Starting phenix.real_space_refine on Fri Aug 2 22:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/08_2024/8ter_41198.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/08_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_41198/08_2024/8ter_41198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/08_2024/8ter_41198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/08_2024/8ter_41198.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ter_41198/08_2024/8ter_41198.cif" } 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-5409/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: 4.28, per 1000 atoms: 0.74 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: 2.00 Conformation dependent library (CDL) restraints added in 999.2 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: 0.97 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: 1.58 Time building geometry restraints manager: 2.21 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 3.040 nonbonded pdb=" OG SER S 277 " pdb=" O HOH S 401 " model vdw 2.351 3.040 nonbonded pdb=" OG SER Q 277 " pdb=" O HOH Q 401 " model vdw 2.351 3.040 nonbonded pdb=" OG SER C 277 " pdb=" O HOH C 401 " model vdw 2.351 3.040 nonbonded pdb=" OG SER E 277 " pdb=" O HOH E 401 " model vdw 2.352 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.890 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- 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 : 0.662 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: 0.8390 time to fit residues: 83.4906 Evaluate side-chains 85 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 0.9980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 54 optimal weight: 0.3980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 293 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: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1506 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= 0.185 Angle : 0.525 3.601 7680 Z= 0.260 Chirality : 0.040 0.113 700 Planarity : 0.004 0.023 1080 Dihedral : 3.147 8.574 760 Min Nonbonded Distance : 2.691 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.76 % Allowed : 10.17 % Favored : 82.07 % 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 (0.15), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.11), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE E 288 TYR 0.007 0.001 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: 45 poor density : 92 time to evaluate : 0.684 Fit side-chains REVERT: E 293 GLN cc_start: 0.8196 (mt0) cc_final: 0.7915 (mt0) REVERT: J 293 GLN cc_start: 0.8207 (mt0) cc_final: 0.7826 (mt0) REVERT: L 293 GLN cc_start: 0.8278 (mt0) cc_final: 0.7936 (mp10) REVERT: M 293 GLN cc_start: 0.8345 (mt0) cc_final: 0.8029 (mt0) REVERT: O 293 GLN cc_start: 0.8244 (mt0) cc_final: 0.7835 (mt0) REVERT: R 297 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8693 (p) outliers start: 45 outliers final: 23 residues processed: 114 average time/residue: 0.7999 time to fit residues: 97.3793 Evaluate side-chains 113 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 D residue 285 LEU 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 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 R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 280 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5766 > 50: distance: 32 - 128: 31.861 distance: 35 - 143: 28.487 distance: 47 - 146: 35.002 distance: 110 - 114: 34.667 distance: 114 - 115: 39.880 distance: 116 - 117: 39.293 distance: 119 - 120: 39.697 distance: 120 - 121: 54.914 distance: 120 - 123: 36.679 distance: 121 - 122: 40.657 distance: 121 - 125: 40.365 distance: 123 - 124: 40.293 distance: 125 - 126: 39.027 distance: 126 - 127: 40.704 distance: 126 - 129: 56.324 distance: 127 - 128: 32.130 distance: 130 - 131: 39.846 distance: 131 - 133: 4.704 distance: 132 - 134: 15.117 distance: 133 - 135: 28.426 distance: 134 - 135: 36.957 distance: 135 - 136: 36.916 distance: 137 - 138: 23.198 distance: 137 - 242: 32.614 distance: 138 - 139: 42.427 distance: 138 - 141: 24.158 distance: 139 - 140: 13.323 distance: 139 - 143: 9.774 distance: 140 - 257: 30.629 distance: 141 - 142: 45.613 distance: 143 - 144: 36.258 distance: 144 - 145: 24.494 distance: 144 - 147: 14.970 distance: 145 - 146: 21.364 distance: 145 - 152: 14.361 distance: 147 - 148: 11.114 distance: 148 - 149: 21.942 distance: 149 - 150: 14.432 distance: 149 - 151: 20.902 distance: 152 - 153: 28.630 distance: 152 - 260: 16.630 distance: 153 - 154: 8.518 distance: 153 - 156: 13.841 distance: 154 - 155: 16.536 distance: 154 - 161: 25.843 distance: 156 - 157: 22.862 distance: 158 - 159: 3.565 distance: 158 - 160: 17.908 distance: 161 - 162: 16.148 distance: 162 - 163: 24.957 distance: 162 - 165: 15.050 distance: 163 - 164: 15.684 distance: 163 - 168: 25.377 distance: 165 - 166: 25.776 distance: 165 - 167: 20.655 distance: 169 - 170: 21.107 distance: 170 - 171: 23.814 distance: 170 - 172: 21.476 distance: 172 - 173: 34.539 distance: 172 - 178: 41.224 distance: 173 - 174: 42.156 distance: 173 - 176: 9.605 distance: 174 - 175: 34.198 distance: 174 - 179: 39.654 distance: 177 - 178: 56.035 distance: 179 - 180: 7.348 distance: 180 - 181: 40.977 distance: 180 - 183: 3.340 distance: 181 - 182: 17.782 distance: 181 - 188: 28.495 distance: 182 - 302: 30.789 distance: 184 - 185: 22.108 distance: 185 - 186: 18.036 distance: 185 - 187: 27.058