Starting phenix.real_space_refine on Thu Mar 21 02:37:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/03_2024/7t8c_25744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/03_2024/7t8c_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_25744/03_2024/7t8c_25744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/03_2024/7t8c_25744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/03_2024/7t8c_25744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8c_25744/03_2024/7t8c_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 14.23, 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: 10.69 Conformation dependent library (CDL) restraints added in 4.2 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: 3.40 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: 10.29 Time building geometry restraints manager: 11.62 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.010 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 69.970 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.730 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 122 HIS 0.002 0.000 HIS E 552 PHE 0.004 0.001 PHE E 111 TYR 0.004 0.001 TYR B 602 ARG 0.001 0.000 ARG G 303 *********************** 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 : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7598 (mtp) cc_final: 0.7171 (mtp) REVERT: A 179 MET cc_start: 0.6924 (ptp) cc_final: 0.5858 (tpt) REVERT: A 204 LEU cc_start: 0.7696 (mt) cc_final: 0.7416 (mp) REVERT: A 206 PHE cc_start: 0.7601 (m-80) cc_final: 0.7377 (m-80) REVERT: A 282 THR cc_start: 0.7186 (p) cc_final: 0.5671 (t) REVERT: A 299 GLU cc_start: 0.6479 (tt0) cc_final: 0.6169 (tt0) REVERT: A 313 ARG cc_start: 0.7309 (tpt-90) cc_final: 0.7068 (tpt-90) REVERT: A 316 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 321 PHE cc_start: 0.7409 (m-10) cc_final: 0.6932 (m-80) REVERT: A 470 LYS cc_start: 0.8373 (mttt) cc_final: 0.8021 (mttt) REVERT: A 496 THR cc_start: 0.7460 (m) cc_final: 0.7163 (p) REVERT: A 501 MET cc_start: 0.8068 (mtp) cc_final: 0.7700 (mtp) REVERT: A 509 ASP cc_start: 0.7104 (m-30) cc_final: 0.5361 (m-30) REVERT: A 610 PHE cc_start: 0.8679 (t80) cc_final: 0.8347 (t80) outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.2211 time to fit residues: 36.2124 Evaluate side-chains 112 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 0.0370 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 chunk 279 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 170 optimal weight: 0.0270 chunk 208 optimal weight: 0.0980 chunk 324 optimal weight: 0.7980 overall best weight: 0.0534 ------------------------------------------------------------------------------- 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: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 29610 Z= 0.135 Angle : 0.539 8.106 40103 Z= 0.273 Chirality : 0.041 0.127 4438 Planarity : 0.004 0.029 5187 Dihedral : 3.373 16.292 3941 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: 0.87 (0.15), residues: 3521 helix: 1.58 (0.15), residues: 1288 sheet: 0.67 (0.20), residues: 833 loop : -0.36 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 158 HIS 0.004 0.001 HIS G 552 PHE 0.019 0.001 PHE C 520 TYR 0.012 0.001 TYR D 537 ARG 0.004 0.000 ARG E 192 *********************** 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 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: B 79 ARG cc_start: 0.6649 (ptt180) cc_final: 0.6447 (ptt-90) REVERT: B 104 ILE cc_start: 0.8053 (mm) cc_final: 0.7582 (tp) REVERT: B 179 MET cc_start: 0.7372 (ptp) cc_final: 0.7101 (tpt) REVERT: B 283 LEU cc_start: 0.8307 (mt) cc_final: 0.8050 (mt) REVERT: B 285 ARG cc_start: 0.7304 (mtm-85) cc_final: 0.7066 (mtt180) REVERT: B 299 GLU cc_start: 0.6940 (tt0) cc_final: 0.6449 (tt0) REVERT: B 304 ILE cc_start: 0.7192 (mt) cc_final: 0.6938 (mp) REVERT: B 316 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7567 (mt-10) REVERT: B 321 PHE cc_start: 0.7502 (m-10) cc_final: 0.7062 (m-10) REVERT: B 323 ARG cc_start: 0.7307 (ttm170) cc_final: 0.6641 (tmm-80) REVERT: B 357 ARG cc_start: 0.7045 (mtm110) cc_final: 0.6801 (mtm-85) REVERT: B 423 THR cc_start: 0.6719 (p) cc_final: 0.6508 (t) REVERT: B 455 MET cc_start: 0.7766 (mtp) cc_final: 0.7425 (mtp) REVERT: B 509 ASP cc_start: 0.7145 (m-30) cc_final: 0.6745 (m-30) REVERT: B 510 ILE cc_start: 0.8175 (mm) cc_final: 0.7751 (mm) REVERT: B 522 MET cc_start: 0.7983 (mtp) cc_final: 0.7545 (mtp) REVERT: B 543 ARG cc_start: 0.6550 (tpt170) cc_final: 0.6038 (ttt180) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2017 time to fit residues: 32.4779 Evaluate side-chains 107 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.9990 chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 0.0770 chunk 220 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 324 optimal weight: 0.7980 chunk 350 optimal weight: 0.6980 chunk 289 optimal weight: 0.7980 chunk 322 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 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: 0.5997 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29610 Z= 0.172 Angle : 0.561 6.725 40103 Z= 0.289 Chirality : 0.042 0.134 4438 Planarity : 0.005 0.067 5187 Dihedral : 3.863 19.872 3941 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: 0.49 (0.15), residues: 3521 helix: 1.34 (0.15), residues: 1309 sheet: 0.28 (0.20), residues: 840 loop : -0.56 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 363 HIS 0.003 0.001 HIS F 512 PHE 0.023 0.002 PHE A 370 TYR 0.011 0.002 TYR G 602 ARG 0.005 0.001 ARG F 371 *********************** 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 : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ILE cc_start: 0.8059 (mm) cc_final: 0.7650 (tp) REVERT: B 179 MET cc_start: 0.7461 (ptp) cc_final: 0.7128 (tpt) REVERT: B 206 PHE cc_start: 0.8345 (m-80) cc_final: 0.8049 (m-80) REVERT: B 283 LEU cc_start: 0.8217 (mt) cc_final: 0.7992 (mt) REVERT: B 285 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7364 (mtt180) REVERT: B 295 LEU cc_start: 0.8629 (mt) cc_final: 0.8390 (mt) REVERT: B 299 GLU cc_start: 0.6979 (tt0) cc_final: 0.6433 (tt0) REVERT: B 304 ILE cc_start: 0.7424 (mt) cc_final: 0.7148 (mp) REVERT: B 313 ARG cc_start: 0.8266 (tmm-80) cc_final: 0.8006 (tmm-80) REVERT: B 316 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7723 (mt-10) REVERT: B 321 PHE cc_start: 0.7876 (m-10) cc_final: 0.7272 (m-10) REVERT: B 323 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7111 (ttt-90) REVERT: B 423 THR cc_start: 0.7026 (p) cc_final: 0.6766 (t) REVERT: B 437 VAL cc_start: 0.6488 (t) cc_final: 0.6248 (p) REVERT: B 451 LEU cc_start: 0.7865 (tp) cc_final: 0.7342 (tp) REVERT: B 455 MET cc_start: 0.7951 (mtp) cc_final: 0.7460 (mtp) REVERT: B 509 ASP cc_start: 0.7201 (m-30) cc_final: 0.6303 (m-30) REVERT: B 510 ILE cc_start: 0.8539 (mm) cc_final: 0.8163 (tp) REVERT: B 522 MET cc_start: 0.8069 (mtp) cc_final: 0.7529 (mtp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2058 time to fit residues: 31.4145 Evaluate side-chains 112 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 0.4980 chunk 244 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 35 optimal weight: 0.0170 chunk 154 optimal weight: 6.9990 chunk 218 optimal weight: 0.0670 chunk 325 optimal weight: 0.9990 chunk 345 optimal weight: 0.8980 chunk 170 optimal weight: 0.0370 chunk 308 optimal weight: 0.0970 chunk 92 optimal weight: 0.3980 overall best weight: 0.1232 ------------------------------------------------------------------------------- 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 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.4881 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= 0.130 Angle : 0.521 6.643 40103 Z= 0.263 Chirality : 0.041 0.129 4438 Planarity : 0.004 0.036 5187 Dihedral : 3.586 18.779 3941 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 0.43 (0.15), residues: 3521 helix: 1.27 (0.15), residues: 1295 sheet: 0.33 (0.20), residues: 847 loop : -0.63 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 392 HIS 0.002 0.000 HIS G 512 PHE 0.018 0.001 PHE D 478 TYR 0.011 0.001 TYR G 602 ARG 0.006 0.000 ARG F 453 *********************** 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 113 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ILE cc_start: 0.7999 (mm) cc_final: 0.7480 (tp) REVERT: B 179 MET cc_start: 0.7436 (ptp) cc_final: 0.7119 (tpt) REVERT: B 206 PHE cc_start: 0.8288 (m-80) cc_final: 0.8025 (m-80) REVERT: B 285 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7324 (mtt180) REVERT: B 295 LEU cc_start: 0.8508 (mt) cc_final: 0.8231 (mt) REVERT: B 299 GLU cc_start: 0.7041 (tt0) cc_final: 0.6407 (tt0) REVERT: B 304 ILE cc_start: 0.7137 (mt) cc_final: 0.6884 (mp) REVERT: B 316 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 321 PHE cc_start: 0.7664 (m-10) cc_final: 0.7204 (m-10) REVERT: B 323 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7198 (ttt-90) REVERT: B 357 ARG cc_start: 0.7086 (mtm110) cc_final: 0.6524 (mtm110) REVERT: B 392 TRP cc_start: 0.6159 (m-90) cc_final: 0.5824 (m-90) REVERT: B 437 VAL cc_start: 0.6545 (t) cc_final: 0.6241 (p) REVERT: B 453 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7713 (mtp180) REVERT: B 509 ASP cc_start: 0.6726 (m-30) cc_final: 0.6214 (m-30) REVERT: B 510 ILE cc_start: 0.8439 (mm) cc_final: 0.8053 (tp) REVERT: B 522 MET cc_start: 0.8013 (mtp) cc_final: 0.7600 (mtp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2070 time to fit residues: 27.7923 Evaluate side-chains 107 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 0.5980 chunk 195 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 142 optimal weight: 0.0470 chunk 294 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 309 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.4482 ------------------------------------------------------------------------------- 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 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.5412 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= 0.139 Angle : 0.533 7.221 40103 Z= 0.270 Chirality : 0.041 0.134 4438 Planarity : 0.003 0.041 5187 Dihedral : 3.637 18.889 3941 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.23 (0.15), residues: 1337 sheet: 0.03 (0.19), residues: 889 loop : -0.58 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 307 HIS 0.003 0.001 HIS D 110 PHE 0.012 0.001 PHE A 301 TYR 0.013 0.001 TYR C 602 ARG 0.004 0.000 ARG E 453 *********************** 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 121 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ILE cc_start: 0.7995 (mm) cc_final: 0.7522 (tp) REVERT: B 105 ASP cc_start: 0.7481 (t0) cc_final: 0.7172 (t0) REVERT: B 179 MET cc_start: 0.7491 (ptp) cc_final: 0.7177 (tpt) REVERT: B 206 PHE cc_start: 0.8244 (m-80) cc_final: 0.7934 (m-80) REVERT: B 248 PHE cc_start: 0.7258 (t80) cc_final: 0.5338 (t80) REVERT: B 285 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.7137 (mtt180) REVERT: B 295 LEU cc_start: 0.8634 (mt) cc_final: 0.8344 (mt) REVERT: B 299 GLU cc_start: 0.7297 (tt0) cc_final: 0.6633 (tt0) REVERT: B 304 ILE cc_start: 0.7166 (mt) cc_final: 0.6947 (mp) REVERT: B 321 PHE cc_start: 0.7864 (m-10) cc_final: 0.7216 (m-10) REVERT: B 323 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7257 (ttt-90) REVERT: B 324 LYS cc_start: 0.8818 (mttt) cc_final: 0.8588 (mttt) REVERT: B 357 ARG cc_start: 0.7631 (mtm110) cc_final: 0.7168 (mtm110) REVERT: B 437 VAL cc_start: 0.6751 (t) cc_final: 0.6492 (p) REVERT: B 455 MET cc_start: 0.8000 (mtp) cc_final: 0.7770 (mtp) REVERT: B 495 ARG cc_start: 0.8373 (tpt170) cc_final: 0.8026 (tpt90) REVERT: B 500 THR cc_start: 0.8593 (m) cc_final: 0.8370 (p) REVERT: B 509 ASP cc_start: 0.7081 (m-30) cc_final: 0.6262 (m-30) REVERT: B 522 MET cc_start: 0.8177 (mtp) cc_final: 0.7745 (mtp) REVERT: B 544 LYS cc_start: 0.8793 (pttm) cc_final: 0.8563 (pttm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2061 time to fit residues: 29.7798 Evaluate side-chains 108 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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: 0.0980 chunk 310 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 345 optimal weight: 0.7980 chunk 286 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 0.0870 chunk 114 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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** B 519 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.5926 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= 0.136 Angle : 0.532 9.784 40103 Z= 0.265 Chirality : 0.041 0.139 4438 Planarity : 0.003 0.036 5187 Dihedral : 3.606 18.285 3941 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 0.42 (0.15), residues: 3521 helix: 1.24 (0.15), residues: 1330 sheet: 0.04 (0.20), residues: 847 loop : -0.42 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 158 HIS 0.003 0.001 HIS G 512 PHE 0.015 0.001 PHE A 478 TYR 0.015 0.002 TYR A 471 ARG 0.002 0.000 ARG B 79 *********************** 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 120 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ILE cc_start: 0.7986 (mm) cc_final: 0.7424 (tp) REVERT: B 179 MET cc_start: 0.7595 (ptp) cc_final: 0.7204 (tpt) REVERT: B 283 LEU cc_start: 0.8125 (mt) cc_final: 0.7886 (mt) REVERT: B 285 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7287 (mtt180) REVERT: B 299 GLU cc_start: 0.7100 (tt0) cc_final: 0.6664 (tt0) REVERT: B 304 ILE cc_start: 0.7047 (mt) cc_final: 0.6716 (mp) REVERT: B 321 PHE cc_start: 0.7907 (m-10) cc_final: 0.7310 (m-10) REVERT: B 323 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7430 (ttt-90) REVERT: B 355 ILE cc_start: 0.8430 (mt) cc_final: 0.8222 (mt) REVERT: B 357 ARG cc_start: 0.7441 (mtm110) cc_final: 0.6882 (mtm110) REVERT: B 437 VAL cc_start: 0.6946 (t) cc_final: 0.6633 (p) REVERT: B 447 SER cc_start: 0.6521 (t) cc_final: 0.6293 (t) REVERT: B 453 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7817 (mtp85) REVERT: B 455 MET cc_start: 0.7992 (mtp) cc_final: 0.7769 (mtp) REVERT: B 496 THR cc_start: 0.8527 (m) cc_final: 0.8234 (p) REVERT: B 509 ASP cc_start: 0.6959 (m-30) cc_final: 0.6369 (m-30) REVERT: B 522 MET cc_start: 0.8064 (mtp) cc_final: 0.7742 (mtp) REVERT: B 544 LYS cc_start: 0.8834 (pttm) cc_final: 0.8567 (pttm) REVERT: B 550 ASN cc_start: 0.8651 (t0) cc_final: 0.8449 (t0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2042 time to fit residues: 29.4083 Evaluate side-chains 107 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 4.9990 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 0.3980 chunk 252 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 290 optimal weight: 0.0970 chunk 192 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 209 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS ** 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: 0.6344 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29610 Z= 0.183 Angle : 0.582 8.870 40103 Z= 0.298 Chirality : 0.042 0.151 4438 Planarity : 0.004 0.036 5187 Dihedral : 4.034 18.533 3941 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 0.04 (0.15), residues: 3521 helix: 0.81 (0.15), residues: 1386 sheet: 0.10 (0.20), residues: 826 loop : -0.75 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 158 HIS 0.004 0.001 HIS E 405 PHE 0.037 0.002 PHE A 370 TYR 0.016 0.002 TYR C 471 ARG 0.003 0.000 ARG B 394 *********************** 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 132 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ILE cc_start: 0.8031 (mm) cc_final: 0.7549 (tp) REVERT: B 105 ASP cc_start: 0.7172 (t70) cc_final: 0.6602 (t0) REVERT: B 107 THR cc_start: 0.8003 (m) cc_final: 0.7754 (p) REVERT: B 179 MET cc_start: 0.7761 (ptp) cc_final: 0.7284 (tpt) REVERT: B 206 PHE cc_start: 0.7827 (m-80) cc_final: 0.7429 (m-80) REVERT: B 299 GLU cc_start: 0.7680 (tt0) cc_final: 0.7108 (tt0) REVERT: B 304 ILE cc_start: 0.7205 (mt) cc_final: 0.6961 (mp) REVERT: B 306 PHE cc_start: 0.8065 (m-80) cc_final: 0.7751 (m-80) REVERT: B 321 PHE cc_start: 0.8057 (m-10) cc_final: 0.7338 (m-10) REVERT: B 333 VAL cc_start: 0.8615 (t) cc_final: 0.8316 (m) REVERT: B 360 LEU cc_start: 0.7921 (mt) cc_final: 0.7694 (mt) REVERT: B 406 ARG cc_start: 0.7134 (mpp-170) cc_final: 0.6899 (mpt180) REVERT: B 453 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7930 (mtp85) REVERT: B 455 MET cc_start: 0.8230 (mtp) cc_final: 0.7992 (mtp) REVERT: B 470 LYS cc_start: 0.7952 (mttt) cc_final: 0.7710 (mttt) REVERT: B 495 ARG cc_start: 0.8393 (tpt90) cc_final: 0.8154 (tpt170) REVERT: B 496 THR cc_start: 0.8388 (m) cc_final: 0.8065 (p) REVERT: B 497 VAL cc_start: 0.8548 (m) cc_final: 0.8215 (m) REVERT: B 501 MET cc_start: 0.8374 (mtm) cc_final: 0.8161 (mtm) REVERT: B 502 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B 509 ASP cc_start: 0.6952 (m-30) cc_final: 0.6018 (m-30) REVERT: B 522 MET cc_start: 0.8087 (mtp) cc_final: 0.7711 (mtp) REVERT: B 544 LYS cc_start: 0.9097 (pttm) cc_final: 0.8750 (pttm) REVERT: B 550 ASN cc_start: 0.8730 (t0) cc_final: 0.8249 (t0) REVERT: B 584 ASP cc_start: 0.5867 (m-30) cc_final: 0.5137 (m-30) REVERT: B 604 GLN cc_start: 0.7561 (tt0) cc_final: 0.7347 (tm-30) REVERT: B 608 ASN cc_start: 0.8476 (t0) cc_final: 0.8113 (t0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1989 time to fit residues: 31.4360 Evaluate side-chains 114 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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: 0.0050 chunk 137 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.0060 chunk 218 optimal weight: 0.9990 chunk 234 optimal weight: 0.0670 chunk 170 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 270 optimal weight: 0.2980 overall best weight: 0.0948 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29610 Z= 0.156 Angle : 0.614 8.172 40103 Z= 0.302 Chirality : 0.042 0.136 4438 Planarity : 0.004 0.037 5187 Dihedral : 3.956 15.521 3941 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 0.27 (0.15), residues: 3521 helix: 1.22 (0.15), residues: 1267 sheet: 0.03 (0.20), residues: 882 loop : -0.61 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 165 HIS 0.002 0.000 HIS G 512 PHE 0.029 0.002 PHE E 370 TYR 0.014 0.001 TYR F 471 ARG 0.005 0.000 ARG C 323 *********************** 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 125 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ILE cc_start: 0.7748 (mm) cc_final: 0.7163 (tp) REVERT: B 105 ASP cc_start: 0.6729 (t70) cc_final: 0.6444 (t70) REVERT: B 111 PHE cc_start: 0.6636 (p90) cc_final: 0.6067 (p90) REVERT: B 163 PRO cc_start: 0.6368 (Cg_exo) cc_final: 0.6045 (Cg_endo) REVERT: B 179 MET cc_start: 0.7686 (ptp) cc_final: 0.7102 (tpt) REVERT: B 206 PHE cc_start: 0.7796 (m-80) cc_final: 0.7356 (m-80) REVERT: B 250 LEU cc_start: 0.8205 (tp) cc_final: 0.7994 (tp) REVERT: B 266 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 285 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6593 (mmm-85) REVERT: B 299 GLU cc_start: 0.7460 (tt0) cc_final: 0.6912 (tt0) REVERT: B 304 ILE cc_start: 0.6963 (mt) cc_final: 0.6721 (mp) REVERT: B 306 PHE cc_start: 0.7879 (m-80) cc_final: 0.7151 (m-80) REVERT: B 321 PHE cc_start: 0.7763 (m-10) cc_final: 0.7329 (m-10) REVERT: B 323 ARG cc_start: 0.8281 (tpp80) cc_final: 0.8007 (tpp80) REVERT: B 332 LEU cc_start: 0.7539 (mt) cc_final: 0.7180 (mt) REVERT: B 333 VAL cc_start: 0.8623 (t) cc_final: 0.8253 (m) REVERT: B 360 LEU cc_start: 0.7857 (mt) cc_final: 0.7580 (pt) REVERT: B 376 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8310 (mp0) REVERT: B 383 ASN cc_start: 0.8022 (t0) cc_final: 0.7782 (t0) REVERT: B 453 ARG cc_start: 0.8360 (mtp180) cc_final: 0.7904 (mtp85) REVERT: B 495 ARG cc_start: 0.8393 (tpt90) cc_final: 0.7979 (tpt90) REVERT: B 496 THR cc_start: 0.8432 (m) cc_final: 0.8085 (p) REVERT: B 501 MET cc_start: 0.8231 (mtm) cc_final: 0.7985 (mtm) REVERT: B 502 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7999 (tm-30) REVERT: B 509 ASP cc_start: 0.6722 (m-30) cc_final: 0.6411 (m-30) REVERT: B 522 MET cc_start: 0.8161 (mtp) cc_final: 0.7955 (mtp) REVERT: B 539 ILE cc_start: 0.8400 (mt) cc_final: 0.8179 (mt) REVERT: B 544 LYS cc_start: 0.8954 (pttm) cc_final: 0.8564 (pttm) REVERT: B 604 GLN cc_start: 0.7430 (tt0) cc_final: 0.7197 (tm-30) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2149 time to fit residues: 32.3921 Evaluate side-chains 114 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 0.7980 chunk 329 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 320 optimal weight: 1.9990 chunk 192 optimal weight: 0.3980 chunk 139 optimal weight: 0.0570 chunk 251 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 289 optimal weight: 0.4980 chunk 303 optimal weight: 0.9980 chunk 319 optimal weight: 0.0770 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.7825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29610 Z= 0.154 Angle : 0.605 7.865 40103 Z= 0.301 Chirality : 0.043 0.156 4438 Planarity : 0.004 0.037 5187 Dihedral : 3.966 16.782 3941 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.71 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: 0.04 (0.15), residues: 3521 helix: 0.90 (0.15), residues: 1274 sheet: 0.10 (0.20), residues: 889 loop : -0.76 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 158 HIS 0.002 0.000 HIS G 512 PHE 0.027 0.001 PHE G 370 TYR 0.013 0.001 TYR B 602 ARG 0.003 0.000 ARG E 156 *********************** 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 120 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8490 (mp10) cc_final: 0.7878 (mp10) REVERT: B 104 ILE cc_start: 0.7730 (mm) cc_final: 0.7159 (tp) REVERT: B 111 PHE cc_start: 0.6659 (p90) cc_final: 0.6125 (p90) REVERT: B 179 MET cc_start: 0.7716 (ptp) cc_final: 0.7237 (tpt) REVERT: B 206 PHE cc_start: 0.7713 (m-80) cc_final: 0.7313 (m-80) REVERT: B 250 LEU cc_start: 0.8221 (tp) cc_final: 0.7987 (tp) REVERT: B 266 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 285 ARG cc_start: 0.7086 (mtt180) cc_final: 0.6518 (mmm-85) REVERT: B 299 GLU cc_start: 0.7548 (tt0) cc_final: 0.6979 (tt0) REVERT: B 304 ILE cc_start: 0.6966 (mt) cc_final: 0.6747 (mp) REVERT: B 306 PHE cc_start: 0.7936 (m-80) cc_final: 0.7581 (m-80) REVERT: B 320 LEU cc_start: 0.8681 (mp) cc_final: 0.8418 (mm) REVERT: B 321 PHE cc_start: 0.7891 (m-10) cc_final: 0.7197 (m-10) REVERT: B 333 VAL cc_start: 0.8618 (t) cc_final: 0.8292 (m) REVERT: B 406 ARG cc_start: 0.6870 (mpp-170) cc_final: 0.6603 (mpt180) REVERT: B 453 ARG cc_start: 0.8412 (mtp180) cc_final: 0.7923 (mtp85) REVERT: B 495 ARG cc_start: 0.8364 (tpt90) cc_final: 0.7995 (tpt90) REVERT: B 496 THR cc_start: 0.8412 (m) cc_final: 0.8061 (p) REVERT: B 501 MET cc_start: 0.8223 (mtm) cc_final: 0.7885 (mtm) REVERT: B 502 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 509 ASP cc_start: 0.7184 (m-30) cc_final: 0.6558 (m-30) REVERT: B 522 MET cc_start: 0.8143 (mtp) cc_final: 0.7755 (mtp) REVERT: B 544 LYS cc_start: 0.9027 (pttm) cc_final: 0.8604 (pttp) REVERT: B 604 GLN cc_start: 0.7556 (tt0) cc_final: 0.7353 (tm-30) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1877 time to fit residues: 27.2461 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 ------------------------------------------------------------------------------- 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: 1.9990 chunk 339 optimal weight: 3.9990 chunk 206 optimal weight: 0.3980 chunk 160 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 218 optimal weight: 0.0270 chunk 173 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.8229 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= 0.154 Angle : 0.597 7.133 40103 Z= 0.296 Chirality : 0.043 0.162 4438 Planarity : 0.003 0.036 5187 Dihedral : 3.924 15.372 3941 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % 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: 0.20 (0.15), residues: 3521 helix: 1.04 (0.15), residues: 1232 sheet: 0.19 (0.19), residues: 896 loop : -0.64 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 158 HIS 0.002 0.001 HIS D 110 PHE 0.028 0.001 PHE F 370 TYR 0.014 0.002 TYR C 602 ARG 0.004 0.000 ARG F 334 ********************** 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 120 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8581 (mp10) cc_final: 0.8272 (mp10) REVERT: B 104 ILE cc_start: 0.7704 (mm) cc_final: 0.7350 (tp) REVERT: B 179 MET cc_start: 0.7789 (ptp) cc_final: 0.7194 (tpt) REVERT: B 206 PHE cc_start: 0.7657 (m-80) cc_final: 0.7326 (m-80) REVERT: B 250 LEU cc_start: 0.8182 (tp) cc_final: 0.7923 (tp) REVERT: B 266 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 285 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6631 (mmm-85) REVERT: B 299 GLU cc_start: 0.7381 (tt0) cc_final: 0.6905 (tt0) REVERT: B 304 ILE cc_start: 0.6970 (mt) cc_final: 0.6738 (mp) REVERT: B 320 LEU cc_start: 0.8668 (mp) cc_final: 0.8435 (mm) REVERT: B 321 PHE cc_start: 0.7900 (m-10) cc_final: 0.7330 (m-10) REVERT: B 329 ARG cc_start: 0.6911 (ptt180) cc_final: 0.6639 (ptt180) REVERT: B 453 ARG cc_start: 0.8459 (mtp180) cc_final: 0.7938 (mtp85) REVERT: B 495 ARG cc_start: 0.8373 (tpt90) cc_final: 0.7864 (tpt90) REVERT: B 497 VAL cc_start: 0.8679 (m) cc_final: 0.8265 (m) REVERT: B 501 MET cc_start: 0.8373 (mtm) cc_final: 0.8066 (mtm) REVERT: B 502 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7848 (tm-30) REVERT: B 509 ASP cc_start: 0.6913 (m-30) cc_final: 0.6268 (m-30) REVERT: B 522 MET cc_start: 0.8016 (mtp) cc_final: 0.7718 (mtp) REVERT: B 544 LYS cc_start: 0.8957 (pttm) cc_final: 0.8661 (pttm) REVERT: B 608 ASN cc_start: 0.8906 (t0) cc_final: 0.8444 (t0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2037 time to fit residues: 29.4314 Evaluate side-chains 112 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 0.3980 chunk 301 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 283 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 291 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.146416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.114852 restraints weight = 9080.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.119205 restraints weight = 5994.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.122359 restraints weight = 4446.577| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.8860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29610 Z= 0.168 Angle : 0.597 6.917 40103 Z= 0.299 Chirality : 0.043 0.145 4438 Planarity : 0.003 0.035 5187 Dihedral : 4.135 16.748 3941 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.08 (0.15), residues: 3521 helix: 0.91 (0.15), residues: 1267 sheet: 0.50 (0.20), residues: 833 loop : -0.96 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 363 HIS 0.002 0.001 HIS A 75 PHE 0.027 0.001 PHE C 370 TYR 0.016 0.002 TYR F 602 ARG 0.003 0.000 ARG B 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.44 seconds wall clock time: 65 minutes 29.66 seconds (3929.66 seconds total)