cc_final: 0.8244 (mp)
REVERT: H   83 TYR cc_start: 0.8123 (m-80) cc_final: 0.7737 (m-80)
REVERT: H  119 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.6475 (t)
REVERT: H  155 TYR cc_start: 0.7851 (p90) cc_final: 0.7544 (p90)
REVERT: L   25 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7718 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8006 (m-30) cc_final: 0.7752 (m-30)
REVERT: L   91 GLN cc_start: 0.8627 (pp30) cc_final: 0.8329 (pp30)
REVERT: L  109 ARG cc_start: 0.7666 (ptm160) cc_final: 0.7325 (ptm160)
REVERT: L  150 LYS cc_start: 0.8227 (mttt) cc_final: 0.7735 (mmmt)
REVERT: L  177 SER cc_start: 0.8631 (m) cc_final: 0.8312 (m)
REVERT: L  196 GLU cc_start: 0.7900 (tt0) cc_final: 0.7524 (pt0)
  outliers start: 24
  outliers final: 17
  residues processed: 206
  average time/residue: 0.1751
  time to fit residues: 50.7531
Evaluate side-chains
  199 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
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  184 ASP
Chi-restraints excluded: chain A residue  192 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  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   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  126 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 22 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 24 optimal weight:    0.2980
   chunk 31 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 GLN
B 210 HIS
** 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 = 0.4157 r_free = 0.4157 target = 0.170891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.125041 restraints weight = 11360.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.67
r_work: 0.3451 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    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 = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.4161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8271  Z= 0.221
  Angle     :  0.602   9.528  11279  Z= 0.294
  Chirality :  0.043   0.215   1308
  Planarity :  0.004   0.083   1413
  Dihedral  :  6.529  82.502   1163
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.54 %
    Favored  : 76.78 %
  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:  0.04 (0.26), residues: 1023
  helix:  1.69 (0.31), residues: 264
  sheet: -0.65 (0.29), residues: 320
  loop : -0.34 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 182 
 HIS   0.010   0.001   HIS L 190 
 PHE   0.026   0.002   PHE H 132 
 TYR   0.025   0.002   TYR L 141 
 ARG   0.003   0.000   ARG B 236 

*********************** 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
  201 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5702 (m-30)
REVERT: A  193 TYR cc_start: 0.7657 (m-10) cc_final: 0.7453 (m-80)
REVERT: A  235 LYS cc_start: 0.7781 (mttt) cc_final: 0.7493 (mtpp)
REVERT: A  239 ARG cc_start: 0.6730 (mtp180) cc_final: 0.6514 (ptm160)
REVERT: A  323 TRP cc_start: 0.8268 (p-90) cc_final: 0.7997 (t60)
REVERT: A  339 ASN cc_start: 0.8517 (m-40) cc_final: 0.8178 (m-40)
REVERT: B   58 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8481 (t)
REVERT: H   76 ASP cc_start: 0.8019 (t0) cc_final: 0.7743 (t0)
REVERT: H   79 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7549 (pttt)
REVERT: H   83 TYR cc_start: 0.7953 (m-80) cc_final: 0.7444 (m-80)
REVERT: H  119 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.6884 (t)
REVERT: L   25 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7629 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8055 (m-30) cc_final: 0.7760 (m-30)
REVERT: L   91 GLN cc_start: 0.8636 (pp30) cc_final: 0.8236 (pp30)
REVERT: L  109 ARG cc_start: 0.7694 (ptm160) cc_final: 0.7180 (ptm160)
REVERT: L  177 SER cc_start: 0.8785 (m) cc_final: 0.8383 (m)
REVERT: L  196 GLU cc_start: 0.7925 (tt0) cc_final: 0.7301 (pt0)
  outliers start: 23
  outliers final: 19
  residues processed: 195
  average time/residue: 0.1656
  time to fit residues: 46.1250
Evaluate side-chains
  192 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
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  184 ASP
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 45 optimal weight:    0.1980
   chunk 46 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0770
   chunk 5 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
A 329 ASN
H 181 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 = 0.4157 r_free = 0.4157 target = 0.170410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.125537 restraints weight = 11265.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.62
r_work: 0.3466 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8271  Z= 0.197
  Angle     :  0.607  10.258  11279  Z= 0.295
  Chirality :  0.042   0.207   1308
  Planarity :  0.004   0.088   1413
  Dihedral  :  6.487  82.513   1163
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.35 %
    Favored  : 75.38 %
  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:  0.13 (0.26), residues: 1023
  helix:  1.71 (0.32), residues: 264
  sheet: -0.61 (0.29), residues: 332
  loop : -0.21 (0.29), residues: 427

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   0.023   0.001   PHE H 132 
 TYR   0.022   0.002   TYR L 141 
 ARG   0.003   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
  214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 186
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8957 (tpp) cc_final: 0.8361 (mmm)
REVERT: A  184 ASP cc_start: 0.6035 (OUTLIER) cc_final: 0.5457 (m-30)
REVERT: A  193 TYR cc_start: 0.7633 (m-10) cc_final: 0.7388 (m-80)
REVERT: A  235 LYS cc_start: 0.7738 (mttt) cc_final: 0.7447 (mtpp)
REVERT: A  239 ARG cc_start: 0.6760 (mtp180) cc_final: 0.6559 (ptm160)
REVERT: A  323 TRP cc_start: 0.8236 (p-90) cc_final: 0.7968 (t60)
REVERT: A  339 ASN cc_start: 0.8538 (m-40) cc_final: 0.8261 (m110)
REVERT: B   58 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8502 (t)
REVERT: H   76 ASP cc_start: 0.7973 (t0) cc_final: 0.7717 (t0)
REVERT: H   79 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7520 (pttt)
REVERT: H   83 TYR cc_start: 0.7962 (m-80) cc_final: 0.7456 (m-80)
REVERT: H  119 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.6874 (t)
REVERT: L   23 THR cc_start: 0.8320 (m) cc_final: 0.8060 (p)
REVERT: L   25 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7653 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8035 (m-30) cc_final: 0.7660 (m-30)
REVERT: L   91 GLN cc_start: 0.8706 (pp30) cc_final: 0.8216 (pp30)
REVERT: L  109 ARG cc_start: 0.7675 (ptm160) cc_final: 0.7149 (ptm160)
REVERT: L  177 SER cc_start: 0.8787 (m) cc_final: 0.8393 (m)
REVERT: L  196 GLU cc_start: 0.7925 (tt0) cc_final: 0.7518 (pt0)
  outliers start: 28
  outliers final: 22
  residues processed: 204
  average time/residue: 0.1688
  time to fit residues: 48.8738
Evaluate side-chains
  204 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
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  184 ASP
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
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   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:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 61 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 57 optimal weight:    0.4980
   chunk 101 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0970
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** 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 = 0.4144 r_free = 0.4144 target = 0.169402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.124407 restraints weight = 11386.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.62
r_work: 0.3449 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.4405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8271  Z= 0.211
  Angle     :  0.635  11.115  11279  Z= 0.307
  Chirality :  0.043   0.210   1308
  Planarity :  0.004   0.082   1413
  Dihedral  :  6.485  82.025   1163
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 23.22 %
    Favored  : 73.75 %
  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:  0.18 (0.26), residues: 1023
  helix:  1.74 (0.32), residues: 264
  sheet: -0.59 (0.29), residues: 332
  loop : -0.16 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 181 
 HIS   0.011   0.001   HIS L 190 
 PHE   0.029   0.002   PHE H 132 
 TYR   0.021   0.002   TYR H 155 
 ARG   0.003   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
  209 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8937 (tpp) cc_final: 0.8360 (mmm)
REVERT: A  154 THR cc_start: 0.8518 (m) cc_final: 0.8212 (p)
REVERT: A  184 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5549 (m-30)
REVERT: A  235 LYS cc_start: 0.7739 (mttt) cc_final: 0.7403 (mtpp)
REVERT: A  239 ARG cc_start: 0.6756 (mtp180) cc_final: 0.6552 (ptm160)
REVERT: A  323 TRP cc_start: 0.8206 (p-90) cc_final: 0.7925 (t60)
REVERT: A  339 ASN cc_start: 0.8528 (m-40) cc_final: 0.8261 (m110)
REVERT: B   58 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8506 (t)
REVERT: H    9 GLU cc_start: 0.7339 (pm20) cc_final: 0.7108 (pm20)
REVERT: H   68 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8434 (ttpp)
REVERT: H  119 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.6866 (t)
REVERT: L   23 THR cc_start: 0.8399 (m) cc_final: 0.8098 (p)
REVERT: L   25 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7646 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8040 (m-30) cc_final: 0.7635 (m-30)
REVERT: L  109 ARG cc_start: 0.7701 (ptm160) cc_final: 0.7162 (ptm160)
REVERT: L  150 LYS cc_start: 0.8202 (mttt) cc_final: 0.7517 (mmmt)
REVERT: L  177 SER cc_start: 0.8762 (m) cc_final: 0.8544 (p)
REVERT: L  196 GLU cc_start: 0.7947 (tt0) cc_final: 0.7563 (pt0)
  outliers start: 26
  outliers final: 22
  residues processed: 201
  average time/residue: 0.1666
  time to fit residues: 47.3764
Evaluate side-chains
  203 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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  184 ASP
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  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   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain L residue   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:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0870
   chunk 6 optimal weight:    0.3980
   chunk 95 optimal weight:    0.0770
   chunk 48 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.4916

-------------------------------------------------------------------------------
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 = 0.4153 r_free = 0.4153 target = 0.170194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.132316 restraints weight = 11189.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 3.21
r_work: 0.3411 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3491
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3491 r_free = 0.3491    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 = 0.3491 r_free = 0.3491    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3491
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.4542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8271  Z= 0.218
  Angle     :  0.643  11.766  11279  Z= 0.313
  Chirality :  0.043   0.217   1308
  Planarity :  0.005   0.082   1413
  Dihedral  :  6.472  81.548   1163
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.87 %
    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:  0.17 (0.26), residues: 1023
  helix:  1.69 (0.32), residues: 264
  sheet: -0.59 (0.29), residues: 332
  loop : -0.14 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 181 
 HIS   0.011   0.001   HIS L 190 
 PHE   0.027   0.002   PHE H 132 
 TYR   0.021   0.002   TYR H 155 
 ARG   0.005   0.000   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
  204 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 177
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8898 (tpp) cc_final: 0.8354 (mmm)
REVERT: A  154 THR cc_start: 0.8540 (m) cc_final: 0.8230 (p)
REVERT: A  184 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.5632 (m-30)
REVERT: A  235 LYS cc_start: 0.7739 (mttt) cc_final: 0.7413 (mtpp)
REVERT: A  323 TRP cc_start: 0.8202 (p-90) cc_final: 0.7970 (t60)
REVERT: A  328 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8138 (t80)
REVERT: A  339 ASN cc_start: 0.8553 (m-40) cc_final: 0.8305 (m110)
REVERT: B   58 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8523 (t)
REVERT: H   79 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7839 (pttt)
REVERT: H  119 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7346 (p)
REVERT: L   23 THR cc_start: 0.8452 (m) cc_final: 0.8207 (p)
REVERT: L   25 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7717 (mtp-110)
REVERT: L   71 ASP cc_start: 0.8099 (m-30) cc_final: 0.7685 (m-30)
REVERT: L  109 ARG cc_start: 0.7734 (ptm160) cc_final: 0.7185 (ptm160)
REVERT: L  177 SER cc_start: 0.8808 (m) cc_final: 0.8381 (m)
REVERT: L  196 GLU cc_start: 0.7906 (tt0) cc_final: 0.7303 (pt0)
  outliers start: 27
  outliers final: 22
  residues processed: 197
  average time/residue: 0.1710
  time to fit residues: 47.8545
Evaluate side-chains
  199 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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  184 ASP
Chi-restraints excluded: chain A residue  225 PHE
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   55 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  172 GLN
Chi-restraints excluded: chain B residue  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   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain L residue   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:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.8984

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.165762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.120181 restraints weight = 11234.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.60
r_work: 0.3383 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    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 = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8271  Z= 0.294
  Angle     :  0.665  11.911  11279  Z= 0.326
  Chirality :  0.043   0.227   1308
  Planarity :  0.005   0.081   1413
  Dihedral  :  6.484  79.523   1163
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.34 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.77 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.04 (0.26), residues: 1023
  helix:  1.57 (0.32), residues: 264
  sheet: -0.67 (0.29), residues: 333
  loop : -0.20 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 181 
 HIS   0.009   0.001   HIS L 190 
 PHE   0.027   0.002   PHE H 132 
 TYR   0.021   0.002   TYR L 141 
 ARG   0.005   0.001   ARG A 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4906.77 seconds
wall clock time: 85 minutes 36.58 seconds (5136.58 seconds total)