Starting phenix.real_space_refine on Sun Mar 10 22:54:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/03_2024/8ter_41198.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/03_2024/8ter_41198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/03_2024/8ter_41198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/03_2024/8ter_41198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/03_2024/8ter_41198.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/03_2024/8ter_41198.pdb" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 3 Type Number sf(0) Gaussians C 3420 2.51 5 N 960 2.21 5 O 1400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5780 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "D" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "E" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "G" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "H" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "I" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "J" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "K" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "L" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "M" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "N" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "O" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "P" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "Q" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "R" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "S" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "T" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "N" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "O" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Q" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 3.16, per 1000 atoms: 0.55 Number of scatterers: 5780 At special positions: 0 Unit cell: (64.141, 69.531, 65.758, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1400 8.00 N 960 7.00 C 3420 6.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 985.6 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 62.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'P' and resid 266 through 273 removed outlier: 6.824A pdb=" N ILE L 270 " --> pdb=" O GLY P 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN P 271 " --> pdb=" O ILE L 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR L 272 " --> pdb=" O GLN P 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER P 273 " --> pdb=" O TYR L 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE H 270 " --> pdb=" O GLY L 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN L 271 " --> pdb=" O ILE H 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR H 272 " --> pdb=" O GLN L 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER L 273 " --> pdb=" O TYR H 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 270 " --> pdb=" O GLY H 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN H 271 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR D 272 " --> pdb=" O GLN H 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER H 273 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 270 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN D 271 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A 272 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER D 273 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN A 267 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE E 270 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY A 269 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR E 272 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN A 271 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN E 267 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE I 270 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY E 269 " --> pdb=" O ILE I 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR I 272 " --> pdb=" O GLY E 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN E 271 " --> pdb=" O TYR I 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN I 267 " --> pdb=" O TYR M 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE M 270 " --> pdb=" O GLN I 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY I 269 " --> pdb=" O ILE M 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR M 272 " --> pdb=" O GLY I 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN I 271 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN M 267 " --> pdb=" O TYR Q 268 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE Q 270 " --> pdb=" O GLN M 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY M 269 " --> pdb=" O ILE Q 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR Q 272 " --> pdb=" O GLY M 269 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLN M 271 " --> pdb=" O TYR Q 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN Q 267 " --> pdb=" O TYR T 268 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE T 270 " --> pdb=" O GLN Q 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY Q 269 " --> pdb=" O ILE T 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR T 272 " --> pdb=" O GLY Q 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN Q 271 " --> pdb=" O TYR T 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 276 through 279 removed outlier: 6.279A pdb=" N TYR L 276 " --> pdb=" O SER P 277 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLN P 279 " --> pdb=" O TYR L 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN L 278 " --> pdb=" O GLN P 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR H 276 " --> pdb=" O SER L 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN L 279 " --> pdb=" O TYR H 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN H 278 " --> pdb=" O GLN L 279 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR D 276 " --> pdb=" O SER H 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN H 279 " --> pdb=" O TYR D 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN D 278 " --> pdb=" O GLN H 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR A 276 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLN D 279 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN A 278 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 283 through 293 removed outlier: 6.437A pdb=" N GLN L 284 " --> pdb=" O LEU P 285 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN P 287 " --> pdb=" O GLN L 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN L 286 " --> pdb=" O GLN P 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN P 289 " --> pdb=" O GLN L 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE L 288 " --> pdb=" O GLN P 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR P 291 " --> pdb=" O PHE L 288 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY L 290 " --> pdb=" O TYR P 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN P 293 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY L 292 " --> pdb=" O GLN P 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN H 284 " --> pdb=" O LEU L 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN L 287 " --> pdb=" O GLN H 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN H 286 " --> pdb=" O GLN L 287 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLN L 289 " --> pdb=" O GLN H 286 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE H 288 " --> pdb=" O GLN L 289 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR L 291 " --> pdb=" O PHE H 288 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY H 290 " --> pdb=" O TYR L 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN L 293 " --> pdb=" O GLY H 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY H 292 " --> pdb=" O GLN L 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN D 284 " --> pdb=" O LEU H 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN H 287 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN D 286 " --> pdb=" O GLN H 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN H 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE D 288 " --> pdb=" O GLN H 289 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR H 291 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY D 290 " --> pdb=" O TYR H 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN H 293 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY D 292 " --> pdb=" O GLN H 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 284 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN D 287 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 286 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN D 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 288 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR D 291 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY A 290 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN D 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY A 292 " --> pdb=" O GLN D 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 296 through 298 removed outlier: 6.450A pdb=" N THR L 296 " --> pdb=" O SER P 297 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR H 296 " --> pdb=" O SER L 297 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR D 296 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR A 296 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 266 through 273 removed outlier: 6.824A pdb=" N ILE N 270 " --> pdb=" O GLY R 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN R 271 " --> pdb=" O ILE N 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR N 272 " --> pdb=" O GLN R 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER R 273 " --> pdb=" O TYR N 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE J 270 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN N 271 " --> pdb=" O ILE J 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR J 272 " --> pdb=" O GLN N 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER N 273 " --> pdb=" O TYR J 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE F 270 " --> pdb=" O GLY J 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN J 271 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR F 272 " --> pdb=" O GLN J 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER J 273 " --> pdb=" O TYR F 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 270 " --> pdb=" O GLY F 269 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN F 271 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR B 272 " --> pdb=" O GLN F 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER F 273 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN B 267 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 270 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLY B 269 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR C 272 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N GLN B 271 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN C 267 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE G 270 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY C 269 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR G 272 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN C 271 " --> pdb=" O TYR G 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN G 267 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE K 270 " --> pdb=" O GLN G 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY G 269 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR K 272 " --> pdb=" O GLY G 269 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLN G 271 " --> pdb=" O TYR K 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN K 267 " --> pdb=" O TYR O 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE O 270 " --> pdb=" O GLN K 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY K 269 " --> pdb=" O ILE O 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR O 272 " --> pdb=" O GLY K 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN K 271 " --> pdb=" O TYR O 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN O 267 " --> pdb=" O TYR S 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE S 270 " --> pdb=" O GLN O 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY O 269 " --> pdb=" O ILE S 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR S 272 " --> pdb=" O GLY O 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN O 271 " --> pdb=" O TYR S 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 276 through 279 removed outlier: 6.279A pdb=" N TYR N 276 " --> pdb=" O SER R 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN R 279 " --> pdb=" O TYR N 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN N 278 " --> pdb=" O GLN R 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR J 276 " --> pdb=" O SER N 277 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLN N 279 " --> pdb=" O TYR J 276 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN J 278 " --> pdb=" O GLN N 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 276 " --> pdb=" O SER J 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN J 279 " --> pdb=" O TYR F 276 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN F 278 " --> pdb=" O GLN J 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR B 276 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN F 279 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN B 278 " --> pdb=" O GLN F 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 283 through 293 removed outlier: 6.437A pdb=" N GLN N 284 " --> pdb=" O LEU R 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN R 287 " --> pdb=" O GLN N 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN N 286 " --> pdb=" O GLN R 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN R 289 " --> pdb=" O GLN N 286 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE N 288 " --> pdb=" O GLN R 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR R 291 " --> pdb=" O PHE N 288 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY N 290 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLN R 293 " --> pdb=" O GLY N 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY N 292 " --> pdb=" O GLN R 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN J 284 " --> pdb=" O LEU N 285 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN N 287 " --> pdb=" O GLN J 284 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN J 286 " --> pdb=" O GLN N 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN N 289 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE J 288 " --> pdb=" O GLN N 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR N 291 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY J 290 " --> pdb=" O TYR N 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN N 293 " --> pdb=" O GLY J 290 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY J 292 " --> pdb=" O GLN N 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN F 284 " --> pdb=" O LEU J 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN J 287 " --> pdb=" O GLN F 284 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN F 286 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN J 289 " --> pdb=" O GLN F 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE F 288 " --> pdb=" O GLN J 289 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR J 291 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY F 290 " --> pdb=" O TYR J 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN J 293 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY F 292 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 284 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN F 287 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN B 286 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN F 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE B 288 " --> pdb=" O GLN F 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR F 291 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY B 290 " --> pdb=" O TYR F 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN F 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 292 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 296 through 298 removed outlier: 6.450A pdb=" N THR N 296 " --> pdb=" O SER R 297 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR J 296 " --> pdb=" O SER N 297 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR F 296 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 296 " --> pdb=" O SER F 297 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 960 1.29 - 1.35: 940 1.35 - 1.42: 759 1.42 - 1.48: 821 1.48 - 1.55: 2200 Bond restraints: 5680 Sorted by residual: bond pdb=" CG GLN J 266 " pdb=" CD GLN J 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" CG GLN S 266 " pdb=" CD GLN S 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CG GLN Q 266 " pdb=" CD GLN Q 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CG GLN E 266 " pdb=" CD GLN E 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CG GLN D 266 " pdb=" CD GLN D 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 ... (remaining 5675 not shown) Histogram of bond angle deviations from ideal: 102.80 - 108.04: 364 108.04 - 113.29: 2352 113.29 - 118.53: 1484 118.53 - 123.77: 3400 123.77 - 129.02: 80 Bond angle restraints: 7680 Sorted by residual: angle pdb=" CA THR D 280 " pdb=" CB THR D 280 " pdb=" CG2 THR D 280 " ideal model delta sigma weight residual 110.50 114.37 -3.87 1.70e+00 3.46e-01 5.19e+00 angle pdb=" CA THR K 280 " pdb=" CB THR K 280 " pdb=" CG2 THR K 280 " ideal model delta sigma weight residual 110.50 114.37 -3.87 1.70e+00 3.46e-01 5.18e+00 angle pdb=" CA THR G 280 " pdb=" CB THR G 280 " pdb=" CG2 THR G 280 " ideal model delta sigma weight residual 110.50 114.37 -3.87 1.70e+00 3.46e-01 5.17e+00 angle pdb=" CA THR J 280 " pdb=" CB THR J 280 " pdb=" CG2 THR J 280 " ideal model delta sigma weight residual 110.50 114.36 -3.86 1.70e+00 3.46e-01 5.16e+00 angle pdb=" CA THR E 280 " pdb=" CB THR E 280 " pdb=" CG2 THR E 280 " ideal model delta sigma weight residual 110.50 114.36 -3.86 1.70e+00 3.46e-01 5.15e+00 ... (remaining 7675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.32: 2660 13.32 - 26.63: 420 26.63 - 39.95: 160 39.95 - 53.26: 80 53.26 - 66.58: 40 Dihedral angle restraints: 3360 sinusoidal: 1360 harmonic: 2000 Sorted by residual: dihedral pdb=" CA GLN I 266 " pdb=" CB GLN I 266 " pdb=" CG GLN I 266 " pdb=" CD GLN I 266 " ideal model delta sinusoidal sigma weight residual 180.00 134.27 45.73 3 1.50e+01 4.44e-03 8.22e+00 dihedral pdb=" CA GLN C 266 " pdb=" CB GLN C 266 " pdb=" CG GLN C 266 " pdb=" CD GLN C 266 " ideal model delta sinusoidal sigma weight residual 180.00 134.28 45.72 3 1.50e+01 4.44e-03 8.22e+00 dihedral pdb=" CA GLN Q 266 " pdb=" CB GLN Q 266 " pdb=" CG GLN Q 266 " pdb=" CD GLN Q 266 " ideal model delta sinusoidal sigma weight residual 180.00 134.28 45.72 3 1.50e+01 4.44e-03 8.22e+00 ... (remaining 3357 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.025: 254 0.025 - 0.047: 226 0.047 - 0.070: 100 0.070 - 0.093: 80 0.093 - 0.116: 40 Chirality restraints: 700 Sorted by residual: chirality pdb=" CB THR I 280 " pdb=" CA THR I 280 " pdb=" OG1 THR I 280 " pdb=" CG2 THR I 280 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CB THR R 280 " pdb=" CA THR R 280 " pdb=" OG1 THR R 280 " pdb=" CG2 THR R 280 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CB THR S 280 " pdb=" CA THR S 280 " pdb=" OG1 THR S 280 " pdb=" CG2 THR S 280 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 697 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 289 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" CD GLN E 289 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN E 289 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN E 289 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 289 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLN S 289 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN S 289 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN S 289 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 289 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" CD GLN K 289 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN K 289 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN K 289 " 0.013 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1566 2.81 - 3.33: 4067 3.33 - 3.86: 11742 3.86 - 4.38: 14891 4.38 - 4.90: 26124 Nonbonded interactions: 58390 Sorted by model distance: nonbonded pdb=" OG SER O 277 " pdb=" O HOH O 401 " model vdw 2.289 2.440 nonbonded pdb=" OG SER S 277 " pdb=" O HOH S 401 " model vdw 2.351 2.440 nonbonded pdb=" OG SER Q 277 " pdb=" O HOH Q 401 " model vdw 2.351 2.440 nonbonded pdb=" OG SER C 277 " pdb=" O HOH C 401 " model vdw 2.351 2.440 nonbonded pdb=" OG SER E 277 " pdb=" O HOH E 401 " model vdw 2.352 2.440 ... (remaining 58385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.640 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.800 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 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 : 0.007 0.034 5680 Z= 0.443 Angle : 0.894 5.077 7680 Z= 0.474 Chirality : 0.048 0.116 700 Planarity : 0.007 0.023 1080 Dihedral : 18.428 66.580 2120 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % 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: -4.34 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.003 PHE D 288 TYR 0.016 0.006 TYR R 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.684 Fit side-chains REVERT: G 293 GLN cc_start: 0.8370 (mt0) cc_final: 0.8141 (mt0) REVERT: J 293 GLN cc_start: 0.8356 (mt0) cc_final: 0.7953 (mt0) REVERT: K 293 GLN cc_start: 0.8479 (mt0) cc_final: 0.8263 (mt0) REVERT: L 293 GLN cc_start: 0.8405 (mt0) cc_final: 0.8033 (mp10) REVERT: M 293 GLN cc_start: 0.8468 (mt0) cc_final: 0.8116 (mt0) REVERT: N 266 GLN cc_start: 0.8810 (mt0) cc_final: 0.8487 (mt0) REVERT: R 293 GLN cc_start: 0.8485 (mt0) cc_final: 0.8279 (mt0) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.8088 time to fit residues: 80.6317 Evaluate side-chains 85 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 298 GLN B 267 GLN B 298 GLN C 267 GLN C 298 GLN D 267 GLN D 298 GLN E 267 GLN E 298 GLN F 267 GLN F 298 GLN G 267 GLN G 298 GLN H 267 GLN H 298 GLN I 267 GLN I 293 GLN I 298 GLN J 267 GLN J 298 GLN K 267 GLN K 298 GLN L 267 GLN L 298 GLN M 267 GLN M 298 GLN N 267 GLN N 293 GLN N 298 GLN O 267 GLN O 298 GLN P 267 GLN P 293 GLN P 298 GLN Q 267 GLN Q 298 GLN R 266 GLN R 267 GLN R 298 GLN S 267 GLN S 298 GLN T 267 GLN T 293 GLN T 298 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5680 Z= 0.330 Angle : 0.609 4.286 7680 Z= 0.310 Chirality : 0.042 0.115 700 Planarity : 0.004 0.029 1080 Dihedral : 3.398 8.208 760 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.93 % Allowed : 9.14 % Favored : 82.93 % 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: -4.00 (0.15), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.003 PHE E 288 TYR 0.010 0.002 TYR H 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 91 time to evaluate : 0.589 Fit side-chains REVERT: E 293 GLN cc_start: 0.8269 (mt0) cc_final: 0.7958 (mt0) REVERT: I 285 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8987 (tt) REVERT: J 293 GLN cc_start: 0.8286 (mt0) cc_final: 0.7931 (mt0) REVERT: L 293 GLN cc_start: 0.8319 (mt0) cc_final: 0.7947 (mp10) REVERT: M 266 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: M 293 GLN cc_start: 0.8411 (mt0) cc_final: 0.8067 (mt0) REVERT: O 266 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8071 (mt0) outliers start: 46 outliers final: 29 residues processed: 113 average time/residue: 0.7878 time to fit residues: 95.3914 Evaluate side-chains 118 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 0.0980 chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 0.0870 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 overall best weight: 3.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN K 293 GLN N 293 GLN P 293 GLN T 293 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 5680 Z= 0.299 Angle : 0.573 4.943 7680 Z= 0.288 Chirality : 0.040 0.109 700 Planarity : 0.004 0.029 1080 Dihedral : 3.251 8.268 760 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 8.45 % Allowed : 9.14 % Favored : 82.41 % 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: -4.00 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE E 288 TYR 0.009 0.001 TYR C 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 95 time to evaluate : 0.673 Fit side-chains REVERT: B 266 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: E 293 GLN cc_start: 0.8270 (mt0) cc_final: 0.7969 (mt0) REVERT: H 266 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: I 285 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9032 (tt) REVERT: J 293 GLN cc_start: 0.8258 (mt0) cc_final: 0.7874 (mt0) REVERT: L 293 GLN cc_start: 0.8312 (mt0) cc_final: 0.7909 (mp10) REVERT: M 266 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: M 293 GLN cc_start: 0.8405 (mt0) cc_final: 0.8121 (mt0) REVERT: N 285 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8725 (tt) REVERT: O 266 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8064 (mt0) outliers start: 49 outliers final: 30 residues processed: 113 average time/residue: 0.8005 time to fit residues: 96.6815 Evaluate side-chains 128 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN D 266 GLN D 293 GLN F 266 GLN G 293 GLN H 293 GLN I 293 GLN K 293 GLN N 293 GLN P 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 5680 Z= 0.311 Angle : 0.576 4.268 7680 Z= 0.290 Chirality : 0.040 0.121 700 Planarity : 0.004 0.030 1080 Dihedral : 3.275 8.404 760 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 8.28 % Allowed : 10.52 % Favored : 81.21 % 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: -3.98 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.003 PHE E 288 TYR 0.012 0.001 TYR R 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 93 time to evaluate : 0.658 Fit side-chains REVERT: B 266 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: E 293 GLN cc_start: 0.8251 (mt0) cc_final: 0.7957 (mt0) REVERT: H 266 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8516 (mt0) REVERT: I 285 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9014 (tt) REVERT: J 293 GLN cc_start: 0.8271 (mt0) cc_final: 0.7877 (mt0) REVERT: L 293 GLN cc_start: 0.8304 (mt0) cc_final: 0.7894 (mp10) REVERT: M 266 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: M 293 GLN cc_start: 0.8444 (mt0) cc_final: 0.8093 (mt0) REVERT: N 285 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8744 (tt) REVERT: O 266 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8038 (mt0) outliers start: 48 outliers final: 32 residues processed: 111 average time/residue: 0.8295 time to fit residues: 98.2950 Evaluate side-chains 130 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN D 266 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN K 293 GLN N 293 GLN R 266 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 5680 Z= 0.310 Angle : 0.574 4.223 7680 Z= 0.288 Chirality : 0.040 0.124 700 Planarity : 0.004 0.029 1080 Dihedral : 3.265 8.474 760 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 8.62 % Allowed : 11.72 % Favored : 79.66 % 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: -3.97 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE E 288 TYR 0.012 0.001 TYR R 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 92 time to evaluate : 0.688 Fit side-chains REVERT: B 266 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: H 266 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: I 285 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9046 (tt) REVERT: J 293 GLN cc_start: 0.8270 (mt0) cc_final: 0.7903 (mt0) REVERT: L 293 GLN cc_start: 0.8302 (mt0) cc_final: 0.7987 (mt0) REVERT: M 266 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: O 266 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8062 (mt0) outliers start: 50 outliers final: 32 residues processed: 111 average time/residue: 0.7793 time to fit residues: 92.5691 Evaluate side-chains 127 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN C 293 GLN D 266 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN K 293 GLN M 293 GLN N 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 5680 Z= 0.375 Angle : 0.607 4.284 7680 Z= 0.308 Chirality : 0.042 0.137 700 Planarity : 0.004 0.030 1080 Dihedral : 3.352 8.753 760 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 8.28 % Allowed : 12.59 % Favored : 79.14 % 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: -3.94 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.003 PHE E 288 TYR 0.013 0.001 TYR R 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 92 time to evaluate : 0.612 Fit side-chains REVERT: B 266 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: H 266 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: I 285 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9054 (tt) REVERT: J 293 GLN cc_start: 0.8272 (mt0) cc_final: 0.7901 (mt0) REVERT: L 293 GLN cc_start: 0.8309 (mt0) cc_final: 0.7989 (mt0) REVERT: M 266 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: O 266 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8042 (mt0) outliers start: 48 outliers final: 31 residues processed: 109 average time/residue: 0.8636 time to fit residues: 100.2763 Evaluate side-chains 125 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 89 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN D 266 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN K 293 GLN M 293 GLN N 293 GLN P 293 GLN R 266 GLN S 279 GLN T 279 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5680 Z= 0.198 Angle : 0.524 5.315 7680 Z= 0.256 Chirality : 0.038 0.115 700 Planarity : 0.003 0.027 1080 Dihedral : 3.132 8.217 760 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.41 % Allowed : 14.14 % Favored : 78.45 % 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: -4.00 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE G 288 TYR 0.010 0.001 TYR R 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 94 time to evaluate : 0.695 Fit side-chains REVERT: H 266 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8504 (mt0) REVERT: J 293 GLN cc_start: 0.8251 (mt0) cc_final: 0.7877 (mt0) REVERT: L 293 GLN cc_start: 0.8268 (mt0) cc_final: 0.7940 (mt0) REVERT: N 285 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8716 (tt) outliers start: 43 outliers final: 26 residues processed: 110 average time/residue: 0.8356 time to fit residues: 98.0461 Evaluate side-chains 120 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 279 GLN B 293 GLN C 293 GLN D 266 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN K 293 GLN M 293 GLN N 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 5680 Z= 0.488 Angle : 0.665 5.352 7680 Z= 0.339 Chirality : 0.045 0.219 700 Planarity : 0.004 0.032 1080 Dihedral : 3.451 9.173 760 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 7.41 % Allowed : 14.31 % Favored : 78.28 % 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: -3.92 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.004 PHE J 288 TYR 0.015 0.002 TYR R 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 90 time to evaluate : 0.738 Fit side-chains REVERT: H 266 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: J 293 GLN cc_start: 0.8289 (mt0) cc_final: 0.7913 (mt0) REVERT: L 293 GLN cc_start: 0.8327 (mt0) cc_final: 0.8004 (mt0) outliers start: 43 outliers final: 29 residues processed: 105 average time/residue: 0.7641 time to fit residues: 85.8814 Evaluate side-chains 120 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN C 293 GLN D 266 GLN G 293 GLN H 293 GLN K 293 GLN L 283 GLN M 293 GLN N 293 GLN R 266 GLN S 279 GLN T 279 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5680 Z= 0.166 Angle : 0.516 6.090 7680 Z= 0.249 Chirality : 0.038 0.125 700 Planarity : 0.003 0.026 1080 Dihedral : 3.137 8.756 760 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.86 % Allowed : 16.21 % Favored : 77.93 % 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: -3.99 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE I 288 TYR 0.009 0.001 TYR R 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 90 time to evaluate : 0.706 Fit side-chains REVERT: H 266 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8496 (mt0) REVERT: J 293 GLN cc_start: 0.8242 (mt0) cc_final: 0.7856 (mt0) REVERT: L 293 GLN cc_start: 0.8253 (mt0) cc_final: 0.7920 (mt0) outliers start: 34 outliers final: 21 residues processed: 102 average time/residue: 0.8630 time to fit residues: 93.7651 Evaluate side-chains 113 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 293 GLN D 293 GLN G 293 GLN H 293 GLN K 293 GLN M 293 GLN N 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 5680 Z= 0.313 Angle : 0.588 5.662 7680 Z= 0.291 Chirality : 0.042 0.203 700 Planarity : 0.004 0.028 1080 Dihedral : 3.255 8.997 760 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.55 % Allowed : 15.34 % Favored : 78.10 % 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: -3.98 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE E 288 TYR 0.013 0.001 TYR R 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 91 time to evaluate : 0.664 Fit side-chains REVERT: H 266 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: J 293 GLN cc_start: 0.8260 (mt0) cc_final: 0.7885 (mt0) REVERT: L 293 GLN cc_start: 0.8285 (mt0) cc_final: 0.7954 (mt0) outliers start: 38 outliers final: 24 residues processed: 102 average time/residue: 0.8222 time to fit residues: 89.4820 Evaluate side-chains 116 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 293 GLN D 266 GLN D 293 GLN G 293 GLN H 293 GLN K 293 GLN M 293 GLN N 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086363 restraints weight = 6627.376| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 0.65 r_work: 0.3168 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.041 5680 Z= 0.598 Angle : 0.723 6.013 7680 Z= 0.372 Chirality : 0.051 0.294 700 Planarity : 0.005 0.034 1080 Dihedral : 3.569 9.670 760 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 6.21 % Allowed : 16.03 % Favored : 77.76 % 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: -3.89 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.004 PHE J 288 TYR 0.017 0.002 TYR R 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.23 seconds wall clock time: 43 minutes 17.75 seconds (2597.75 seconds total)