Starting phenix.real_space_refine (version: dev) on Wed Dec 14 02:02:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/12_2022/8eax_27989.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/12_2022/8eax_27989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/12_2022/8eax_27989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/12_2022/8eax_27989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/12_2022/8eax_27989.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/12_2022/8eax_27989.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.027 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 439": "OD1" <-> "OD2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A ASP 606": "OD1" <-> "OD2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A ASP 687": "OD1" <-> "OD2" Residue "A ASP 704": "OD1" <-> "OD2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 539": "OD1" <-> "OD2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B ASP 559": "OD1" <-> "OD2" Residue "B ASP 605": "OD1" <-> "OD2" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B ASP 626": "OD1" <-> "OD2" Residue "B GLU 627": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 687": "OD1" <-> "OD2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 439": "OD1" <-> "OD2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C ASP 453": "OD1" <-> "OD2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C ASP 478": "OD1" <-> "OD2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C GLU 520": "OE1" <-> "OE2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C GLU 553": "OE1" <-> "OE2" Residue "C ASP 559": "OD1" <-> "OD2" Residue "C ASP 606": "OD1" <-> "OD2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C ASP 626": "OD1" <-> "OD2" Residue "C ASP 679": "OD1" <-> "OD2" Residue "C ASP 687": "OD1" <-> "OD2" Residue "C GLU 700": "OE1" <-> "OE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D ASP 453": "OD1" <-> "OD2" Residue "D ASP 475": "OD1" <-> "OD2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 552": "OE1" <-> "OE2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D GLU 627": "OE1" <-> "OE2" Residue "D ASP 670": "OD1" <-> "OD2" Residue "D GLU 675": "OE1" <-> "OE2" Residue "D ASP 679": "OD1" <-> "OD2" Residue "D TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 700": "OE1" <-> "OE2" Residue "E ASP 439": "OD1" <-> "OD2" Residue "E ASP 447": "OD1" <-> "OD2" Residue "E ASP 453": "OD1" <-> "OD2" Residue "E ASP 461": "OD1" <-> "OD2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "E ASP 606": "OD1" <-> "OD2" Residue "E GLU 663": "OE1" <-> "OE2" Residue "E GLU 675": "OE1" <-> "OE2" Residue "E ASP 687": "OD1" <-> "OD2" Residue "E ASP 704": "OD1" <-> "OD2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 427": "OD1" <-> "OD2" Residue "F ASP 443": "OD1" <-> "OD2" Residue "F ASP 447": "OD1" <-> "OD2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "F ASP 475": "OD1" <-> "OD2" Residue "F PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 539": "OD1" <-> "OD2" Residue "F GLU 551": "OE1" <-> "OE2" Residue "F ASP 559": "OD1" <-> "OD2" Residue "F ASP 605": "OD1" <-> "OD2" Residue "F ASP 606": "OD1" <-> "OD2" Residue "F ASP 626": "OD1" <-> "OD2" Residue "F GLU 627": "OE1" <-> "OE2" Residue "F GLU 663": "OE1" <-> "OE2" Residue "F GLU 674": "OE1" <-> "OE2" Residue "F TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 687": "OD1" <-> "OD2" Residue "F GLU 715": "OE1" <-> "OE2" Residue "G PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 439": "OD1" <-> "OD2" Residue "G ASP 447": "OD1" <-> "OD2" Residue "G ASP 453": "OD1" <-> "OD2" Residue "G ASP 474": "OD1" <-> "OD2" Residue "G ASP 478": "OD1" <-> "OD2" Residue "G GLU 515": "OE1" <-> "OE2" Residue "G GLU 520": "OE1" <-> "OE2" Residue "G GLU 524": "OE1" <-> "OE2" Residue "G GLU 551": "OE1" <-> "OE2" Residue "G GLU 553": "OE1" <-> "OE2" Residue "G ASP 559": "OD1" <-> "OD2" Residue "G ASP 606": "OD1" <-> "OD2" Residue "G ASP 624": "OD1" <-> "OD2" Residue "G ASP 626": "OD1" <-> "OD2" Residue "G ASP 679": "OD1" <-> "OD2" Residue "G ASP 687": "OD1" <-> "OD2" Residue "G GLU 700": "OE1" <-> "OE2" Residue "H PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 418": "OE1" <-> "OE2" Residue "H TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 439": "OD1" <-> "OD2" Residue "H ASP 447": "OD1" <-> "OD2" Residue "H ASP 453": "OD1" <-> "OD2" Residue "H ASP 475": "OD1" <-> "OD2" Residue "H PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 552": "OE1" <-> "OE2" Residue "H ASP 624": "OD1" <-> "OD2" Residue "H GLU 627": "OE1" <-> "OE2" Residue "H ASP 670": "OD1" <-> "OD2" Residue "H GLU 675": "OE1" <-> "OE2" Residue "H ASP 679": "OD1" <-> "OD2" Residue "H TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 700": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18458 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2333 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2293 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 2329 Chain: "C" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2329 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2274 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2272 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Conformer: "B" Number of residues, atoms: 289, 2272 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 bond proxies already assigned to first conformer: 2310 Chain: "E" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2333 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 2293 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 2329 Chain: "G" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2329 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 2274 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2272 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Conformer: "B" Number of residues, atoms: 289, 2272 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 bond proxies already assigned to first conformer: 2310 Time building chain proxies: 14.70, per 1000 atoms: 0.80 Number of scatterers: 18458 At special positions: 0 Unit cell: (141.93, 138.61, 87.98, 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 120 16.00 O 3426 8.00 N 3174 7.00 C 11738 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: 7.07 Conformation dependent library (CDL) restraints added in 4.3 seconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 414 through 423 removed outlier: 3.899A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 removed outlier: 3.669A pdb=" N TYR A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.553A pdb=" N ALA A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.595A pdb=" N VAL A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.622A pdb=" N PHE A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.719A pdb=" N THR A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 530 through 546 removed outlier: 3.551A pdb=" N GLN A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 removed outlier: 3.576A pdb=" N TYR A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 removed outlier: 4.020A pdb=" N PHE A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 610 removed outlier: 3.674A pdb=" N LEU A 593 " --> pdb=" O CYS A 589 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.600A pdb=" N SER A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 654 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 675 removed outlier: 3.904A pdb=" N PHE A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 701 removed outlier: 4.377A pdb=" N ASP A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 689 " --> pdb=" O MET A 685 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 718 removed outlier: 3.999A pdb=" N ARG A 718 " --> pdb=" O GLU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'B' and resid 415 through 423 removed outlier: 3.630A pdb=" N VAL B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 removed outlier: 3.526A pdb=" N ASP B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.687A pdb=" N ILE B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 477 removed outlier: 4.249A pdb=" N LYS B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.518A pdb=" N ILE B 492 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 514 removed outlier: 3.924A pdb=" N TYR B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 545 removed outlier: 3.605A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 4.411A pdb=" N ARG B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 removed outlier: 4.124A pdb=" N PHE B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 568 " --> pdb=" O GLN B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 611 removed outlier: 3.614A pdb=" N GLN B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.545A pdb=" N HIS B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.910A pdb=" N ASN B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 676 removed outlier: 3.645A pdb=" N LEU B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 693 removed outlier: 3.614A pdb=" N THR B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 688 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 689 " --> pdb=" O MET B 685 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 690 " --> pdb=" O MET B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 703 removed outlier: 3.622A pdb=" N ILE B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 4.299A pdb=" N LEU B 714 " --> pdb=" O MET B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 429 removed outlier: 3.709A pdb=" N ILE C 429 " --> pdb=" O PRO C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 removed outlier: 4.512A pdb=" N ASP C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 478 removed outlier: 3.602A pdb=" N VAL C 456 " --> pdb=" O PRO C 452 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 3.952A pdb=" N ILE C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 517 removed outlier: 3.607A pdb=" N THR C 498 " --> pdb=" O GLY C 494 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 499 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN C 500 " --> pdb=" O ALA C 496 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.935A pdb=" N GLU C 524 " --> pdb=" O SER C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 546 removed outlier: 3.680A pdb=" N GLN C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 562 removed outlier: 3.632A pdb=" N TYR C 555 " --> pdb=" O GLU C 551 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 561 " --> pdb=" O MET C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 575 removed outlier: 4.082A pdb=" N PHE C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 610 removed outlier: 3.880A pdb=" N GLN C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C 607 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 643 through 658 removed outlier: 3.561A pdb=" N LEU C 647 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 654 " --> pdb=" O VAL C 650 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 673 removed outlier: 3.535A pdb=" N GLU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 700 removed outlier: 4.245A pdb=" N ASP C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL C 690 " --> pdb=" O MET C 686 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 691 " --> pdb=" O ASP C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.536A pdb=" N LEU C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 714 " --> pdb=" O MET C 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 709 through 714' Processing helix chain 'D' and resid 415 through 423 removed outlier: 3.793A pdb=" N LYS D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 421 " --> pdb=" O PHE D 417 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 423' Processing helix chain 'D' and resid 423 through 431 removed outlier: 3.814A pdb=" N SER D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 450 removed outlier: 3.941A pdb=" N ILE D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TRP D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 478 removed outlier: 4.606A pdb=" N LYS D 458 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 471 " --> pdb=" O HIS D 467 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 473 " --> pdb=" O SER D 469 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 removed outlier: 3.570A pdb=" N ILE D 492 " --> pdb=" O THR D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 514 removed outlier: 3.830A pdb=" N TYR D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 507 " --> pdb=" O THR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 545 removed outlier: 3.879A pdb=" N VAL D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 530 " --> pdb=" O MET D 526 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.667A pdb=" N TYR D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG D 556 " --> pdb=" O GLU D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 removed outlier: 4.035A pdb=" N PHE D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 568 " --> pdb=" O GLN D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 611 removed outlier: 3.574A pdb=" N SER D 588 " --> pdb=" O THR D 584 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS D 589 " --> pdb=" O LYS D 585 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 592 " --> pdb=" O SER D 588 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU D 593 " --> pdb=" O CYS D 589 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS D 604 " --> pdb=" O CYS D 600 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 607 " --> pdb=" O ILE D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 636 Processing helix chain 'D' and resid 643 through 649 removed outlier: 3.645A pdb=" N LEU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 676 removed outlier: 3.516A pdb=" N VAL D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 669 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU D 674 " --> pdb=" O ASP D 670 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 703 removed outlier: 3.535A pdb=" N ARG D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D 687 " --> pdb=" O SER D 683 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS D 689 " --> pdb=" O MET D 685 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 690 " --> pdb=" O MET D 686 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 701 " --> pdb=" O GLY D 697 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 703 " --> pdb=" O ILE D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 717 removed outlier: 4.018A pdb=" N LEU D 714 " --> pdb=" O ARG D 711 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 717 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 423 removed outlier: 3.899A pdb=" N ALA E 420 " --> pdb=" O PHE E 416 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 422 " --> pdb=" O GLU E 418 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E 423 " --> pdb=" O LYS E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 431 removed outlier: 3.669A pdb=" N TYR E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 429 " --> pdb=" O PRO E 425 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 450 removed outlier: 3.553A pdb=" N ALA E 444 " --> pdb=" O GLN E 440 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 445 " --> pdb=" O PHE E 441 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP E 447 " --> pdb=" O ASP E 443 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 478 removed outlier: 3.595A pdb=" N VAL E 456 " --> pdb=" O PRO E 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS E 458 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL E 465 " --> pdb=" O ASP E 461 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 494 removed outlier: 3.622A pdb=" N PHE E 493 " --> pdb=" O THR E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 515 removed outlier: 3.719A pdb=" N THR E 498 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 499 " --> pdb=" O SER E 495 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN E 500 " --> pdb=" O ALA E 496 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE E 507 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS E 508 " --> pdb=" O TYR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 527 Processing helix chain 'E' and resid 530 through 546 removed outlier: 3.551A pdb=" N GLN E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN E 536 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR E 544 " --> pdb=" O LEU E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 562 removed outlier: 3.576A pdb=" N TYR E 555 " --> pdb=" O GLU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 574 removed outlier: 4.020A pdb=" N PHE E 566 " --> pdb=" O THR E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 610 removed outlier: 3.674A pdb=" N LEU E 593 " --> pdb=" O CYS E 589 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN E 602 " --> pdb=" O GLY E 598 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP E 605 " --> pdb=" O PHE E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 638 Processing helix chain 'E' and resid 643 through 658 removed outlier: 3.600A pdb=" N SER E 652 " --> pdb=" O LEU E 648 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR E 653 " --> pdb=" O ASN E 649 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY E 654 " --> pdb=" O VAL E 650 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 655 " --> pdb=" O LEU E 651 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 675 removed outlier: 3.904A pdb=" N PHE E 667 " --> pdb=" O GLU E 663 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 701 removed outlier: 4.377A pdb=" N ASP E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 688 " --> pdb=" O VAL E 684 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS E 689 " --> pdb=" O MET E 685 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 690 " --> pdb=" O MET E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 714 Processing helix chain 'E' and resid 715 through 718 removed outlier: 3.999A pdb=" N ARG E 718 " --> pdb=" O GLU E 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 715 through 718' Processing helix chain 'F' and resid 415 through 423 removed outlier: 3.630A pdb=" N VAL F 421 " --> pdb=" O PHE F 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU F 423 " --> pdb=" O LYS F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 431 removed outlier: 3.526A pdb=" N ASP F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 450 removed outlier: 3.687A pdb=" N ILE F 442 " --> pdb=" O ARG F 438 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP F 443 " --> pdb=" O ASP F 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 445 " --> pdb=" O PHE F 441 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN F 446 " --> pdb=" O ILE F 442 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP F 447 " --> pdb=" O ASP F 443 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP F 448 " --> pdb=" O ALA F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 477 removed outlier: 4.249A pdb=" N LYS F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F 473 " --> pdb=" O SER F 469 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE F 476 " --> pdb=" O LEU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 removed outlier: 3.518A pdb=" N ILE F 492 " --> pdb=" O THR F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 514 removed outlier: 3.924A pdb=" N TYR F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE F 507 " --> pdb=" O THR F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 545 removed outlier: 3.605A pdb=" N SER F 528 " --> pdb=" O GLU F 524 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU F 532 " --> pdb=" O SER F 528 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE F 533 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP F 539 " --> pdb=" O GLY F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 562 removed outlier: 4.411A pdb=" N ARG F 556 " --> pdb=" O GLU F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 572 removed outlier: 4.124A pdb=" N PHE F 566 " --> pdb=" O THR F 562 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 589 Processing helix chain 'F' and resid 590 through 611 removed outlier: 3.614A pdb=" N GLN F 602 " --> pdb=" O GLY F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 636 removed outlier: 3.545A pdb=" N HIS F 636 " --> pdb=" O LEU F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 649 removed outlier: 3.910A pdb=" N ASN F 649 " --> pdb=" O MET F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 676 removed outlier: 3.645A pdb=" N LEU F 669 " --> pdb=" O LYS F 665 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE F 672 " --> pdb=" O VAL F 668 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU F 673 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU F 675 " --> pdb=" O ILE F 671 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS F 676 " --> pdb=" O ILE F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 677 through 693 removed outlier: 3.614A pdb=" N THR F 681 " --> pdb=" O SER F 677 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG F 682 " --> pdb=" O LEU F 678 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU F 688 " --> pdb=" O VAL F 684 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS F 689 " --> pdb=" O MET F 685 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL F 690 " --> pdb=" O MET F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 703 removed outlier: 3.622A pdb=" N ILE F 699 " --> pdb=" O GLU F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 714 removed outlier: 4.299A pdb=" N LEU F 714 " --> pdb=" O MET F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 717 No H-bonds generated for 'chain 'F' and resid 715 through 717' Processing helix chain 'G' and resid 415 through 419 Processing helix chain 'G' and resid 423 through 429 removed outlier: 3.709A pdb=" N ILE G 429 " --> pdb=" O PRO G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 450 removed outlier: 4.512A pdb=" N ASP G 447 " --> pdb=" O ASP G 443 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP G 448 " --> pdb=" O ALA G 444 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G 449 " --> pdb=" O LEU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 478 removed outlier: 3.602A pdb=" N VAL G 456 " --> pdb=" O PRO G 452 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS G 458 " --> pdb=" O VAL G 454 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS G 460 " --> pdb=" O VAL G 456 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 461 " --> pdb=" O GLY G 457 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 462 " --> pdb=" O LYS G 458 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL G 465 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 472 " --> pdb=" O ASN G 468 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 473 " --> pdb=" O SER G 469 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE G 476 " --> pdb=" O LEU G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 494 removed outlier: 3.952A pdb=" N ILE G 492 " --> pdb=" O SER G 488 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 493 " --> pdb=" O THR G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 517 removed outlier: 3.607A pdb=" N THR G 498 " --> pdb=" O GLY G 494 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL G 499 " --> pdb=" O SER G 495 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN G 500 " --> pdb=" O ALA G 496 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE G 507 " --> pdb=" O THR G 503 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER G 517 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 525 removed outlier: 3.935A pdb=" N GLU G 524 " --> pdb=" O SER G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 546 removed outlier: 3.680A pdb=" N GLN G 534 " --> pdb=" O MET G 530 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN G 536 " --> pdb=" O LEU G 532 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP G 539 " --> pdb=" O GLY G 535 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR G 544 " --> pdb=" O LEU G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 562 removed outlier: 3.632A pdb=" N TYR G 555 " --> pdb=" O GLU G 551 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS G 561 " --> pdb=" O MET G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 575 removed outlier: 4.082A pdb=" N PHE G 566 " --> pdb=" O THR G 562 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 586 through 610 removed outlier: 3.880A pdb=" N GLN G 602 " --> pdb=" O GLY G 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 603 " --> pdb=" O ARG G 599 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR G 607 " --> pdb=" O ILE G 603 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 638 Processing helix chain 'G' and resid 643 through 658 removed outlier: 3.561A pdb=" N LEU G 647 " --> pdb=" O SER G 643 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY G 654 " --> pdb=" O VAL G 650 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG G 655 " --> pdb=" O LEU G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 663 through 673 removed outlier: 3.535A pdb=" N GLU G 673 " --> pdb=" O LEU G 669 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 700 removed outlier: 4.245A pdb=" N ASP G 687 " --> pdb=" O SER G 683 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL G 690 " --> pdb=" O MET G 686 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN G 691 " --> pdb=" O ASP G 687 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 714 removed outlier: 3.536A pdb=" N LEU G 713 " --> pdb=" O ALA G 709 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 714 " --> pdb=" O MET G 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 709 through 714' Processing helix chain 'H' and resid 415 through 423 removed outlier: 3.793A pdb=" N LYS H 419 " --> pdb=" O ILE H 415 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA H 420 " --> pdb=" O PHE H 416 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL H 421 " --> pdb=" O PHE H 417 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU H 423 " --> pdb=" O LYS H 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 415 through 423' Processing helix chain 'H' and resid 423 through 431 removed outlier: 3.814A pdb=" N SER H 431 " --> pdb=" O ASP H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 450 removed outlier: 3.941A pdb=" N ILE H 442 " --> pdb=" O ARG H 438 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP H 443 " --> pdb=" O ASP H 439 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP H 447 " --> pdb=" O ASP H 443 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TRP H 448 " --> pdb=" O ALA H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 478 removed outlier: 4.606A pdb=" N LYS H 458 " --> pdb=" O VAL H 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 471 " --> pdb=" O HIS H 467 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE H 476 " --> pdb=" O LEU H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 492 removed outlier: 3.570A pdb=" N ILE H 492 " --> pdb=" O THR H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 514 removed outlier: 3.830A pdb=" N TYR H 504 " --> pdb=" O ASN H 500 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 507 " --> pdb=" O THR H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 545 removed outlier: 3.879A pdb=" N VAL H 525 " --> pdb=" O SER H 521 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 529 " --> pdb=" O VAL H 525 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET H 530 " --> pdb=" O MET H 526 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE H 531 " --> pdb=" O ASN H 527 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU H 532 " --> pdb=" O SER H 528 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE H 533 " --> pdb=" O ILE H 529 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN H 534 " --> pdb=" O MET H 530 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP H 539 " --> pdb=" O GLY H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 550 through 562 removed outlier: 3.667A pdb=" N TYR H 555 " --> pdb=" O GLU H 551 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG H 556 " --> pdb=" O GLU H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 572 removed outlier: 4.035A pdb=" N PHE H 566 " --> pdb=" O THR H 562 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE H 568 " --> pdb=" O GLN H 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 611 removed outlier: 3.574A pdb=" N SER H 588 " --> pdb=" O THR H 584 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS H 589 " --> pdb=" O LYS H 585 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU H 590 " --> pdb=" O ILE H 586 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG H 592 " --> pdb=" O SER H 588 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU H 593 " --> pdb=" O CYS H 589 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS H 604 " --> pdb=" O CYS H 600 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 607 " --> pdb=" O ILE H 603 " (cutoff:3.500A) Processing helix chain 'H' and resid 631 through 636 Processing helix chain 'H' and resid 643 through 649 removed outlier: 3.645A pdb=" N LEU H 647 " --> pdb=" O SER H 643 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN H 649 " --> pdb=" O MET H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 663 through 676 removed outlier: 3.516A pdb=" N VAL H 668 " --> pdb=" O GLN H 664 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU H 669 " --> pdb=" O LYS H 665 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU H 673 " --> pdb=" O LEU H 669 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU H 674 " --> pdb=" O ASP H 670 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU H 675 " --> pdb=" O ILE H 671 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS H 676 " --> pdb=" O ILE H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 676 through 703 removed outlier: 3.535A pdb=" N ARG H 682 " --> pdb=" O LEU H 678 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP H 687 " --> pdb=" O SER H 683 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS H 689 " --> pdb=" O MET H 685 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL H 690 " --> pdb=" O MET H 686 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA H 694 " --> pdb=" O VAL H 690 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY H 697 " --> pdb=" O ARG H 693 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE H 701 " --> pdb=" O GLY H 697 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU H 702 " --> pdb=" O ARG H 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU H 703 " --> pdb=" O ILE H 699 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 717 removed outlier: 4.018A pdb=" N LEU H 714 " --> pdb=" O ARG H 711 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU H 717 " --> pdb=" O LEU H 714 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2643 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: 4.62 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6124 1.34 - 1.46: 3484 1.46 - 1.58: 8970 1.58 - 1.70: 0 1.70 - 1.81: 216 Bond restraints: 18794 Sorted by residual: bond pdb=" CA PRO D 582 " pdb=" C PRO D 582 " ideal model delta sigma weight residual 1.528 1.519 0.010 9.10e-03 1.21e+04 1.12e+00 bond pdb=" CA PRO H 582 " pdb=" C PRO H 582 " ideal model delta sigma weight residual 1.528 1.519 0.010 9.10e-03 1.21e+04 1.12e+00 bond pdb=" CA ILE F 581 " pdb=" CB ILE F 581 " ideal model delta sigma weight residual 1.540 1.567 -0.027 2.70e-02 1.37e+03 1.02e+00 bond pdb=" CA ILE B 581 " pdb=" CB ILE B 581 " ideal model delta sigma weight residual 1.540 1.567 -0.027 2.70e-02 1.37e+03 1.02e+00 bond pdb=" CB ILE H 507 " pdb=" CG2 ILE H 507 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.84e-01 ... (remaining 18789 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.05: 384 106.05 - 113.05: 10080 113.05 - 120.04: 7074 120.04 - 127.04: 7660 127.04 - 134.04: 202 Bond angle restraints: 25400 Sorted by residual: angle pdb=" CA MET H 710 " pdb=" CB MET H 710 " pdb=" CG MET H 710 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" CA MET D 710 " pdb=" CB MET D 710 " pdb=" CG MET D 710 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" CA LEU B 610 " pdb=" CB LEU B 610 " pdb=" CG LEU B 610 " ideal model delta sigma weight residual 116.30 126.72 -10.42 3.50e+00 8.16e-02 8.86e+00 angle pdb=" CA LEU F 610 " pdb=" CB LEU F 610 " pdb=" CG LEU F 610 " ideal model delta sigma weight residual 116.30 126.72 -10.42 3.50e+00 8.16e-02 8.86e+00 angle pdb=" CA LYS C 676 " pdb=" CB LYS C 676 " pdb=" CG LYS C 676 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.62e+00 ... (remaining 25395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10334 17.84 - 35.68: 842 35.68 - 53.52: 166 53.52 - 71.36: 38 71.36 - 89.20: 40 Dihedral angle restraints: 11420 sinusoidal: 4604 harmonic: 6816 Sorted by residual: dihedral pdb=" CA THR F 653 " pdb=" C THR F 653 " pdb=" N GLY F 654 " pdb=" CA GLY F 654 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA THR B 653 " pdb=" C THR B 653 " pdb=" N GLY B 654 " pdb=" CA GLY B 654 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA THR C 661 " pdb=" C THR C 661 " pdb=" N LEU C 662 " pdb=" CA LEU C 662 " ideal model delta harmonic sigma weight residual 180.00 162.61 17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1892 0.045 - 0.089: 882 0.089 - 0.133: 120 0.133 - 0.178: 14 0.178 - 0.222: 2 Chirality restraints: 2910 Sorted by residual: chirality pdb=" CB ILE B 581 " pdb=" CA ILE B 581 " pdb=" CG1 ILE B 581 " pdb=" CG2 ILE B 581 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE F 581 " pdb=" CA ILE F 581 " pdb=" CG1 ILE F 581 " pdb=" CG2 ILE F 581 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU D 482 " pdb=" CB LEU D 482 " pdb=" CD1 LEU D 482 " pdb=" CD2 LEU D 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 2907 not shown) Planarity restraints: 3248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 451 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO D 452 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 452 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 452 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 451 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO H 452 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 452 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 452 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 581 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO D 582 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 582 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 582 " 0.026 5.00e-02 4.00e+02 ... (remaining 3245 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2840 2.75 - 3.29: 20086 3.29 - 3.83: 27423 3.83 - 4.36: 33849 4.36 - 4.90: 53418 Nonbonded interactions: 137616 Sorted by model distance: nonbonded pdb=" O MET G 660 " pdb=" OG1 THR G 661 " model vdw 2.213 2.440 nonbonded pdb=" O MET C 660 " pdb=" OG1 THR C 661 " model vdw 2.213 2.440 nonbonded pdb=" OD2 ASP A 606 " pdb=" OG SER A 631 " model vdw 2.246 2.440 nonbonded pdb=" OD2 ASP E 606 " pdb=" OG SER E 631 " model vdw 2.246 2.440 nonbonded pdb=" O VAL C 650 " pdb=" OG1 THR C 653 " model vdw 2.249 2.440 ... (remaining 137611 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' and (resid 414 through 437 or resid 439 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 577 o \ r resid 581 through 584 or (resid 585 through 587 and (name N or name CA or name \ C or name O or name CB )) or resid 588 through 591 or (resid 592 and (name N or \ name CA or name C or name O or name CB )) or resid 593 through 611 or resid 624 \ through 652 or (resid 653 and (name N or name CA or name C or name O or name CB \ )) or resid 654 or (resid 655 and (name N or name CA or name C or name O or nam \ e CB )) or resid 656 through 663 or (resid 664 through 665 and (name N or name C \ A or name C or name O or name CB )) or resid 666 through 703 or (resid 704 and ( \ name N or name CA or name C or name O or name CB )) or resid 705 through 706 or \ (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 708 \ through 710 or (resid 711 and (name N or name CA or name C or name O or name CB \ )) or resid 712 through 717)) selection = (chain 'B' and (resid 414 through 437 or resid 439 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 577 o \ r (resid 581 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 82 or (resid 583 through 587 and (name N or name CA or name C or name O or name \ CB )) or resid 588 through 591 or (resid 592 and (name N or name CA or name C or \ name O or name CB )) or resid 593 through 672 or (resid 673 and (name N or name \ CA or name C or name O or name CB )) or resid 674 through 703 or (resid 704 and \ (name N or name CA or name C or name O or name CB )) or resid 705 through 706 o \ r (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 08 through 710 or (resid 711 and (name N or name CA or name C or name O or name \ CB )) or resid 712 through 717)) selection = (chain 'C' and (resid 414 through 437 or resid 439 through 577 or resid 581 thro \ ugh 583 or (resid 584 through 587 and (name N or name CA or name C or name O or \ name CB )) or resid 588 through 591 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 611 or resid 624 through 652 or \ (resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ or (resid 655 and (name N or name CA or name C or name O or name CB )) or resid \ 656 through 663 or (resid 664 through 665 and (name N or name CA or name C or n \ ame O or name CB )) or resid 666 through 672 or (resid 673 and (name N or name C \ A or name C or name O or name CB )) or resid 674 through 703 or (resid 704 and ( \ name N or name CA or name C or name O or name CB )) or resid 705 through 706 or \ (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 708 \ through 710 or (resid 711 and (name N or name CA or name C or name O or name CB \ )) or resid 712 through 717)) selection = (chain 'D' and (resid 414 through 437 or resid 439 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 577 o \ r (resid 581 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 82 through 583 or (resid 584 through 587 and (name N or name CA or name C or nam \ e O or name CB )) or resid 588 through 652 or (resid 653 and (name N or name CA \ or name C or name O or name CB )) or resid 654 or (resid 655 and (name N or name \ CA or name C or name O or name CB )) or resid 656 through 663 or (resid 664 thr \ ough 665 and (name N or name CA or name C or name O or name CB )) or resid 666 t \ hrough 672 or (resid 673 and (name N or name CA or name C or name O or name CB ) \ ) or resid 674 through 717)) selection = (chain 'E' and (resid 414 through 437 or resid 439 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 577 o \ r resid 581 through 584 or (resid 585 through 587 and (name N or name CA or name \ C or name O or name CB )) or resid 588 through 591 or (resid 592 and (name N or \ name CA or name C or name O or name CB )) or resid 593 through 611 or resid 624 \ through 652 or (resid 653 and (name N or name CA or name C or name O or name CB \ )) or resid 654 or (resid 655 and (name N or name CA or name C or name O or nam \ e CB )) or resid 656 through 663 or (resid 664 through 665 and (name N or name C \ A or name C or name O or name CB )) or resid 666 through 703 or (resid 704 and ( \ name N or name CA or name C or name O or name CB )) or resid 705 through 706 or \ (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 708 \ through 710 or (resid 711 and (name N or name CA or name C or name O or name CB \ )) or resid 712 through 717)) selection = (chain 'F' and (resid 414 through 437 or resid 439 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 577 o \ r (resid 581 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 82 or (resid 583 through 587 and (name N or name CA or name C or name O or name \ CB )) or resid 588 through 591 or (resid 592 and (name N or name CA or name C or \ name O or name CB )) or resid 593 through 672 or (resid 673 and (name N or name \ CA or name C or name O or name CB )) or resid 674 through 703 or (resid 704 and \ (name N or name CA or name C or name O or name CB )) or resid 705 through 706 o \ r (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 08 through 710 or (resid 711 and (name N or name CA or name C or name O or name \ CB )) or resid 712 through 717)) selection = (chain 'G' and (resid 414 through 437 or resid 439 through 577 or resid 581 thro \ ugh 583 or (resid 584 through 587 and (name N or name CA or name C or name O or \ name CB )) or resid 588 through 591 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 611 or resid 624 through 652 or \ (resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ or (resid 655 and (name N or name CA or name C or name O or name CB )) or resid \ 656 through 663 or (resid 664 through 665 and (name N or name CA or name C or n \ ame O or name CB )) or resid 666 through 672 or (resid 673 and (name N or name C \ A or name C or name O or name CB )) or resid 674 through 703 or (resid 704 and ( \ name N or name CA or name C or name O or name CB )) or resid 705 through 706 or \ (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 708 \ through 710 or (resid 711 and (name N or name CA or name C or name O or name CB \ )) or resid 712 through 717)) selection = (chain 'H' and (resid 414 through 437 or resid 439 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 577 o \ r (resid 581 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 82 through 583 or (resid 584 through 587 and (name N or name CA or name C or nam \ e O or name CB )) or resid 588 through 652 or (resid 653 and (name N or name CA \ or name C or name O or name CB )) or resid 654 or (resid 655 and (name N or name \ CA or name C or name O or name CB )) or resid 656 through 663 or (resid 664 thr \ ough 665 and (name N or name CA or name C or name O or name CB )) or resid 666 t \ hrough 672 or (resid 673 and (name N or name CA or name C or name O or name CB ) \ ) or resid 674 through 717)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11738 2.51 5 N 3174 2.21 5 O 3426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.630 Check model and map are aligned: 0.280 Convert atoms to be neutral: 0.160 Process input model: 52.380 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 18794 Z= 0.291 Angle : 0.834 10.416 25400 Z= 0.421 Chirality : 0.046 0.222 2910 Planarity : 0.005 0.048 3248 Dihedral : 14.959 89.197 6988 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.77 % Favored : 89.79 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.15), residues: 2296 helix: -2.50 (0.10), residues: 1514 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 656 time to evaluate : 1.934 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 661 average time/residue: 0.3087 time to fit residues: 301.8948 Evaluate side-chains 570 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 569 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1777 time to fit residues: 3.5622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS A 440 GLN A 477 GLN A 479 ASN A 527 ASN A 536 GLN A 591 HIS A 644 HIS A 649 ASN A 666 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 649 ASN C 446 ASN C 523 GLN C 587 GLN C 664 GLN D 414 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 HIS D 641 GLN D 644 HIS ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 HIS E 440 GLN E 468 ASN E 477 GLN E 479 ASN E 527 ASN E 536 GLN E 644 HIS E 649 ASN E 666 GLN ** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 547 HIS G 446 ASN G 523 GLN G 649 ASN G 664 GLN H 414 HIS ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 GLN H 636 HIS H 641 GLN H 644 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 18794 Z= 0.249 Angle : 0.780 12.271 25400 Z= 0.387 Chirality : 0.044 0.184 2910 Planarity : 0.005 0.052 3248 Dihedral : 4.689 24.408 2498 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.28 % Favored : 93.46 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.17), residues: 2296 helix: -0.97 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 597 time to evaluate : 2.168 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 30 residues processed: 620 average time/residue: 0.3106 time to fit residues: 283.8321 Evaluate side-chains 595 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 565 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1934 time to fit residues: 13.0593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN A 468 ASN A 644 HIS A 666 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 HIS ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN E 644 HIS ** G 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS H 644 HIS ** H 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 18794 Z= 0.220 Angle : 0.740 12.689 25400 Z= 0.362 Chirality : 0.042 0.253 2910 Planarity : 0.004 0.050 3248 Dihedral : 4.473 22.422 2498 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2296 helix: -0.49 (0.13), residues: 1574 sheet: None (None), residues: 0 loop : -1.78 (0.23), residues: 722 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 580 time to evaluate : 2.353 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 596 average time/residue: 0.3124 time to fit residues: 272.5899 Evaluate side-chains 579 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 560 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1573 time to fit residues: 8.6560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 107 optimal weight: 0.0030 chunk 22 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 139 optimal weight: 0.4980 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN B 467 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS E 657 HIS E 666 GLN F 534 GLN ** G 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 18794 Z= 0.195 Angle : 0.717 14.087 25400 Z= 0.345 Chirality : 0.041 0.253 2910 Planarity : 0.004 0.047 3248 Dihedral : 4.312 19.882 2498 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2296 helix: -0.21 (0.13), residues: 1562 sheet: None (None), residues: 0 loop : -1.53 (0.23), residues: 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 576 time to evaluate : 2.062 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 588 average time/residue: 0.3100 time to fit residues: 269.1379 Evaluate side-chains 575 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 560 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1627 time to fit residues: 7.7055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 152 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS E 666 GLN F 534 GLN ** G 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS ** H 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18794 Z= 0.218 Angle : 0.723 15.263 25400 Z= 0.349 Chirality : 0.041 0.250 2910 Planarity : 0.004 0.048 3248 Dihedral : 4.292 18.396 2498 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2296 helix: -0.15 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -1.82 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 566 time to evaluate : 2.165 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 577 average time/residue: 0.3259 time to fit residues: 275.0732 Evaluate side-chains 572 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 558 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1657 time to fit residues: 7.5237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.4980 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN A 666 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN ** D 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS E 666 GLN F 534 GLN ** G 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS H 666 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18794 Z= 0.218 Angle : 0.732 15.571 25400 Z= 0.351 Chirality : 0.041 0.221 2910 Planarity : 0.004 0.054 3248 Dihedral : 4.242 17.012 2498 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.18), residues: 2296 helix: -0.00 (0.13), residues: 1606 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 567 time to evaluate : 2.099 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: symmetry clash outliers start: 25 outliers final: 11 residues processed: 575 average time/residue: 0.3394 time to fit residues: 287.3908 Evaluate side-chains 565 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 554 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1743 time to fit residues: 6.6272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 HIS A 666 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN D 545 ASN D 636 HIS D 666 GLN ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS E 666 GLN F 534 GLN G 664 GLN H 636 HIS ** H 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 18794 Z= 0.223 Angle : 0.745 16.518 25400 Z= 0.357 Chirality : 0.041 0.264 2910 Planarity : 0.004 0.053 3248 Dihedral : 4.242 17.466 2498 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2296 helix: 0.10 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : -1.71 (0.24), residues: 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 576 time to evaluate : 1.916 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: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 584 average time/residue: 0.3130 time to fit residues: 267.0964 Evaluate side-chains 576 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 565 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1710 time to fit residues: 6.2518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 149 optimal weight: 0.0060 chunk 108 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 172 optimal weight: 0.0770 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN A 666 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS D 636 HIS D 689 HIS ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS E 649 ASN E 666 GLN F 467 HIS F 534 GLN H 636 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 18794 Z= 0.191 Angle : 0.744 16.824 25400 Z= 0.351 Chirality : 0.040 0.309 2910 Planarity : 0.004 0.054 3248 Dihedral : 4.156 20.916 2498 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2296 helix: 0.26 (0.13), residues: 1592 sheet: None (None), residues: 0 loop : -1.54 (0.24), residues: 704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 567 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 575 average time/residue: 0.3161 time to fit residues: 268.5382 Evaluate side-chains 559 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 551 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1611 time to fit residues: 5.5526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 185 optimal weight: 0.4980 chunk 193 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 HIS ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS H 602 GLN H 636 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 18794 Z= 0.241 Angle : 0.783 16.278 25400 Z= 0.373 Chirality : 0.042 0.281 2910 Planarity : 0.004 0.064 3248 Dihedral : 4.231 21.051 2498 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2296 helix: 0.24 (0.13), residues: 1622 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 674 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 561 time to evaluate : 2.075 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: symmetry clash outliers start: 17 outliers final: 5 residues processed: 565 average time/residue: 0.3204 time to fit residues: 265.0349 Evaluate side-chains 562 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 557 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2364 time to fit residues: 4.9994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 0.0670 chunk 227 optimal weight: 3.9990 chunk 209 optimal weight: 0.1980 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.0470 chunk 143 optimal weight: 0.8980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN C 536 GLN ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS F 534 GLN H 636 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 18794 Z= 0.210 Angle : 0.783 16.792 25400 Z= 0.372 Chirality : 0.041 0.326 2910 Planarity : 0.004 0.078 3248 Dihedral : 4.248 21.478 2498 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2296 helix: 0.31 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 672 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 553 time to evaluate : 2.186 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: symmetry clash outliers start: 5 outliers final: 2 residues processed: 555 average time/residue: 0.3215 time to fit residues: 261.7724 Evaluate side-chains 546 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 544 time to evaluate : 2.205 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1572 time to fit residues: 3.6871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 55 optimal weight: 0.0030 chunk 166 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 chunk 181 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 159 optimal weight: 0.8980 overall best weight: 0.4248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN E 644 HIS F 534 GLN H 636 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.158440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124798 restraints weight = 51411.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132741 restraints weight = 24480.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136402 restraints weight = 12306.502| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 18794 Z= 0.207 Angle : 0.782 16.892 25400 Z= 0.371 Chirality : 0.041 0.296 2910 Planarity : 0.004 0.087 3248 Dihedral : 4.218 21.881 2498 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2296 helix: 0.41 (0.14), residues: 1616 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 680 =============================================================================== Job complete usr+sys time: 4865.25 seconds wall clock time: 89 minutes 42.58 seconds (5382.58 seconds total)