Starting phenix.real_space_refine on Mon Nov 20 05:28:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/11_2023/7t8c_25744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/11_2023/7t8c_25744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/11_2023/7t8c_25744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/11_2023/7t8c_25744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/11_2023/7t8c_25744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/11_2023/7t8c_25744.pdb" } resolution = 4.5 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= 0.001 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 18480 2.51 5 N 5075 2.21 5 O 5292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 28952 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4136 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4136 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4136 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4136 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4136 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4136 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4136 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 14.28, per 1000 atoms: 0.49 Number of scatterers: 28952 At special positions: 0 Unit cell: (187.266, 188.324, 83.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 5292 8.00 N 5075 7.00 C 18480 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: 10.06 Conformation dependent library (CDL) restraints added in 5.2 seconds 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6762 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 28 sheets defined 44.2% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 56 through 68 removed outlier: 3.606A pdb=" N HIS A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 170 through 181 Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.528A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 291 through 299 Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.826A pdb=" N LYS A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA A 388 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.825A pdb=" N ILE A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'A' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.790A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 68 removed outlier: 3.606A pdb=" N HIS B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 170 through 181 Processing helix chain 'B' and resid 186 through 194 removed outlier: 3.528A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 266 through 276 Processing helix chain 'B' and resid 291 through 299 Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 311 through 325 removed outlier: 3.825A pdb=" N LYS B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 341 through 349 Processing helix chain 'B' and resid 352 through 358 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.095A pdb=" N ALA B 388 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.824A pdb=" N ILE B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 493 through 509 Processing helix chain 'B' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 550 Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.790A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 68 removed outlier: 3.605A pdb=" N HIS C 67 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 170 through 181 Processing helix chain 'C' and resid 186 through 194 removed outlier: 3.529A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 291 through 299 Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 311 through 325 removed outlier: 3.825A pdb=" N LYS C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 325 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'C' and resid 352 through 358 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA C 388 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.825A pdb=" N ILE C 401 " --> pdb=" O ASP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'C' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 550 Processing helix chain 'C' and resid 578 through 583 removed outlier: 3.789A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 68 removed outlier: 3.605A pdb=" N HIS D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 186 through 194 removed outlier: 3.527A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 291 through 299 Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 311 through 325 removed outlier: 3.826A pdb=" N LYS D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 341 through 349 Processing helix chain 'D' and resid 352 through 358 Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA D 388 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.824A pdb=" N ILE D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE D 424 " --> pdb=" O GLY D 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE D 425 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 461 Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 493 through 509 Processing helix chain 'D' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 550 Processing helix chain 'D' and resid 578 through 583 removed outlier: 3.789A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.605A pdb=" N HIS E 67 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 170 through 181 Processing helix chain 'E' and resid 186 through 194 removed outlier: 3.529A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 266 through 276 Processing helix chain 'E' and resid 291 through 299 Proline residue: E 296 - end of helix Processing helix chain 'E' and resid 311 through 325 removed outlier: 3.825A pdb=" N LYS E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 325 " --> pdb=" O PHE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 352 through 358 Processing helix chain 'E' and resid 370 through 372 No H-bonds generated for 'chain 'E' and resid 370 through 372' Processing helix chain 'E' and resid 373 through 383 Processing helix chain 'E' and resid 384 through 388 removed outlier: 4.095A pdb=" N ALA E 388 " --> pdb=" O GLU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.825A pdb=" N ILE E 401 " --> pdb=" O ASP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE E 424 " --> pdb=" O GLY E 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE E 425 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER E 426 " --> pdb=" O THR E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 461 Processing helix chain 'E' and resid 471 through 479 Processing helix chain 'E' and resid 493 through 509 Processing helix chain 'E' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY E 523 " --> pdb=" O GLN E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 550 Processing helix chain 'E' and resid 578 through 583 removed outlier: 3.789A pdb=" N GLU E 582 " --> pdb=" O LYS E 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 68 removed outlier: 3.604A pdb=" N HIS F 67 " --> pdb=" O TYR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 154 through 160 Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 170 through 181 Processing helix chain 'F' and resid 186 through 194 removed outlier: 3.529A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 266 through 276 Processing helix chain 'F' and resid 291 through 299 Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 311 through 325 removed outlier: 3.826A pdb=" N LYS F 324 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 325 " --> pdb=" O PHE F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 341 through 349 Processing helix chain 'F' and resid 352 through 358 Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 373 through 383 Processing helix chain 'F' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA F 388 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.824A pdb=" N ILE F 401 " --> pdb=" O ASP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 426 " --> pdb=" O THR F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 461 Processing helix chain 'F' and resid 471 through 479 Processing helix chain 'F' and resid 493 through 509 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY F 523 " --> pdb=" O GLN F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 550 Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.790A pdb=" N GLU F 582 " --> pdb=" O LYS F 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 68 removed outlier: 3.605A pdb=" N HIS G 67 " --> pdb=" O TYR G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 154 through 160 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 170 through 181 Processing helix chain 'G' and resid 186 through 194 removed outlier: 3.529A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 244 Processing helix chain 'G' and resid 266 through 276 Processing helix chain 'G' and resid 291 through 299 Proline residue: G 296 - end of helix Processing helix chain 'G' and resid 311 through 325 removed outlier: 3.825A pdb=" N LYS G 324 " --> pdb=" O LEU G 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 325 " --> pdb=" O PHE G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 328 No H-bonds generated for 'chain 'G' and resid 326 through 328' Processing helix chain 'G' and resid 341 through 349 Processing helix chain 'G' and resid 352 through 358 Processing helix chain 'G' and resid 370 through 372 No H-bonds generated for 'chain 'G' and resid 370 through 372' Processing helix chain 'G' and resid 373 through 383 Processing helix chain 'G' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA G 388 " --> pdb=" O GLU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 403 removed outlier: 3.825A pdb=" N ILE G 401 " --> pdb=" O ASP G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 434 removed outlier: 3.534A pdb=" N PHE G 424 " --> pdb=" O GLY G 420 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 425 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER G 426 " --> pdb=" O THR G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 461 Processing helix chain 'G' and resid 471 through 479 Processing helix chain 'G' and resid 493 through 509 Processing helix chain 'G' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY G 523 " --> pdb=" O GLN G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 550 Processing helix chain 'G' and resid 578 through 583 removed outlier: 3.789A pdb=" N GLU G 582 " --> pdb=" O LYS G 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.788A pdb=" N GLY A 120 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 6.314A pdb=" N LEU A 204 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 221 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A 206 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 219 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP A 208 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL A 260 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP A 307 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU A 262 " --> pdb=" O TRP A 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 304 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.452A pdb=" N THR G 439 " --> pdb=" O TYR G 484 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET G 486 " --> pdb=" O THR G 439 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP G 441 " --> pdb=" O MET G 486 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL G 513 " --> pdb=" O THR G 554 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL G 556 " --> pdb=" O VAL G 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE G 515 " --> pdb=" O VAL G 556 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU G 410 " --> pdb=" O ASN G 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU G 587 " --> pdb=" O LEU G 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL G 412 " --> pdb=" O LEU G 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU G 589 " --> pdb=" O VAL G 412 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR G 414 " --> pdb=" O LEU G 589 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP G 591 " --> pdb=" O THR G 414 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN G 622 " --> pdb=" O THR G 627 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR G 627 " --> pdb=" O ASN G 622 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.645A pdb=" N THR A 627 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 622 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 410 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU A 587 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 412 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU A 589 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 414 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP A 591 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 513 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 556 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 515 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR A 439 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET A 486 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP A 441 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.789A pdb=" N GLY B 120 " --> pdb=" O PHE B 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU B 204 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 221 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE B 206 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 219 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP B 208 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL B 260 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP B 307 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU B 262 " --> pdb=" O TRP B 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 304 " --> pdb=" O PHE B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 627 through 629 removed outlier: 3.645A pdb=" N THR B 627 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 622 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 410 " --> pdb=" O ASN B 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 587 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 412 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU B 589 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 414 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP B 591 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 513 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL B 556 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 515 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 439 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET B 486 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP B 441 " --> pdb=" O MET B 486 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 485 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 368 " --> pdb=" O PHE B 485 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.789A pdb=" N GLY C 120 " --> pdb=" O PHE C 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU C 204 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU C 221 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE C 206 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 219 " --> pdb=" O PHE C 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 208 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL C 260 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP C 307 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU C 262 " --> pdb=" O TRP C 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 304 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 483 through 485 removed outlier: 6.452A pdb=" N THR C 439 " --> pdb=" O TYR C 484 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 513 " --> pdb=" O THR C 554 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL C 556 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 515 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU C 410 " --> pdb=" O ASN C 585 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU C 587 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 412 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU C 589 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 414 " --> pdb=" O LEU C 589 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASP C 591 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN C 622 " --> pdb=" O THR C 627 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 627 " --> pdb=" O ASN C 622 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.788A pdb=" N GLY D 120 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU D 204 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D 221 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE D 206 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU D 219 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP D 208 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL D 260 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP D 307 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU D 262 " --> pdb=" O TRP D 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE D 304 " --> pdb=" O PHE D 331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 483 through 485 removed outlier: 6.452A pdb=" N THR D 439 " --> pdb=" O TYR D 484 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 513 " --> pdb=" O THR D 554 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL D 556 " --> pdb=" O VAL D 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE D 515 " --> pdb=" O VAL D 556 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU D 410 " --> pdb=" O ASN D 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU D 587 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 412 " --> pdb=" O LEU D 587 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU D 589 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D 414 " --> pdb=" O LEU D 589 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASP D 591 " --> pdb=" O THR D 414 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN D 622 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 627 " --> pdb=" O ASN D 622 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.789A pdb=" N GLY E 120 " --> pdb=" O PHE E 111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU E 204 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU E 221 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE E 206 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU E 219 " --> pdb=" O PHE E 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP E 208 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL E 260 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP E 307 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 262 " --> pdb=" O TRP E 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 304 " --> pdb=" O PHE E 331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 627 through 629 removed outlier: 3.645A pdb=" N THR E 627 " --> pdb=" O ASN E 622 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN E 622 " --> pdb=" O THR E 627 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU E 410 " --> pdb=" O ASN E 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU E 587 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL E 412 " --> pdb=" O LEU E 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU E 589 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR E 414 " --> pdb=" O LEU E 589 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASP E 591 " --> pdb=" O THR E 414 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL E 513 " --> pdb=" O THR E 554 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL E 556 " --> pdb=" O VAL E 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE E 515 " --> pdb=" O VAL E 556 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR E 439 " --> pdb=" O TYR E 484 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N MET E 486 " --> pdb=" O THR E 439 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP E 441 " --> pdb=" O MET E 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.788A pdb=" N GLY F 120 " --> pdb=" O PHE F 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU F 204 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU F 221 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE F 206 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU F 219 " --> pdb=" O PHE F 206 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP F 208 " --> pdb=" O ARG F 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 280 through 282 removed outlier: 6.643A pdb=" N VAL F 260 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP F 307 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU F 262 " --> pdb=" O TRP F 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE F 304 " --> pdb=" O PHE F 331 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 627 through 629 removed outlier: 3.645A pdb=" N THR F 627 " --> pdb=" O ASN F 622 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN F 622 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU F 410 " --> pdb=" O ASN F 585 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU F 587 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL F 412 " --> pdb=" O LEU F 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU F 589 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR F 414 " --> pdb=" O LEU F 589 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASP F 591 " --> pdb=" O THR F 414 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL F 513 " --> pdb=" O THR F 554 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL F 556 " --> pdb=" O VAL F 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 515 " --> pdb=" O VAL F 556 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR F 439 " --> pdb=" O TYR F 484 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET F 486 " --> pdb=" O THR F 439 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP F 441 " --> pdb=" O MET F 486 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 71 through 72 removed outlier: 3.788A pdb=" N GLY G 120 " --> pdb=" O PHE G 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU G 204 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU G 221 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE G 206 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU G 219 " --> pdb=" O PHE G 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP G 208 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL G 260 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP G 307 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU G 262 " --> pdb=" O TRP G 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE G 304 " --> pdb=" O PHE G 331 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3300 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: 11.56 Time building geometry restraints manager: 11.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9587 1.34 - 1.46: 6823 1.46 - 1.58: 13046 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 29610 Sorted by residual: bond pdb=" C ARG F 199 " pdb=" N PRO F 200 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.36e-02 5.41e+03 5.25e-01 bond pdb=" C ARG D 199 " pdb=" N PRO D 200 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.36e-02 5.41e+03 5.08e-01 bond pdb=" C ARG E 199 " pdb=" N PRO E 200 " ideal model delta sigma weight residual 1.335 1.345 -0.009 1.36e-02 5.41e+03 4.59e-01 bond pdb=" C ARG A 199 " pdb=" N PRO A 200 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.39e-01 bond pdb=" C ARG C 199 " pdb=" N PRO C 200 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.36e-01 ... (remaining 29605 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.27: 1084 107.27 - 113.94: 16302 113.94 - 120.62: 11985 120.62 - 127.30: 10396 127.30 - 133.98: 336 Bond angle restraints: 40103 Sorted by residual: angle pdb=" C SER F 447 " pdb=" N ASN F 448 " pdb=" CA ASN F 448 " ideal model delta sigma weight residual 120.38 124.55 -4.17 1.46e+00 4.69e-01 8.16e+00 angle pdb=" C SER C 447 " pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 120.38 124.54 -4.16 1.46e+00 4.69e-01 8.11e+00 angle pdb=" C SER A 447 " pdb=" N ASN A 448 " pdb=" CA ASN A 448 " ideal model delta sigma weight residual 120.38 124.53 -4.15 1.46e+00 4.69e-01 8.09e+00 angle pdb=" C SER G 447 " pdb=" N ASN G 448 " pdb=" CA ASN G 448 " ideal model delta sigma weight residual 120.38 124.52 -4.14 1.46e+00 4.69e-01 8.04e+00 angle pdb=" C SER D 447 " pdb=" N ASN D 448 " pdb=" CA ASN D 448 " ideal model delta sigma weight residual 120.38 124.51 -4.13 1.46e+00 4.69e-01 8.02e+00 ... (remaining 40098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 17054 16.61 - 33.23: 523 33.23 - 49.84: 35 49.84 - 66.46: 0 66.46 - 83.07: 7 Dihedral angle restraints: 17619 sinusoidal: 7196 harmonic: 10423 Sorted by residual: dihedral pdb=" N ARG D 202 " pdb=" CA ARG D 202 " pdb=" CB ARG D 202 " pdb=" CG ARG D 202 " ideal model delta sinusoidal sigma weight residual -60.00 -103.25 43.25 3 1.50e+01 4.44e-03 7.77e+00 dihedral pdb=" N ARG G 202 " pdb=" CA ARG G 202 " pdb=" CB ARG G 202 " pdb=" CG ARG G 202 " ideal model delta sinusoidal sigma weight residual -60.00 -103.24 43.24 3 1.50e+01 4.44e-03 7.77e+00 dihedral pdb=" N ARG B 202 " pdb=" CA ARG B 202 " pdb=" CB ARG B 202 " pdb=" CG ARG B 202 " ideal model delta sinusoidal sigma weight residual -60.00 -103.23 43.23 3 1.50e+01 4.44e-03 7.77e+00 ... (remaining 17616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2784 0.026 - 0.052: 1047 0.052 - 0.078: 290 0.078 - 0.104: 214 0.104 - 0.130: 103 Chirality restraints: 4438 Sorted by residual: chirality pdb=" CA ILE C 238 " pdb=" N ILE C 238 " pdb=" C ILE C 238 " pdb=" CB ILE C 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE G 238 " pdb=" N ILE G 238 " pdb=" C ILE G 238 " pdb=" CB ILE G 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 4435 not shown) Planarity restraints: 5187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 199 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.11e-01 pdb=" N PRO G 200 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO G 200 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 200 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 199 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.98e-01 pdb=" N PRO A 200 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 199 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.96e-01 pdb=" N PRO F 200 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " 0.013 5.00e-02 4.00e+02 ... (remaining 5184 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9996 2.86 - 3.37: 26536 3.37 - 3.88: 47144 3.88 - 4.39: 52962 4.39 - 4.90: 87777 Nonbonded interactions: 224415 Sorted by model distance: nonbonded pdb=" O LEU D 272 " pdb=" OG1 THR D 276 " model vdw 2.347 2.440 nonbonded pdb=" O LEU A 272 " pdb=" OG1 THR A 276 " model vdw 2.347 2.440 nonbonded pdb=" O LEU E 272 " pdb=" OG1 THR E 276 " model vdw 2.348 2.440 nonbonded pdb=" O LEU F 272 " pdb=" OG1 THR F 276 " model vdw 2.348 2.440 nonbonded pdb=" O LEU B 272 " pdb=" OG1 THR B 276 " model vdw 2.348 2.440 ... (remaining 224410 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' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 4.320 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: 0.030 Extract box with map and model: 14.420 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 74.480 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 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 : 0.001 0.025 29610 Z= 0.094 Angle : 0.416 4.822 40103 Z= 0.222 Chirality : 0.037 0.130 4438 Planarity : 0.003 0.024 5187 Dihedral : 7.595 83.072 10857 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.41 % Allowed : 2.71 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.76 (0.15), residues: 3521 helix: 1.41 (0.14), residues: 1295 sheet: 0.76 (0.19), residues: 833 loop : -0.45 (0.17), residues: 1393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.2234 time to fit residues: 36.5054 Evaluate side-chains 110 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 0.0980 chunk 270 optimal weight: 0.0070 chunk 150 optimal weight: 3.9990 chunk 92 optimal weight: 0.0670 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 0.0020 chunk 279 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 170 optimal weight: 0.0270 chunk 208 optimal weight: 1.9990 chunk 324 optimal weight: 0.7980 overall best weight: 0.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 HIS ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 29610 Z= 0.144 Angle : 0.547 7.944 40103 Z= 0.277 Chirality : 0.041 0.131 4438 Planarity : 0.004 0.029 5187 Dihedral : 3.457 15.992 3941 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.85 (0.15), residues: 3521 helix: 1.53 (0.15), residues: 1288 sheet: 0.71 (0.20), residues: 833 loop : -0.38 (0.17), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2107 time to fit residues: 34.0904 Evaluate side-chains 112 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 269 optimal weight: 0.0270 chunk 220 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 324 optimal weight: 0.5980 chunk 350 optimal weight: 0.6980 chunk 289 optimal weight: 0.0970 chunk 322 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 29610 Z= 0.150 Angle : 0.555 7.343 40103 Z= 0.283 Chirality : 0.042 0.138 4438 Planarity : 0.004 0.044 5187 Dihedral : 3.752 18.512 3941 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.46 (0.15), residues: 3521 helix: 1.31 (0.15), residues: 1337 sheet: 0.57 (0.20), residues: 826 loop : -0.83 (0.18), residues: 1358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2096 time to fit residues: 32.1037 Evaluate side-chains 110 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 0.0570 chunk 244 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 218 optimal weight: 0.0870 chunk 325 optimal weight: 0.0970 chunk 345 optimal weight: 0.9980 chunk 170 optimal weight: 0.0370 chunk 308 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 overall best weight: 0.1152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29610 Z= 0.133 Angle : 0.531 7.134 40103 Z= 0.270 Chirality : 0.041 0.124 4438 Planarity : 0.004 0.034 5187 Dihedral : 3.703 18.511 3941 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.31 (0.15), residues: 3521 helix: 1.15 (0.15), residues: 1337 sheet: 0.54 (0.20), residues: 833 loop : -0.92 (0.17), residues: 1351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2275 time to fit residues: 31.4261 Evaluate side-chains 103 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 0.7980 chunk 195 optimal weight: 0.0020 chunk 5 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 294 optimal weight: 0.0370 chunk 238 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 309 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29610 Z= 0.139 Angle : 0.539 6.899 40103 Z= 0.277 Chirality : 0.041 0.134 4438 Planarity : 0.003 0.032 5187 Dihedral : 3.793 19.516 3941 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.34 (0.15), residues: 3521 helix: 1.16 (0.15), residues: 1337 sheet: 0.43 (0.20), residues: 833 loop : -0.78 (0.18), residues: 1351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1984 time to fit residues: 26.1310 Evaluate side-chains 101 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 0.0050 chunk 310 optimal weight: 2.9990 chunk 68 optimal weight: 0.0040 chunk 202 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 345 optimal weight: 0.6980 chunk 286 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 29610 Z= 0.137 Angle : 0.526 6.655 40103 Z= 0.269 Chirality : 0.042 0.168 4438 Planarity : 0.003 0.031 5187 Dihedral : 3.676 16.798 3941 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.47 (0.15), residues: 3521 helix: 1.13 (0.15), residues: 1344 sheet: 0.52 (0.20), residues: 833 loop : -0.57 (0.17), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1947 time to fit residues: 26.3620 Evaluate side-chains 103 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 0.4980 chunk 252 optimal weight: 2.9990 chunk 195 optimal weight: 0.0770 chunk 290 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 344 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 209 optimal weight: 0.0970 chunk 158 optimal weight: 3.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29610 Z= 0.156 Angle : 0.596 8.298 40103 Z= 0.302 Chirality : 0.043 0.158 4438 Planarity : 0.004 0.030 5187 Dihedral : 3.863 16.438 3941 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.28 (0.15), residues: 3521 helix: 1.00 (0.14), residues: 1330 sheet: 0.41 (0.20), residues: 840 loop : -0.69 (0.17), residues: 1351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2019 time to fit residues: 28.3057 Evaluate side-chains 105 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 0.9980 chunk 137 optimal weight: 0.0020 chunk 205 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 218 optimal weight: 0.0000 chunk 234 optimal weight: 0.0170 chunk 170 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 270 optimal weight: 0.0270 overall best weight: 0.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 29610 Z= 0.141 Angle : 0.580 7.719 40103 Z= 0.289 Chirality : 0.043 0.190 4438 Planarity : 0.004 0.030 5187 Dihedral : 3.736 15.314 3941 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.32 (0.15), residues: 3521 helix: 1.02 (0.14), residues: 1323 sheet: 0.54 (0.20), residues: 833 loop : -0.72 (0.17), residues: 1365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1952 time to fit residues: 27.2330 Evaluate side-chains 103 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 0.8980 chunk 329 optimal weight: 0.0370 chunk 300 optimal weight: 0.8980 chunk 320 optimal weight: 0.0270 chunk 192 optimal weight: 0.6980 chunk 139 optimal weight: 0.0060 chunk 251 optimal weight: 0.7980 chunk 98 optimal weight: 0.0770 chunk 289 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 319 optimal weight: 0.0170 overall best weight: 0.0328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29610 Z= 0.140 Angle : 0.590 7.867 40103 Z= 0.293 Chirality : 0.043 0.171 4438 Planarity : 0.004 0.031 5187 Dihedral : 3.673 15.135 3941 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.36 (0.15), residues: 3521 helix: 1.04 (0.14), residues: 1330 sheet: 0.63 (0.20), residues: 833 loop : -0.76 (0.16), residues: 1358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1898 time to fit residues: 26.3559 Evaluate side-chains 101 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 7.9990 chunk 339 optimal weight: 3.9990 chunk 206 optimal weight: 0.0000 chunk 160 optimal weight: 0.9980 chunk 235 optimal weight: 0.0270 chunk 355 optimal weight: 0.6980 chunk 327 optimal weight: 0.7980 chunk 283 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 218 optimal weight: 0.0040 chunk 173 optimal weight: 0.5980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.7133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29610 Z= 0.144 Angle : 0.586 8.514 40103 Z= 0.294 Chirality : 0.043 0.186 4438 Planarity : 0.004 0.030 5187 Dihedral : 3.643 15.227 3941 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.60 (0.15), residues: 3521 helix: 1.22 (0.15), residues: 1288 sheet: 0.78 (0.21), residues: 826 loop : -0.54 (0.17), residues: 1407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1987 time to fit residues: 26.3918 Evaluate side-chains 101 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 0.0040 chunk 301 optimal weight: 7.9990 chunk 86 optimal weight: 0.0570 chunk 261 optimal weight: 8.9990 chunk 41 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 118 optimal weight: 0.0470 chunk 291 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 52 optimal weight: 5.9990 overall best weight: 0.1326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.157260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123378 restraints weight = 8720.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.127780 restraints weight = 5942.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131065 restraints weight = 4465.149| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 29610 Z= 0.131 Angle : 0.570 7.783 40103 Z= 0.282 Chirality : 0.042 0.182 4438 Planarity : 0.004 0.031 5187 Dihedral : 3.624 18.097 3941 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.62 (0.15), residues: 3521 helix: 1.22 (0.15), residues: 1288 sheet: 0.78 (0.20), residues: 826 loop : -0.51 (0.17), residues: 1407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3434.68 seconds wall clock time: 64 minutes 52.83 seconds (3892.83 seconds total)