Starting phenix.real_space_refine
on Thu Jun 26 08:31:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cku_45654/06_2025/9cku_45654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cku_45654/06_2025/9cku_45654.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cku_45654/06_2025/9cku_45654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cku_45654/06_2025/9cku_45654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cku_45654/06_2025/9cku_45654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cku_45654/06_2025/9cku_45654.cif"
  }
  resolution = 2.04
  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=   0.003 sd=   1.030
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
     S      52      5.16       5
     C    9534      2.51       5
     N    2721      2.21       5
     O    2992      1.98       5
     H   15361      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 30660
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "A"
      Number of atoms: 4070
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 261, 3972
          Classifications: {'peptide': 261}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
      Conformer: "A"
        Number of residues, atoms: 252, 3858
          Classifications: {'peptide': 252}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 241}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3791
    Chain: "B"
      Number of atoms: 3972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 3972
          Classifications: {'peptide': 261}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "C"
      Number of atoms: 4070
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 261, 3972
          Classifications: {'peptide': 261}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
      Conformer: "B"
        Number of residues, atoms: 253, 3877
          Classifications: {'peptide': 253}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 242}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3810
    Chain: "D"
      Number of atoms: 4089
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 261, 3972
          Classifications: {'peptide': 261}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
      Conformer: "B"
        Number of residues, atoms: 253, 3877
          Classifications: {'peptide': 253}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 242}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3791
    Chain: "E"
      Number of atoms: 4070
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 261, 3972
          Classifications: {'peptide': 261}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
      Conformer: "A"
        Number of residues, atoms: 252, 3858
          Classifications: {'peptide': 252}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 241}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3791
    Chain: "F"
      Number of atoms: 3878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 3878
          Classifications: {'peptide': 254}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 243}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 5928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 5928
          Classifications: {'peptide': 384}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 362}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 453
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 20
          Classifications: {'water': 20}
          Link IDs: {None: 19}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "C"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "D"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "E"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 20
          Classifications: {'water': 20}
          Link IDs: {None: 19}
    Chain: "F"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "G"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
  Residues with excluded nonbonded symmetry interactions: 55
    residue:
      pdb=" N  BALA A 162 " occ=0.50
      ... (8 atoms not shown)
      pdb=" HB3BALA A 162 " occ=0.50
    residue:
      pdb=" N  BALA A 163 " occ=0.50
      ... (8 atoms not shown)
      pdb=" HB3BALA A 163 " occ=0.50
    residue:
      pdb=" N  BALA A 164 " occ=0.50
      ... (8 atoms not shown)
      pdb=" HB3BALA A 164 " occ=0.50
    residue:
      pdb=" N  BALA A 165 " occ=0.50
      ... (8 atoms not shown)
      pdb=" HB3BALA A 165 " occ=0.50
    residue:
      pdb=" N  BARG A 166 " occ=0.50
      ... (22 atoms not shown)
      pdb="HH22BARG A 166 " occ=0.50
    residue:
      pdb=" N  BSER A 167 " occ=0.50
      ... (9 atoms not shown)
      pdb=" HG BSER A 167 " occ=0.50
    residue:
      pdb=" N  BALA A 168 " occ=0.50
      ... (8 atoms not shown)
      pdb=" HB3BALA A 168 " occ=0.50
    residue:
      pdb=" N  BALA A 169 " occ=0.50
      ... (8 atoms not shown)
      pdb=" HB3BALA A 169 " occ=0.50
    residue:
      pdb=" N  BLEU A 170 " occ=0.50
      ... (17 atoms not shown)
      pdb="HD23BLEU A 170 " occ=0.50
    residue:
      pdb=" N  AARG A 171 " occ=0.50
      ... (46 atoms not shown)
      pdb="HH22BARG A 171 " occ=0.50
    residue:
      pdb=" N  AARG A 172 " occ=0.50
      ... (46 atoms not shown)
      pdb="HH22BARG A 172 " occ=0.50
    residue:
      pdb=" N  AVAL A 173 " occ=0.50
      ... (30 atoms not shown)
      pdb="HG23BVAL A 173 " occ=0.50
    ... (remaining 43 not shown)
  Time building chain proxies: 20.91, per 1000 atoms: 0.68
  Number of scatterers: 30660
  At special positions: 0
  Unit cell: (99.825, 111.375, 151.8, 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      52     16.00
     O    2992      8.00
     N    2721      7.00
     C    9534      6.00
     H   15361      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 8.38
  Conformation dependent library (CDL) restraints added in 3.8 seconds
  

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3670

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 17 sheets defined
      48.3% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 24
    Processing helix  chain 'A' and resid 39 through 52
    Processing helix  chain 'A' and resid 53 through 58
      removed outlier: 3.658A  pdb=" N   GLU A  56 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A  58 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 104 through 108
    Processing helix  chain 'A' and resid 109 through 124
    Processing helix  chain 'A' and resid 159 through 167
      removed outlier: 4.185A  pdb=" N  BSER A 167 " --> pdb=" O  BALA A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 213
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 3.664A  pdb=" N   LEU A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 238
      No H-bonds generated for 'chain 'A' and resid 236 through 238'
    Processing helix  chain 'A' and resid 247 through 261
    Processing helix  chain 'B' and resid 20 through 24
    Processing helix  chain 'B' and resid 39 through 52
    Processing helix  chain 'B' and resid 53 through 58
      removed outlier: 3.509A  pdb=" N   GLU B  56 " --> pdb=" O   GLU B  53 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU B  58 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 104 through 108
    Processing helix  chain 'B' and resid 109 through 124
    Processing helix  chain 'B' and resid 159 through 167
      removed outlier: 4.119A  pdb=" N   SER B 167 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 213
    Processing helix  chain 'B' and resid 230 through 235
      removed outlier: 3.643A  pdb=" N   LEU B 234 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 238
      No H-bonds generated for 'chain 'B' and resid 236 through 238'
    Processing helix  chain 'B' and resid 247 through 261
    Processing helix  chain 'C' and resid 20 through 24
    Processing helix  chain 'C' and resid 39 through 52
    Processing helix  chain 'C' and resid 53 through 58
      removed outlier: 3.517A  pdb=" N   GLU C  56 " --> pdb=" O   GLU C  53 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU C  58 " --> pdb=" O   SER C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 104 through 108
    Processing helix  chain 'C' and resid 109 through 124
    Processing helix  chain 'C' and resid 159 through 167
      removed outlier: 4.081A  pdb=" N  ASER C 167 " --> pdb=" O  AALA C 163 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 213
    Processing helix  chain 'C' and resid 230 through 235
      removed outlier: 3.600A  pdb=" N   LEU C 234 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 238
      No H-bonds generated for 'chain 'C' and resid 236 through 238'
    Processing helix  chain 'C' and resid 247 through 261
    Processing helix  chain 'D' and resid 20 through 24
    Processing helix  chain 'D' and resid 39 through 52
    Processing helix  chain 'D' and resid 53 through 58
      removed outlier: 3.571A  pdb=" N   GLU D  56 " --> pdb=" O   GLU D  53 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU D  58 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 104 through 108
    Processing helix  chain 'D' and resid 109 through 124
    Processing helix  chain 'D' and resid 159 through 167
      removed outlier: 3.996A  pdb=" N  ASER D 167 " --> pdb=" O  AALA D 163 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 213
    Processing helix  chain 'D' and resid 230 through 235
      removed outlier: 3.711A  pdb=" N   LEU D 234 " --> pdb=" O   THR D 230 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 236 through 238
      No H-bonds generated for 'chain 'D' and resid 236 through 238'
    Processing helix  chain 'D' and resid 247 through 260
    Processing helix  chain 'E' and resid 20 through 24
    Processing helix  chain 'E' and resid 39 through 52
    Processing helix  chain 'E' and resid 53 through 58
      removed outlier: 3.621A  pdb=" N   LEU E  58 " --> pdb=" O   SER E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 67 through 82
    Processing helix  chain 'E' and resid 104 through 108
    Processing helix  chain 'E' and resid 109 through 124
    Processing helix  chain 'E' and resid 159 through 167
      removed outlier: 4.176A  pdb=" N  BSER E 167 " --> pdb=" O  BALA E 163 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 185 through 213
    Processing helix  chain 'E' and resid 230 through 235
      removed outlier: 3.598A  pdb=" N   LEU E 234 " --> pdb=" O   THR E 230 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 236 through 238
      No H-bonds generated for 'chain 'E' and resid 236 through 238'
    Processing helix  chain 'E' and resid 247 through 260
    Processing helix  chain 'F' and resid 20 through 24
    Processing helix  chain 'F' and resid 39 through 52
    Processing helix  chain 'F' and resid 53 through 58
      removed outlier: 3.671A  pdb=" N   GLU F  56 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 67 through 82
    Processing helix  chain 'F' and resid 104 through 108
    Processing helix  chain 'F' and resid 109 through 124
    Processing helix  chain 'F' and resid 185 through 213
    Processing helix  chain 'F' and resid 230 through 235
    Processing helix  chain 'F' and resid 236 through 238
      No H-bonds generated for 'chain 'F' and resid 236 through 238'
    Processing helix  chain 'F' and resid 247 through 261
    Processing helix  chain 'G' and resid 22 through 39
    Processing helix  chain 'G' and resid 108 through 132
    Processing helix  chain 'G' and resid 166 through 181
      Proline residue:  G 176  - end of helix
    Processing helix  chain 'G' and resid 181 through 186
    Processing helix  chain 'G' and resid 205 through 208
      removed outlier: 4.163A  pdb=" N   ASP G 208 " --> pdb=" O   GLN G 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 205 through 208'
    Processing helix  chain 'G' and resid 251 through 271
      removed outlier: 3.649A  pdb=" N   THR G 262 " --> pdb=" O   LYS G 258 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 275 through 279
    Processing helix  chain 'G' and resid 282 through 292
      removed outlier: 3.600A  pdb=" N   HIS G 288 " --> pdb=" O   VAL G 284 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 310 through 327
    Processing helix  chain 'G' and resid 331 through 351
    Processing helix  chain 'G' and resid 352 through 356
    Processing helix  chain 'G' and resid 359 through 376
    Processing helix  chain 'G' and resid 381 through 392
      removed outlier: 4.436A  pdb=" N   SER G 392 " --> pdb=" O   ASP G 388 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 399 through 407
    Processing helix  chain 'G' and resid 415 through 423
    Processing helix  chain 'H' and resid 36 through 47
      removed outlier: 3.768A  pdb=" N   VAL H  46 " --> pdb=" O   GLU H  42 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 50 through 58
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 33
      removed outlier: 5.434A  pdb=" N   VAL A  26 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   SER A  18 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   THR A  61 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ILE A  90 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ALA A  63 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 154
      removed outlier: 6.602A  pdb=" N   VAL A 140 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLY A 150 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL A 138 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ILE A 152 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE A 136 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 33
      removed outlier: 5.613A  pdb=" N   VAL B  26 " --> pdb=" O   SER B  18 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   SER B  18 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   THR B  61 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   ILE B  90 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ALA B  63 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 154
      removed outlier: 3.926A  pdb=" N   GLY B 149 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 33
      removed outlier: 5.556A  pdb=" N   VAL C  26 " --> pdb=" O   SER C  18 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   SER C  18 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 154
      removed outlier: 3.941A  pdb=" N   GLY C 149 " --> pdb=" O   VAL C 140 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 33
      removed outlier: 5.592A  pdb=" N   VAL D  26 " --> pdb=" O   SER D  18 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   SER D  18 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   THR D  61 " --> pdb=" O   VAL D  88 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 154
      removed outlier: 3.936A  pdb=" N   GLY D 149 " --> pdb=" O   VAL D 140 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 25 through 33
      removed outlier: 5.555A  pdb=" N   VAL E  26 " --> pdb=" O   SER E  18 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   SER E  18 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 147 through 154
      removed outlier: 6.316A  pdb=" N   VAL E 140 " --> pdb=" O   LEU E 148 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLY E 150 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL E 138 " --> pdb=" O   GLY E 150 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   ILE E 152 " --> pdb=" O   ILE E 136 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE E 136 " --> pdb=" O   ILE E 152 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 25 through 33
      removed outlier: 5.514A  pdb=" N   VAL F  26 " --> pdb=" O   SER F  18 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   SER F  18 " --> pdb=" O   VAL F  26 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   THR F  61 " --> pdb=" O   VAL F  88 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 147 through 154
      removed outlier: 4.055A  pdb=" N   GLY F 149 " --> pdb=" O   VAL F 140 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 84 through 85
    Processing sheet with id=AB5, first strand: chain 'G' and resid 12 through 14
    Processing sheet with id=AB6, first strand: chain 'G' and resid 189 through 192
      removed outlier: 6.025A  pdb=" N   GLY G 200 " --> pdb=" O   GLY G 191 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 210 through 215
      removed outlier: 7.256A  pdb=" N   ILE G 224 " --> pdb=" O   GLU G 211 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   GLU G 213 " --> pdb=" O   ILE G 224 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   ASN G 226 " --> pdb=" O   GLU G 213 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   GLY G 215 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 299 through 301

    860 hydrogen bonds defined for protein.
    2403 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: 13.19

  Time building geometry restraints manager: 10.15 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 15341
        1.03 -     1.23: 314
        1.23 -     1.43: 5920
        1.43 -     1.62: 9117
        1.62 -     1.82: 84
  Bond restraints: 30776
  Sorted by residual:
  bond pdb=" N   GLY F 193 "
       pdb=" CA  GLY F 193 "
    ideal  model  delta    sigma   weight residual
    1.454  1.436  0.017 1.29e-02 6.01e+03 1.83e+00
  bond pdb=" CB  VAL B 173 "
       pdb=" CG2 VAL B 173 "
    ideal  model  delta    sigma   weight residual
    1.521  1.557 -0.036 3.30e-02 9.18e+02 1.21e+00
  bond pdb=" C   GLY F 193 "
       pdb=" O   GLY F 193 "
    ideal  model  delta    sigma   weight residual
    1.234  1.221  0.013 1.20e-02 6.94e+03 1.10e+00
  bond pdb=" CB  VAL F  85 "
       pdb=" CG1 VAL F  85 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.09e+00
  bond pdb=" N   GLY E 150 "
       pdb=" CA  GLY E 150 "
    ideal  model  delta    sigma   weight residual
    1.455  1.444  0.011 1.05e-02 9.07e+03 1.08e+00
  ... (remaining 30771 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.38: 55753
        5.38 -    10.76: 19
       10.76 -    16.13: 2
       16.13 -    21.51: 0
       21.51 -    26.89: 9
  Bond angle restraints: 55783
  Sorted by residual:
  angle pdb=" CG1AVAL C 173 "
        pdb=" CB AVAL C 173 "
        pdb=" HB AVAL C 173 "
      ideal   model   delta    sigma   weight residual
     108.00   81.11   26.89 3.00e+00 1.11e-01 8.03e+01
  angle pdb=" CG1 VAL B 173 "
        pdb=" CB  VAL B 173 "
        pdb=" HB  VAL B 173 "
      ideal   model   delta    sigma   weight residual
     108.00   81.12   26.88 3.00e+00 1.11e-01 8.03e+01
  angle pdb=" CG2AVAL C 173 "
        pdb=" CB AVAL C 173 "
        pdb=" HB AVAL C 173 "
      ideal   model   delta    sigma   weight residual
     108.00   81.15   26.85 3.00e+00 1.11e-01 8.01e+01
  angle pdb=" CG2 VAL B 173 "
        pdb=" CB  VAL B 173 "
        pdb=" HB  VAL B 173 "
      ideal   model   delta    sigma   weight residual
     108.00   81.17   26.83 3.00e+00 1.11e-01 8.00e+01
  angle pdb=" CG2AVAL D 173 "
        pdb=" CB AVAL D 173 "
        pdb=" HB AVAL D 173 "
      ideal   model   delta    sigma   weight residual
     108.00   81.28   26.72 3.00e+00 1.11e-01 7.93e+01
  ... (remaining 55778 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 13332
       17.71 -    35.42: 606
       35.42 -    53.13: 261
       53.13 -    70.84: 83
       70.84 -    88.56: 10
  Dihedral angle restraints: 14292
    sinusoidal: 7954
      harmonic: 6338
  Sorted by residual:
  dihedral pdb=" CA  ASN G  88 "
           pdb=" C   ASN G  88 "
           pdb=" N   GLY G  89 "
           pdb=" CA  GLY G  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.17  -19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  TYR G 153 "
           pdb=" C   TYR G 153 "
           pdb=" N   GLY G 154 "
           pdb=" CA  GLY G 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.64  -18.36     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ASP G 247 "
           pdb=" C   ASP G 247 "
           pdb=" N   ALA G 248 "
           pdb=" CA  ALA G 248 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.28   17.72     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 14289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.273: 2510
       0.273 -    0.547: 0
       0.547 -    0.820: 0
       0.820 -    1.094: 0
       1.094 -    1.367: 3
  Chirality restraints: 2513
  Sorted by residual:
  chirality pdb=" CB AVAL D 173 "
            pdb=" CA AVAL D 173 "
            pdb=" CG1AVAL D 173 "
            pdb=" CG2AVAL D 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.26   -1.37 2.00e-01 2.50e+01 4.67e+01
  chirality pdb=" CB AVAL C 173 "
            pdb=" CA AVAL C 173 "
            pdb=" CG1AVAL C 173 "
            pdb=" CG2AVAL C 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.28   -1.35 2.00e-01 2.50e+01 4.53e+01
  chirality pdb=" CB  VAL B 173 "
            pdb=" CA  VAL B 173 "
            pdb=" CG1 VAL B 173 "
            pdb=" CG2 VAL B 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.31   -1.32 2.00e-01 2.50e+01 4.38e+01
  ... (remaining 2510 not shown)

  Planarity restraints: 4629
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 210 "   -0.076 9.50e-02 1.11e+02   3.59e-02 1.51e+01
        pdb=" NE  ARG F 210 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 210 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 210 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 210 "   -0.050 2.00e-02 2.50e+03
        pdb="HH11 ARG F 210 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG F 210 "   -0.011 2.00e-02 2.50e+03
        pdb="HH21 ARG F 210 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG F 210 "    0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 210 "   -0.132 9.50e-02 1.11e+02   5.00e-02 1.48e+01
        pdb=" NE  ARG D 210 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 210 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 210 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 210 "   -0.051 2.00e-02 2.50e+03
        pdb="HH11 ARG D 210 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG D 210 "   -0.011 2.00e-02 2.50e+03
        pdb="HH21 ARG D 210 "   -0.005 2.00e-02 2.50e+03
        pdb="HH22 ARG D 210 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 210 "   -0.140 9.50e-02 1.11e+02   5.13e-02 1.26e+01
        pdb=" NE  ARG E 210 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 210 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 210 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 210 "   -0.047 2.00e-02 2.50e+03
        pdb="HH11 ARG E 210 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG E 210 "   -0.007 2.00e-02 2.50e+03
        pdb="HH21 ARG E 210 "   -0.004 2.00e-02 2.50e+03
        pdb="HH22 ARG E 210 "    0.038 2.00e-02 2.50e+03
  ... (remaining 4626 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1273
        2.19 -     2.79: 62675
        2.79 -     3.39: 88340
        3.39 -     4.00: 119961
        4.00 -     4.60: 180923
  Nonbonded interactions: 453172
  Sorted by model distance:
  nonbonded pdb=" OE1AGLU C 174 "
            pdb=" H  AGLU C 174 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" OE1 GLU B 174 "
            pdb=" H   GLU B 174 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" O  AARG C 166 "
            pdb=" HG ASER C 167 "
     model   vdw
     1.631 2.450
  nonbonded pdb=" OD2 ASP G 116 "
            pdb=" HZ3 LYS G 143 "
     model   vdw
     1.643 2.450
  nonbonded pdb=" O   ARG B 166 "
            pdb=" HG  SER B 167 "
     model   vdw
     1.669 2.450
  ... (remaining 453167 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ 
h 261))
  selection = (chain 'B' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ 
h 261))
  selection = (chain 'C' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ 
h 261))
  selection = (chain 'D' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ 
h 261))
  selection = (chain 'E' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name OD1 or name OD2)) or resid 176 throug \ 
h 261))
  selection = (chain 'F' and (resid 1 through 161 or resid 176 through 261))
}

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=0.50 max=1.00 mean=0.98
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:             3.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.530
  Extract box with map and model:          1.150
  Check model and map are aligned:         0.190
  Set scattering table:                    0.240
  Process input model:                     76.100
  Find NCS groups from input model:        0.920
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   97.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
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      :  0.004   0.045  15415  Z= 0.211
  Angle     :  0.674  10.989  20966  Z= 0.374
  Chirality :  0.068   1.367   2513
  Planarity :  0.006   0.083   2728
  Dihedral  : 11.841  88.556   5621
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.44 (0.18), residues: 1974
  helix:  2.06 (0.18), residues: 735
  sheet:  1.16 (0.24), residues: 393
  loop : -0.09 (0.19), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.005   0.001   HIS E  87 
 PHE   0.016   0.002   PHE E 198 
 TYR   0.014   0.002   TYR G  34 
 ARG   0.015   0.001   ARG B 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10345 (  860)
  hydrogen bonds       : angle       5.81079 ( 2403)
  covalent geometry    : bond        0.00445 (15415)
  covalent geometry    : angle       0.67354 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 2.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8182 (mtp) cc_final: 0.7818 (mtm)
REVERT: A   21 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7882 (mmmm)
REVERT: A   91 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7627 (tp30)
REVERT: B    1 MET cc_start: 0.8475 (mtp) cc_final: 0.8270 (mtp)
REVERT: B   23 HIS cc_start: 0.7773 (m-70) cc_final: 0.7472 (m90)
REVERT: B   87 HIS cc_start: 0.8449 (p90) cc_final: 0.7799 (m90)
REVERT: C   20 MET cc_start: 0.7855 (mtp) cc_final: 0.7410 (mmt)
REVERT: C   87 HIS cc_start: 0.8240 (p90) cc_final: 0.7793 (m-70)
REVERT: D   20 MET cc_start: 0.7685 (mtp) cc_final: 0.7041 (mpt)
REVERT: D   87 HIS cc_start: 0.8350 (p90) cc_final: 0.7948 (m-70)
REVERT: D  259 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7161 (mtt-85)
REVERT: E   53 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7607 (mp0)
REVERT: E   87 HIS cc_start: 0.8533 (p90) cc_final: 0.7900 (m90)
REVERT: F   23 HIS cc_start: 0.7902 (m-70) cc_final: 0.7623 (m90)
REVERT: F   53 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7727 (mp0)
REVERT: F  144 LYS cc_start: 0.8326 (mttt) cc_final: 0.7950 (mtmt)
REVERT: F  230 THR cc_start: 0.8818 (p) cc_final: 0.8559 (t)
  outliers start: 0
  outliers final: 1
  residues processed: 239
  average time/residue: 3.3771
  time to fit residues: 878.9778
Evaluate side-chains
  208 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 2.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   98 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    3.9990
   chunk 148 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 153 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 114 optimal weight:    3.9990
   chunk 177 optimal weight:    2.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
E 260 ASN
F 157 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.140586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.112229 restraints weight = 53770.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.36
r_work: 0.3048 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15415  Z= 0.214
  Angle     :  0.625  11.322  20966  Z= 0.346
  Chirality :  0.067   1.377   2513
  Planarity :  0.006   0.064   2728
  Dihedral  :  4.957  28.095   2163
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  7.22 %
    Favored  : 92.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.13 (0.17), residues: 1974
  helix:  1.73 (0.17), residues: 746
  sheet:  1.15 (0.25), residues: 372
  loop : -0.28 (0.19), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.013   0.001   HIS G 129 
 PHE   0.020   0.002   PHE E 198 
 TYR   0.019   0.003   TYR G  34 
 ARG   0.006   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06044 (  860)
  hydrogen bonds       : angle       5.62694 ( 2403)
  covalent geometry    : bond        0.00449 (15415)
  covalent geometry    : angle       0.62533 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 207
  time to evaluate  : 2.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8201 (mtp) cc_final: 0.7810 (mtm)
REVERT: A   21 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7795 (mmmm)
REVERT: A   91 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7632 (tp30)
REVERT: B   23 HIS cc_start: 0.7828 (m-70) cc_final: 0.7495 (m90)
REVERT: B   87 HIS cc_start: 0.8532 (p90) cc_final: 0.7713 (m90)
REVERT: B  260 ASN cc_start: 0.8416 (m-40) cc_final: 0.8174 (m110)
REVERT: C   20 MET cc_start: 0.7934 (mtp) cc_final: 0.7494 (mmt)
REVERT: C   29 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8166 (tm-30)
REVERT: C   87 HIS cc_start: 0.8418 (p90) cc_final: 0.7873 (m-70)
REVERT: D   20 MET cc_start: 0.7715 (mtp) cc_final: 0.7104 (mpt)
REVERT: D   87 HIS cc_start: 0.8417 (p90) cc_final: 0.7903 (m-70)
REVERT: D  259 ARG cc_start: 0.7618 (ttt90) cc_final: 0.7129 (mtt-85)
REVERT: F   23 HIS cc_start: 0.7897 (m-70) cc_final: 0.7590 (m90)
REVERT: F   53 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7744 (mp0)
REVERT: F  144 LYS cc_start: 0.8399 (mttt) cc_final: 0.7966 (mtmt)
REVERT: G  239 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7941 (tmt90)
  outliers start: 9
  outliers final: 7
  residues processed: 212
  average time/residue: 3.8527
  time to fit residues: 887.6070
Evaluate side-chains
  212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 203
  time to evaluate  : 2.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue  166 ARG
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue  106 LYS
Chi-restraints excluded: chain G residue  239 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 175 optimal weight:    4.9990
   chunk 138 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0870
   chunk 152 optimal weight:    0.0270
   chunk 113 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 105 optimal weight:    4.9990
   overall best weight:    1.4220

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.144699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.116617 restraints weight = 61230.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.43
r_work: 0.3058 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15415  Z= 0.135
  Angle     :  0.529  11.103  20966  Z= 0.289
  Chirality :  0.066   1.418   2513
  Planarity :  0.004   0.041   2728
  Dihedral  :  4.601  26.800   2163
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  7.65 %
    Favored  : 91.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.41 (0.18), residues: 1974
  helix:  2.09 (0.18), residues: 746
  sheet:  1.20 (0.25), residues: 372
  loop : -0.21 (0.19), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.008   0.001   HIS G 129 
 PHE   0.014   0.002   PHE E 198 
 TYR   0.011   0.002   TYR G  34 
 ARG   0.008   0.000   ARG D 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04932 (  860)
  hydrogen bonds       : angle       5.27194 ( 2403)
  covalent geometry    : bond        0.00272 (15415)
  covalent geometry    : angle       0.52898 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 211
  time to evaluate  : 2.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8188 (mtp) cc_final: 0.7819 (mtm)
REVERT: A   21 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7783 (mmmm)
REVERT: A   91 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7613 (tp30)
REVERT: B   23 HIS cc_start: 0.7790 (m-70) cc_final: 0.7454 (m90)
REVERT: B  260 ASN cc_start: 0.8375 (m-40) cc_final: 0.8108 (m110)
REVERT: C   20 MET cc_start: 0.7926 (mtp) cc_final: 0.7476 (mmt)
REVERT: C   29 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8272 (tm-30)
REVERT: C   87 HIS cc_start: 0.8376 (p90) cc_final: 0.7864 (m-70)
REVERT: D   20 MET cc_start: 0.7726 (mtp) cc_final: 0.7107 (mpt)
REVERT: D   87 HIS cc_start: 0.8418 (p90) cc_final: 0.7885 (m90)
REVERT: D  259 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7113 (mtt-85)
REVERT: E   91 GLU cc_start: 0.7058 (mp0) cc_final: 0.6525 (pm20)
REVERT: F   23 HIS cc_start: 0.7890 (m-70) cc_final: 0.7603 (m90)
REVERT: F   53 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7732 (mp0)
REVERT: F  144 LYS cc_start: 0.8397 (mttt) cc_final: 0.7964 (mtmt)
  outliers start: 11
  outliers final: 4
  residues processed: 216
  average time/residue: 3.5005
  time to fit residues: 824.3623
Evaluate side-chains
  211 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 206
  time to evaluate  : 2.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue  106 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 138 optimal weight:    2.9990
   chunk 154 optimal weight:    3.9990
   chunk 182 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 185 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 178 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 137 optimal weight:    1.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.144134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.116197 restraints weight = 59255.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.40
r_work: 0.3053 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15415  Z= 0.148
  Angle     :  0.543  11.049  20966  Z= 0.298
  Chirality :  0.066   1.418   2513
  Planarity :  0.005   0.049   2728
  Dihedral  :  4.656  27.408   2163
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  7.89 %
    Favored  : 91.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.33 (0.18), residues: 1974
  helix:  2.03 (0.18), residues: 746
  sheet:  1.14 (0.25), residues: 381
  loop : -0.26 (0.19), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.004   0.001   HIS E  72 
 PHE   0.016   0.002   PHE E 198 
 TYR   0.013   0.002   TYR G  34 
 ARG   0.008   0.001   ARG D 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05179 (  860)
  hydrogen bonds       : angle       5.32382 ( 2403)
  covalent geometry    : bond        0.00304 (15415)
  covalent geometry    : angle       0.54350 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 208
  time to evaluate  : 2.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8174 (mtp) cc_final: 0.7800 (mtm)
REVERT: A   21 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7812 (mmtm)
REVERT: A   91 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7616 (tp30)
REVERT: B   23 HIS cc_start: 0.7786 (m-70) cc_final: 0.7456 (m90)
REVERT: B  106 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7468 (mptt)
REVERT: B  260 ASN cc_start: 0.8375 (m-40) cc_final: 0.8122 (m110)
REVERT: C   20 MET cc_start: 0.7933 (mtp) cc_final: 0.7490 (mmt)
REVERT: C   29 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8267 (tm-30)
REVERT: C   87 HIS cc_start: 0.8380 (p90) cc_final: 0.7877 (m90)
REVERT: D   20 MET cc_start: 0.7742 (mtp) cc_final: 0.7120 (mpt)
REVERT: D   87 HIS cc_start: 0.8409 (p90) cc_final: 0.7880 (m-70)
REVERT: D  259 ARG cc_start: 0.7615 (ttt90) cc_final: 0.7140 (mtt-85)
REVERT: F   23 HIS cc_start: 0.7892 (m-70) cc_final: 0.7614 (m90)
REVERT: F  144 LYS cc_start: 0.8403 (mttt) cc_final: 0.7979 (mtmt)
  outliers start: 11
  outliers final: 7
  residues processed: 214
  average time/residue: 4.2099
  time to fit residues: 984.9828
Evaluate side-chains
  212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 203
  time to evaluate  : 2.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 LYS
Chi-restraints excluded: chain B residue  144 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue  166 ARG
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue  106 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 140 optimal weight:    3.9990
   chunk 142 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0170
   chunk 21 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    2.2026

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.140818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.111914 restraints weight = 59543.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.44
r_work: 0.3079 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  15415  Z= 0.173
  Angle     :  0.569  11.219  20966  Z= 0.313
  Chirality :  0.066   1.415   2513
  Planarity :  0.005   0.048   2728
  Dihedral  :  4.764  28.543   2163
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.47 %
    Favored  : 91.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.23 (0.18), residues: 1974
  helix:  1.93 (0.18), residues: 746
  sheet:  1.14 (0.25), residues: 381
  loop : -0.33 (0.19), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.005   0.001   HIS D  72 
 PHE   0.018   0.002   PHE E 198 
 TYR   0.015   0.002   TYR G  34 
 ARG   0.010   0.001   ARG D 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05506 (  860)
  hydrogen bonds       : angle       5.42152 ( 2403)
  covalent geometry    : bond        0.00358 (15415)
  covalent geometry    : angle       0.56861 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 203
  time to evaluate  : 2.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8155 (mtp) cc_final: 0.7778 (mtm)
REVERT: A   21 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7786 (mmtm)
REVERT: A   91 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7609 (tp30)
REVERT: B   23 HIS cc_start: 0.7738 (m-70) cc_final: 0.7409 (m90)
REVERT: B  260 ASN cc_start: 0.8384 (m-40) cc_final: 0.8130 (m110)
REVERT: C   20 MET cc_start: 0.7926 (mtp) cc_final: 0.7473 (mmt)
REVERT: C   29 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8251 (tm-30)
REVERT: C   87 HIS cc_start: 0.8408 (p90) cc_final: 0.7889 (m90)
REVERT: C  179 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7741 (ptp-170)
REVERT: D   20 MET cc_start: 0.7751 (mtp) cc_final: 0.7078 (mpt)
REVERT: D   87 HIS cc_start: 0.8421 (p90) cc_final: 0.7854 (m-70)
REVERT: D  259 ARG cc_start: 0.7628 (ttt90) cc_final: 0.7128 (mtt-85)
REVERT: F   23 HIS cc_start: 0.7888 (m-70) cc_final: 0.7584 (m90)
REVERT: F  144 LYS cc_start: 0.8403 (mttt) cc_final: 0.7972 (mtmt)
  outliers start: 15
  outliers final: 7
  residues processed: 210
  average time/residue: 4.9106
  time to fit residues: 1139.2393
Evaluate side-chains
  210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 201
  time to evaluate  : 2.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue  179 ARG
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue  166 ARG
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue  106 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 132 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 133 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 186 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.141215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.112450 restraints weight = 59054.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.43
r_work: 0.3060 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15415  Z= 0.157
  Angle     :  0.550  11.134  20966  Z= 0.302
  Chirality :  0.065   1.414   2513
  Planarity :  0.005   0.055   2728
  Dihedral  :  4.706  28.746   2163
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.96 %
    Favored  : 91.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.28 (0.17), residues: 1974
  helix:  1.98 (0.18), residues: 746
  sheet:  1.16 (0.25), residues: 372
  loop : -0.28 (0.19), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.004   0.001   HIS E  72 
 PHE   0.016   0.002   PHE E 198 
 TYR   0.013   0.002   TYR G  34 
 ARG   0.011   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05230 (  860)
  hydrogen bonds       : angle       5.34635 ( 2403)
  covalent geometry    : bond        0.00322 (15415)
  covalent geometry    : angle       0.55031 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 207
  time to evaluate  : 5.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8118 (mtp) cc_final: 0.7738 (mtm)
REVERT: A   21 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7769 (mmtm)
REVERT: A   91 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7627 (tp30)
REVERT: B   23 HIS cc_start: 0.7724 (m-70) cc_final: 0.7381 (m90)
REVERT: B  106 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7498 (mptt)
REVERT: B  260 ASN cc_start: 0.8381 (m-40) cc_final: 0.8118 (m110)
REVERT: C   20 MET cc_start: 0.7913 (mtp) cc_final: 0.7466 (mmt)
REVERT: C   29 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8268 (tm-30)
REVERT: C   87 HIS cc_start: 0.8388 (p90) cc_final: 0.7868 (m90)
REVERT: C  179 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7753 (ptp-170)
REVERT: D   20 MET cc_start: 0.7740 (mtp) cc_final: 0.7075 (mpt)
REVERT: D   87 HIS cc_start: 0.8412 (p90) cc_final: 0.7838 (m-70)
REVERT: D  259 ARG cc_start: 0.7615 (ttt90) cc_final: 0.7115 (mtt-85)
REVERT: F   23 HIS cc_start: 0.7846 (m-70) cc_final: 0.7548 (m90)
REVERT: F   53 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7505 (mp0)
REVERT: F  144 LYS cc_start: 0.8401 (mttt) cc_final: 0.7954 (mtmt)
REVERT: F  179 ARG cc_start: 0.8261 (ptt90) cc_final: 0.8011 (ptt90)
REVERT: H   46 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7215 (p)
  outliers start: 14
  outliers final: 8
  residues processed: 213
  average time/residue: 4.5145
  time to fit residues: 1059.2008
Evaluate side-chains
  217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 204
  time to evaluate  : 3.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 LYS
Chi-restraints excluded: chain B residue  144 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue  166 ARG
Chi-restraints excluded: chain C residue  179 ARG
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue  166 ARG
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue  106 LYS
Chi-restraints excluded: chain H residue   46 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 130 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 108 optimal weight:    3.9990
   chunk 182 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 186 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 161 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.141352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.112996 restraints weight = 55782.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.39
r_work: 0.3068 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15415  Z= 0.150
  Angle     :  0.546  11.129  20966  Z= 0.299
  Chirality :  0.065   1.414   2513
  Planarity :  0.005   0.072   2728
  Dihedral  :  4.672  28.461   2163
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.08 %
    Favored  : 90.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.31 (0.18), residues: 1974
  helix:  2.01 (0.18), residues: 746
  sheet:  1.17 (0.25), residues: 372
  loop : -0.26 (0.19), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.004   0.001   HIS E  72 
 PHE   0.016   0.002   PHE E 198 
 TYR   0.013   0.002   TYR G  34 
 ARG   0.012   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05143 (  860)
  hydrogen bonds       : angle       5.31658 ( 2403)
  covalent geometry    : bond        0.00308 (15415)
  covalent geometry    : angle       0.54553 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 2.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8128 (mtp) cc_final: 0.7754 (mtm)
REVERT: A   21 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7778 (mmtm)
REVERT: A   91 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7618 (tp30)
REVERT: B   23 HIS cc_start: 0.7729 (m-70) cc_final: 0.7399 (m90)
REVERT: B  260 ASN cc_start: 0.8376 (m-40) cc_final: 0.8110 (m110)
REVERT: C   20 MET cc_start: 0.7907 (mtp) cc_final: 0.7477 (mmt)
REVERT: C   29 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8263 (tm-30)
REVERT: C   87 HIS cc_start: 0.8376 (p90) cc_final: 0.7861 (m90)
REVERT: C  179 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7746 (ptp-170)
REVERT: D   20 MET cc_start: 0.7739 (mtp) cc_final: 0.7085 (mpt)
REVERT: D   87 HIS cc_start: 0.8399 (p90) cc_final: 0.7833 (m-70)
REVERT: D  259 ARG cc_start: 0.7600 (ttt90) cc_final: 0.7116 (mtt-85)
REVERT: F   23 HIS cc_start: 0.7848 (m-70) cc_final: 0.7561 (m90)
REVERT: F  144 LYS cc_start: 0.8394 (mttt) cc_final: 0.7952 (mtmt)
REVERT: H   46 VAL cc_start: 0.7511 (t) cc_final: 0.7221 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 210
  average time/residue: 3.5411
  time to fit residues: 809.9751
Evaluate side-chains
  210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 200
  time to evaluate  : 2.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue  166 ARG
Chi-restraints excluded: chain C residue  179 ARG
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue  166 ARG
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue  106 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 182 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 155 optimal weight:    3.9990
   chunk 187 optimal weight:    3.9990
   chunk 150 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 193 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.141486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.113028 restraints weight = 57668.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.41
r_work: 0.3056 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15415  Z= 0.161
  Angle     :  0.558  11.213  20966  Z= 0.306
  Chirality :  0.066   1.414   2513
  Planarity :  0.005   0.074   2728
  Dihedral  :  4.719  29.091   2163
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.26 %
    Favored  : 90.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.24 (0.17), residues: 1974
  helix:  1.97 (0.18), residues: 746
  sheet:  1.13 (0.25), residues: 381
  loop : -0.34 (0.19), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.004   0.001   HIS E  72 
 PHE   0.017   0.002   PHE E 198 
 TYR   0.014   0.002   TYR G  34 
 ARG   0.013   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05310 (  860)
  hydrogen bonds       : angle       5.36258 ( 2403)
  covalent geometry    : bond        0.00333 (15415)
  covalent geometry    : angle       0.55805 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 205
  time to evaluate  : 2.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8120 (mtp) cc_final: 0.7743 (mtm)
REVERT: A   21 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7787 (mmtm)
REVERT: A   91 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7639 (tp30)
REVERT: B   23 HIS cc_start: 0.7729 (m-70) cc_final: 0.7400 (m90)
REVERT: B  106 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7464 (mptt)
REVERT: B  260 ASN cc_start: 0.8393 (m-40) cc_final: 0.8150 (m110)
REVERT: C   20 MET cc_start: 0.7909 (mtp) cc_final: 0.7469 (mmt)
REVERT: C   29 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8265 (tm-30)
REVERT: C   87 HIS cc_start: 0.8384 (p90) cc_final: 0.7867 (m90)
REVERT: C  179 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7732 (ptp-170)
REVERT: D   20 MET cc_start: 0.7706 (mtp) cc_final: 0.7063 (mpt)
REVERT: D   87 HIS cc_start: 0.8412 (p90) cc_final: 0.7869 (m-70)
REVERT: D  259 ARG cc_start: 0.7610 (ttt90) cc_final: 0.7125 (mtt-85)
REVERT: F   23 HIS cc_start: 0.7844 (m-70) cc_final: 0.7560 (m90)
REVERT: F   53 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7512 (mp0)
REVERT: F  144 LYS cc_start: 0.8402 (mttt) cc_final: 0.7964 (mtmt)
REVERT: H   46 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7209 (p)
  outliers start: 15
  outliers final: 8
  residues processed: 211
  average time/residue: 3.7094
  time to fit residues: 864.5861
Evaluate side-chains
  215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 2.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 LYS
Chi-restraints excluded: chain B residue  144 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue  166 ARG
Chi-restraints excluded: chain C residue  179 ARG
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue  166 ARG
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue  106 LYS
Chi-restraints excluded: chain H residue   46 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 192 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 94 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 189 optimal weight:    5.9990
   chunk 179 optimal weight:    1.9990
   chunk 143 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.140634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.111083 restraints weight = 64745.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.67
r_work: 0.3028 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15415  Z= 0.183
  Angle     :  0.584  11.244  20966  Z= 0.321
  Chirality :  0.065   1.397   2513
  Planarity :  0.005   0.077   2728
  Dihedral  :  4.801  29.522   2163
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  8.63 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.17 (0.17), residues: 1974
  helix:  1.87 (0.18), residues: 746
  sheet:  1.13 (0.25), residues: 381
  loop : -0.36 (0.19), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.005   0.001   HIS E  87 
 PHE   0.019   0.002   PHE E 198 
 TYR   0.016   0.002   TYR G  34 
 ARG   0.013   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05602 (  860)
  hydrogen bonds       : angle       5.44878 ( 2403)
  covalent geometry    : bond        0.00381 (15415)
  covalent geometry    : angle       0.58376 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 201
  time to evaluate  : 2.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8134 (mtp) cc_final: 0.7749 (mtm)
REVERT: A   21 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7778 (mmtm)
REVERT: A   91 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7609 (tp30)
REVERT: B   23 HIS cc_start: 0.7706 (m-70) cc_final: 0.7382 (m90)
REVERT: B  106 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7428 (mptt)
REVERT: B  260 ASN cc_start: 0.8402 (m-40) cc_final: 0.8149 (m110)
REVERT: C   20 MET cc_start: 0.7920 (mtp) cc_final: 0.7447 (mmt)
REVERT: C   29 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8278 (tm-30)
REVERT: C   87 HIS cc_start: 0.8427 (p90) cc_final: 0.7881 (m90)
REVERT: C  179 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7776 (ptp-170)
REVERT: D   20 MET cc_start: 0.7695 (mtp) cc_final: 0.7026 (mpt)
REVERT: D   87 HIS cc_start: 0.8430 (p90) cc_final: 0.7817 (m-70)
REVERT: D  259 ARG cc_start: 0.7626 (ttt90) cc_final: 0.7097 (mtt-85)
REVERT: F   23 HIS cc_start: 0.7819 (m-70) cc_final: 0.7534 (m90)
REVERT: F   53 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7522 (mp0)
REVERT: F  144 LYS cc_start: 0.8436 (mttt) cc_final: 0.7966 (mtmt)
  outliers start: 12
  outliers final: 8
  residues processed: 207
  average time/residue: 3.4711
  time to fit residues: 780.7007
Evaluate side-chains
  210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 198
  time to evaluate  : 2.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 LYS
Chi-restraints excluded: chain B residue  144 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue  166 ARG
Chi-restraints excluded: chain C residue  179 ARG
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue  166 ARG
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue  106 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 147 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 177 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 142 optimal weight:    2.9990
   chunk 118 optimal weight:    0.6980
   chunk 165 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.141865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.113827 restraints weight = 54877.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.37
r_work: 0.3073 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15415  Z= 0.148
  Angle     :  0.543  11.097  20966  Z= 0.297
  Chirality :  0.066   1.410   2513
  Planarity :  0.005   0.070   2728
  Dihedral  :  4.676  28.657   2163
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  8.75 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.30 (0.18), residues: 1974
  helix:  2.00 (0.18), residues: 746
  sheet:  1.16 (0.25), residues: 372
  loop : -0.27 (0.19), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  30 
 HIS   0.004   0.001   HIS E  87 
 PHE   0.015   0.002   PHE E 198 
 TYR   0.012   0.002   TYR G  34 
 ARG   0.012   0.001   ARG D 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05067 (  860)
  hydrogen bonds       : angle       5.30302 ( 2403)
  covalent geometry    : bond        0.00305 (15415)
  covalent geometry    : angle       0.54291 (20966)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 204
  time to evaluate  : 2.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.8103 (mtp) cc_final: 0.7735 (mtm)
REVERT: A   21 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7788 (mmmm)
REVERT: A   91 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7624 (tp30)
REVERT: B   23 HIS cc_start: 0.7724 (m-70) cc_final: 0.7403 (m90)
REVERT: B  260 ASN cc_start: 0.8376 (m-40) cc_final: 0.8137 (m110)
REVERT: C   20 MET cc_start: 0.7912 (mtp) cc_final: 0.7480 (mmt)
REVERT: C   29 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8244 (tm-30)
REVERT: C   87 HIS cc_start: 0.8358 (p90) cc_final: 0.7885 (m90)
REVERT: C  179 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7765 (ptp-170)
REVERT: D   20 MET cc_start: 0.7695 (mtp) cc_final: 0.7061 (mpt)
REVERT: D   87 HIS cc_start: 0.8386 (p90) cc_final: 0.7808 (m-70)
REVERT: D  259 ARG cc_start: 0.7599 (ttt90) cc_final: 0.7121 (mtt-85)
REVERT: F   23 HIS cc_start: 0.7856 (m-70) cc_final: 0.7577 (m90)
REVERT: F   53 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7489 (mp0)
REVERT: F  144 LYS cc_start: 0.8375 (mttt) cc_final: 0.7949 (mtmt)
  outliers start: 10
  outliers final: 8
  residues processed: 209
  average time/residue: 3.6109
  time to fit residues: 822.8956
Evaluate side-chains
  211 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 200
  time to evaluate  : 3.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue  166 ARG
Chi-restraints excluded: chain C residue  179 ARG
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue  166 ARG
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   98 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue  106 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9980
   chunk 115 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 126 optimal weight:    4.9990
   chunk 142 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 169 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 163 optimal weight:    8.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
D  72 HIS
D 104 ASN
H  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.139575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.110595 restraints weight = 60253.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.45
r_work: 0.3056 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  15415  Z= 0.248
  Angle     :  0.654  11.540  20966  Z= 0.363
  Chirality :  0.067   1.404   2513
  Planarity :  0.006   0.088   2728
  Dihedral  :  5.010  30.191   2163
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  1.55 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  8.38 %
    Favored  : 90.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.02 (0.17), residues: 1974
  helix:  1.66 (0.17), residues: 746
  sheet:  1.14 (0.25), residues: 382
  loop : -0.41 (0.19), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP A  30 
 HIS   0.007   0.002   HIS E  87 
 PHE   0.023   0.003   PHE E 198 
 TYR   0.020   0.003   TYR G  34 
 ARG   0.015   0.001   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06373 (  860)
  hydrogen bonds       : angle       5.67764 ( 2403)
  covalent geometry    : bond        0.00523 (15415)
  covalent geometry    : angle       0.65443 (20966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 33481.03 seconds
wall clock time: 582 minutes 22.97 seconds (34942.97 seconds total)