Starting phenix.real_space_refine on Sun Mar 17 17:18:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/03_2024/8eax_27989.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/03_2024/8eax_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_27989/03_2024/8eax_27989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/03_2024/8eax_27989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/03_2024/8eax_27989.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eax_27989/03_2024/8eax_27989.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 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. 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-5265/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: 14.13, per 1000 atoms: 0.77 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: 6.68 Conformation dependent library (CDL) restraints added in 4.9 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: 1.83 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: 4.76 Time building geometry restraints manager: 7.23 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 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.430 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 52.920 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 % Allowed : 4.36 % Favored : 95.35 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 630 HIS 0.012 0.001 HIS G 467 PHE 0.029 0.003 PHE D 533 TYR 0.017 0.002 TYR A 544 ARG 0.005 0.001 ARG B 583 *********************** 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 : 2.169 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 REVERT: A 418 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 439 ASP cc_start: 0.8567 (p0) cc_final: 0.8308 (p0) REVERT: A 460 LYS cc_start: 0.8698 (mttt) cc_final: 0.8432 (mttt) REVERT: A 475 ASP cc_start: 0.7968 (t0) cc_final: 0.7766 (t0) REVERT: A 486 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7839 (mmmt) REVERT: A 491 ASN cc_start: 0.7708 (m-40) cc_final: 0.7389 (m-40) REVERT: A 524 GLU cc_start: 0.8161 (mp0) cc_final: 0.7662 (mp0) REVERT: A 556 ARG cc_start: 0.6200 (tmt170) cc_final: 0.5946 (tmt170) REVERT: A 629 LYS cc_start: 0.7476 (ptmm) cc_final: 0.7131 (ptmm) REVERT: A 645 MET cc_start: 0.7658 (mmm) cc_final: 0.7403 (mmm) REVERT: A 670 ASP cc_start: 0.8196 (p0) cc_final: 0.7821 (p0) REVERT: A 695 GLU cc_start: 0.7285 (tp30) cc_final: 0.6522 (tp30) REVERT: A 700 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6728 (mm-30) REVERT: A 715 GLU cc_start: 0.7911 (mp0) cc_final: 0.7459 (mp0) REVERT: B 440 GLN cc_start: 0.7936 (pp30) cc_final: 0.7675 (pp30) REVERT: B 441 PHE cc_start: 0.8808 (t80) cc_final: 0.8566 (t80) REVERT: B 527 ASN cc_start: 0.7922 (p0) cc_final: 0.7457 (p0) REVERT: B 530 MET cc_start: 0.8201 (mtt) cc_final: 0.7915 (mtm) REVERT: B 536 GLN cc_start: 0.7676 (tm-30) cc_final: 0.6887 (tm-30) REVERT: B 539 ASP cc_start: 0.8033 (t0) cc_final: 0.7747 (t0) REVERT: B 573 LEU cc_start: 0.8329 (tp) cc_final: 0.8050 (tp) REVERT: C 427 ASP cc_start: 0.8014 (t0) cc_final: 0.7607 (t0) REVERT: C 428 TYR cc_start: 0.7844 (t80) cc_final: 0.7576 (t80) REVERT: C 474 ASP cc_start: 0.7770 (t70) cc_final: 0.7461 (t0) REVERT: C 478 ASP cc_start: 0.7130 (m-30) cc_final: 0.6922 (m-30) REVERT: C 679 ASP cc_start: 0.8281 (t0) cc_final: 0.7766 (t0) REVERT: D 503 THR cc_start: 0.8255 (t) cc_final: 0.8053 (m) REVERT: D 506 ILE cc_start: 0.7649 (pt) cc_final: 0.7271 (mt) REVERT: D 536 GLN cc_start: 0.7128 (tm-30) cc_final: 0.6606 (tm-30) REVERT: D 540 LEU cc_start: 0.8036 (mt) cc_final: 0.7695 (mm) REVERT: D 551 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6717 (tm-30) REVERT: D 637 MET cc_start: 0.7500 (ppp) cc_final: 0.7164 (ppp) REVERT: D 685 MET cc_start: 0.7449 (tpt) cc_final: 0.7103 (tpt) REVERT: D 686 MET cc_start: 0.7748 (mmp) cc_final: 0.7460 (mmp) REVERT: D 687 ASP cc_start: 0.7690 (t0) cc_final: 0.7083 (t0) REVERT: E 460 LYS cc_start: 0.8693 (mttt) cc_final: 0.8314 (mtpp) REVERT: E 463 VAL cc_start: 0.8295 (p) cc_final: 0.8086 (m) REVERT: E 468 ASN cc_start: 0.7788 (m110) cc_final: 0.7556 (m110) REVERT: E 484 ARG cc_start: 0.6842 (pmt-80) cc_final: 0.6423 (pmt-80) REVERT: E 491 ASN cc_start: 0.7603 (m-40) cc_final: 0.7231 (m-40) REVERT: E 500 ASN cc_start: 0.8511 (t0) cc_final: 0.8292 (t0) REVERT: E 524 GLU cc_start: 0.8116 (mp0) cc_final: 0.7624 (mp0) REVERT: E 539 ASP cc_start: 0.7675 (t70) cc_final: 0.7453 (t0) REVERT: E 670 ASP cc_start: 0.8119 (p0) cc_final: 0.7829 (p0) REVERT: E 695 GLU cc_start: 0.7236 (tp30) cc_final: 0.5892 (tp30) REVERT: E 698 ARG cc_start: 0.7012 (mtm110) cc_final: 0.6109 (mtm110) REVERT: E 700 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6772 (mm-30) REVERT: E 715 GLU cc_start: 0.7895 (mp0) cc_final: 0.7373 (mp0) REVERT: F 440 GLN cc_start: 0.7946 (pp30) cc_final: 0.7586 (pp30) REVERT: F 441 PHE cc_start: 0.8754 (t80) cc_final: 0.8480 (t80) REVERT: F 463 VAL cc_start: 0.8859 (t) cc_final: 0.8592 (p) REVERT: F 527 ASN cc_start: 0.8058 (p0) cc_final: 0.7661 (p0) REVERT: F 530 MET cc_start: 0.8095 (mtt) cc_final: 0.7833 (mtm) REVERT: F 536 GLN cc_start: 0.7694 (tm-30) cc_final: 0.6848 (tm-30) REVERT: F 539 ASP cc_start: 0.8135 (t0) cc_final: 0.7876 (t0) REVERT: F 544 TYR cc_start: 0.7093 (t80) cc_final: 0.6671 (t80) REVERT: F 560 GLN cc_start: 0.7932 (tt0) cc_final: 0.7721 (tt0) REVERT: F 586 ILE cc_start: 0.8410 (pt) cc_final: 0.7913 (mp) REVERT: G 428 TYR cc_start: 0.7938 (t80) cc_final: 0.7723 (t80) REVERT: G 450 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.8193 (ttp-110) REVERT: G 464 ARG cc_start: 0.7279 (ttp80) cc_final: 0.7045 (ttp80) REVERT: G 474 ASP cc_start: 0.7747 (t70) cc_final: 0.7507 (t0) REVERT: G 515 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7104 (tm-30) REVERT: G 602 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6663 (mm-40) REVERT: G 627 GLU cc_start: 0.5582 (mp0) cc_final: 0.4860 (mp0) REVERT: G 673 GLU cc_start: 0.7697 (pt0) cc_final: 0.7453 (pt0) REVERT: G 679 ASP cc_start: 0.8232 (t0) cc_final: 0.7478 (t0) REVERT: H 506 ILE cc_start: 0.7536 (pt) cc_final: 0.7111 (mt) REVERT: H 536 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6910 (tm-30) REVERT: H 541 PHE cc_start: 0.8289 (t80) cc_final: 0.8052 (t80) REVERT: H 551 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6843 (tm-30) REVERT: H 591 HIS cc_start: 0.7792 (m170) cc_final: 0.7528 (m-70) REVERT: H 637 MET cc_start: 0.7507 (ppp) cc_final: 0.7276 (ppp) REVERT: H 647 LEU cc_start: 0.8313 (mp) cc_final: 0.8101 (mp) REVERT: H 686 MET cc_start: 0.7669 (mmp) cc_final: 0.7440 (mmp) outliers start: 6 outliers final: 1 residues processed: 661 average time/residue: 0.3097 time to fit residues: 301.0185 Evaluate side-chains 574 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 573 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 657 HIS 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: 0.0170 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 0.0980 chunk 207 optimal weight: 4.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 547 HIS B 591 HIS B 649 ASN C 446 ASN C 467 HIS C 523 GLN C 587 GLN C 664 GLN D 414 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN D 644 HIS ** D 691 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 547 HIS G 446 ASN G 523 GLN ** G 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7146 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18794 Z= 0.208 Angle : 0.745 12.553 25400 Z= 0.366 Chirality : 0.042 0.185 2910 Planarity : 0.005 0.052 3248 Dihedral : 4.656 46.800 2500 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.11 % Favored : 93.67 % Rotamer: Outliers : 2.38 % Allowed : 15.05 % Favored : 82.57 % 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: -1.99 (0.17), residues: 2296 helix: -0.90 (0.13), residues: 1554 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 448 HIS 0.011 0.001 HIS B 657 PHE 0.028 0.002 PHE H 441 TYR 0.018 0.001 TYR D 554 ARG 0.007 0.000 ARG E 693 *********************** 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 645 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 597 time to evaluate : 2.073 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: A 440 GLN cc_start: 0.8194 (mt0) cc_final: 0.7690 (mt0) REVERT: A 460 LYS cc_start: 0.8485 (mttt) cc_final: 0.7921 (mtmm) REVERT: A 476 PHE cc_start: 0.8025 (t80) cc_final: 0.7804 (t80) REVERT: A 486 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7890 (mmmt) REVERT: A 491 ASN cc_start: 0.7598 (m-40) cc_final: 0.7282 (m-40) REVERT: A 629 LYS cc_start: 0.7404 (ptmm) cc_final: 0.7149 (ptmm) REVERT: A 645 MET cc_start: 0.7501 (mmm) cc_final: 0.7273 (mmm) REVERT: A 665 LYS cc_start: 0.8248 (tppt) cc_final: 0.8002 (mmtm) REVERT: A 670 ASP cc_start: 0.8004 (p0) cc_final: 0.7754 (p0) REVERT: A 695 GLU cc_start: 0.7125 (tp30) cc_final: 0.6314 (tp30) REVERT: A 696 ILE cc_start: 0.8520 (mm) cc_final: 0.8197 (tp) REVERT: A 700 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 710 MET cc_start: 0.7539 (mmm) cc_final: 0.7194 (mmm) REVERT: A 715 GLU cc_start: 0.7941 (mp0) cc_final: 0.7451 (mp0) REVERT: B 527 ASN cc_start: 0.8060 (p0) cc_final: 0.7630 (p0) REVERT: B 536 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6618 (tm-30) REVERT: B 539 ASP cc_start: 0.8066 (t0) cc_final: 0.7791 (t0) REVERT: B 657 HIS cc_start: 0.5533 (OUTLIER) cc_final: 0.4926 (p-80) REVERT: B 666 GLN cc_start: 0.7952 (mp10) cc_final: 0.7547 (pm20) REVERT: B 682 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7534 (mmm-85) REVERT: B 691 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 428 TYR cc_start: 0.7980 (t80) cc_final: 0.7654 (t80) REVERT: C 432 MET cc_start: 0.6373 (mmm) cc_final: 0.5987 (mtm) REVERT: C 474 ASP cc_start: 0.7845 (t70) cc_final: 0.7598 (t0) REVERT: C 559 ASP cc_start: 0.7590 (t0) cc_final: 0.6996 (t0) REVERT: C 627 GLU cc_start: 0.5556 (mp0) cc_final: 0.5134 (mp0) REVERT: C 645 MET cc_start: 0.6884 (mmm) cc_final: 0.6651 (mpp) REVERT: C 665 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8639 (mtpt) REVERT: D 464 ARG cc_start: 0.7293 (ttp80) cc_final: 0.6781 (ttp80) REVERT: D 469 SER cc_start: 0.7967 (p) cc_final: 0.7648 (t) REVERT: D 573 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8624 (mt) REVERT: D 594 THR cc_start: 0.7880 (m) cc_final: 0.7568 (p) REVERT: D 686 MET cc_start: 0.7676 (mmp) cc_final: 0.7020 (mmp) REVERT: D 687 ASP cc_start: 0.7687 (t70) cc_final: 0.6916 (t0) REVERT: D 691 GLN cc_start: 0.8170 (mt0) cc_final: 0.7714 (mt0) REVERT: E 419 LYS cc_start: 0.7992 (tppt) cc_final: 0.7689 (tppt) REVERT: E 438 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7519 (mtt180) REVERT: E 440 GLN cc_start: 0.8178 (mt0) cc_final: 0.7723 (mt0) REVERT: E 455 LYS cc_start: 0.8663 (tppt) cc_final: 0.8453 (mmtp) REVERT: E 460 LYS cc_start: 0.8487 (mttt) cc_final: 0.7980 (mtmm) REVERT: E 476 PHE cc_start: 0.7789 (t80) cc_final: 0.7533 (t80) REVERT: E 486 LYS cc_start: 0.8232 (mmmt) cc_final: 0.8015 (mmmt) REVERT: E 491 ASN cc_start: 0.7471 (m-40) cc_final: 0.7126 (m-40) REVERT: E 524 GLU cc_start: 0.8090 (mp0) cc_final: 0.7817 (mp0) REVERT: E 557 MET cc_start: 0.7095 (tmm) cc_final: 0.6893 (tmm) REVERT: E 629 LYS cc_start: 0.7346 (ptmm) cc_final: 0.6912 (ptmm) REVERT: E 635 ILE cc_start: 0.8128 (mt) cc_final: 0.7753 (tt) REVERT: E 645 MET cc_start: 0.7503 (mmm) cc_final: 0.7298 (mmm) REVERT: E 666 GLN cc_start: 0.8192 (tp40) cc_final: 0.7960 (tp40) REVERT: E 670 ASP cc_start: 0.8023 (p0) cc_final: 0.7636 (p0) REVERT: E 695 GLU cc_start: 0.7136 (tp30) cc_final: 0.5828 (tp30) REVERT: E 696 ILE cc_start: 0.8540 (mm) cc_final: 0.8313 (tp) REVERT: E 698 ARG cc_start: 0.7088 (mtm110) cc_final: 0.6175 (mtm180) REVERT: E 700 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6962 (mm-30) REVERT: E 710 MET cc_start: 0.7562 (mmm) cc_final: 0.7257 (mmm) REVERT: E 715 GLU cc_start: 0.7856 (mp0) cc_final: 0.7279 (mp0) REVERT: F 515 GLU cc_start: 0.6748 (pt0) cc_final: 0.6448 (pt0) REVERT: F 527 ASN cc_start: 0.8199 (p0) cc_final: 0.7852 (p0) REVERT: F 536 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6755 (tm-30) REVERT: F 539 ASP cc_start: 0.8048 (t0) cc_final: 0.7788 (t0) REVERT: F 626 ASP cc_start: 0.6992 (p0) cc_final: 0.6412 (t70) REVERT: F 666 GLN cc_start: 0.7966 (mp10) cc_final: 0.7657 (pm20) REVERT: F 682 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7424 (mmm-85) REVERT: F 691 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8107 (tm-30) REVERT: G 428 TYR cc_start: 0.8051 (t80) cc_final: 0.7795 (t80) REVERT: G 456 VAL cc_start: 0.8238 (m) cc_final: 0.7985 (t) REVERT: G 539 ASP cc_start: 0.8026 (t0) cc_final: 0.7530 (m-30) REVERT: G 559 ASP cc_start: 0.7472 (t0) cc_final: 0.7211 (t0) REVERT: G 627 GLU cc_start: 0.5460 (mp0) cc_final: 0.5200 (mp0) REVERT: G 667 PHE cc_start: 0.7245 (t80) cc_final: 0.7043 (t80) REVERT: H 442 ILE cc_start: 0.8289 (mt) cc_final: 0.8067 (tp) REVERT: H 469 SER cc_start: 0.7972 (p) cc_final: 0.7685 (t) REVERT: H 539 ASP cc_start: 0.7521 (t0) cc_final: 0.7091 (t0) REVERT: H 551 GLU cc_start: 0.6458 (tm-30) cc_final: 0.6209 (tm-30) REVERT: H 637 MET cc_start: 0.7448 (ppp) cc_final: 0.7107 (ppp) REVERT: H 647 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7605 (mm) REVERT: H 686 MET cc_start: 0.7601 (mmp) cc_final: 0.6952 (mmp) REVERT: H 687 ASP cc_start: 0.7984 (t0) cc_final: 0.7680 (t0) outliers start: 48 outliers final: 18 residues processed: 616 average time/residue: 0.3223 time to fit residues: 289.7247 Evaluate side-chains 585 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 564 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 678 LEU Chi-restraints excluded: chain H residue 647 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 205 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 644 HIS B 512 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 HIS D 644 HIS ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 527 ASN E 560 GLN E 644 HIS G 649 ASN ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS H 644 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18794 Z= 0.224 Angle : 0.707 12.476 25400 Z= 0.346 Chirality : 0.042 0.218 2910 Planarity : 0.004 0.051 3248 Dihedral : 4.395 21.965 2498 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.72 % Allowed : 18.86 % Favored : 78.42 % 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: -1.39 (0.17), residues: 2296 helix: -0.45 (0.13), residues: 1570 sheet: None (None), residues: 0 loop : -1.76 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 448 HIS 0.010 0.001 HIS B 657 PHE 0.050 0.002 PHE C 516 TYR 0.020 0.002 TYR H 504 ARG 0.005 0.000 ARG A 693 *********************** 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 648 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 593 time to evaluate : 1.988 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: A 440 GLN cc_start: 0.8191 (mt0) cc_final: 0.7710 (mt0) REVERT: A 484 ARG cc_start: 0.6638 (pmt-80) cc_final: 0.6136 (pmt-80) REVERT: A 486 LYS cc_start: 0.8257 (mmmt) cc_final: 0.8009 (mmmt) REVERT: A 491 ASN cc_start: 0.7578 (m-40) cc_final: 0.7276 (m-40) REVERT: A 629 LYS cc_start: 0.7414 (ptmm) cc_final: 0.7144 (ptmm) REVERT: A 645 MET cc_start: 0.7421 (mmm) cc_final: 0.7128 (mmm) REVERT: A 670 ASP cc_start: 0.7891 (p0) cc_final: 0.7516 (p0) REVERT: A 695 GLU cc_start: 0.7207 (tp30) cc_final: 0.6537 (tp30) REVERT: A 700 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7041 (mm-30) REVERT: A 710 MET cc_start: 0.7411 (mmm) cc_final: 0.7133 (mmm) REVERT: B 508 LYS cc_start: 0.8264 (tttp) cc_final: 0.7920 (ttpp) REVERT: B 527 ASN cc_start: 0.8056 (p0) cc_final: 0.7664 (p0) REVERT: B 536 GLN cc_start: 0.7218 (tm-30) cc_final: 0.6616 (tm-30) REVERT: B 539 ASP cc_start: 0.8061 (t0) cc_final: 0.7766 (t0) REVERT: B 682 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7591 (mmm-85) REVERT: B 686 MET cc_start: 0.7725 (mmp) cc_final: 0.7503 (mmp) REVERT: B 691 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 428 TYR cc_start: 0.8006 (t80) cc_final: 0.7780 (t80) REVERT: C 474 ASP cc_start: 0.7863 (t70) cc_final: 0.7631 (t0) REVERT: C 559 ASP cc_start: 0.7080 (t0) cc_final: 0.6840 (t0) REVERT: C 696 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8304 (tt) REVERT: D 464 ARG cc_start: 0.7310 (ttp80) cc_final: 0.6820 (ttp80) REVERT: D 469 SER cc_start: 0.7961 (p) cc_final: 0.7714 (t) REVERT: D 594 THR cc_start: 0.7916 (m) cc_final: 0.7691 (p) REVERT: D 663 GLU cc_start: 0.7713 (pm20) cc_final: 0.7248 (pm20) REVERT: D 667 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: D 685 MET cc_start: 0.7166 (tpt) cc_final: 0.6558 (tpt) REVERT: D 686 MET cc_start: 0.7750 (mmp) cc_final: 0.7123 (mmp) REVERT: D 687 ASP cc_start: 0.7749 (t70) cc_final: 0.7436 (t0) REVERT: E 419 LYS cc_start: 0.8025 (tppt) cc_final: 0.7724 (tppt) REVERT: E 438 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7527 (mtt180) REVERT: E 440 GLN cc_start: 0.8174 (mt0) cc_final: 0.7736 (mt0) REVERT: E 460 LYS cc_start: 0.8409 (mttt) cc_final: 0.7950 (mtmm) REVERT: E 491 ASN cc_start: 0.7494 (m-40) cc_final: 0.7149 (m-40) REVERT: E 629 LYS cc_start: 0.7329 (ptmm) cc_final: 0.6933 (ptmm) REVERT: E 666 GLN cc_start: 0.8276 (tp40) cc_final: 0.7942 (tp40) REVERT: E 670 ASP cc_start: 0.7959 (p0) cc_final: 0.7512 (p0) REVERT: E 693 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7833 (ttm-80) REVERT: E 695 GLU cc_start: 0.7265 (tp30) cc_final: 0.6066 (tp30) REVERT: E 696 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8364 (tp) REVERT: E 698 ARG cc_start: 0.7271 (mtm110) cc_final: 0.6261 (mtm180) REVERT: E 700 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7054 (mm-30) REVERT: E 710 MET cc_start: 0.7568 (mmm) cc_final: 0.7313 (mmm) REVERT: E 715 GLU cc_start: 0.7891 (mp0) cc_final: 0.7284 (mp0) REVERT: F 419 LYS cc_start: 0.7687 (tppt) cc_final: 0.7203 (tppt) REVERT: F 515 GLU cc_start: 0.6772 (pt0) cc_final: 0.6436 (pt0) REVERT: F 527 ASN cc_start: 0.8174 (p0) cc_final: 0.7900 (p0) REVERT: F 536 GLN cc_start: 0.7265 (tm-30) cc_final: 0.6733 (tm-30) REVERT: F 539 ASP cc_start: 0.8104 (t0) cc_final: 0.7904 (t0) REVERT: F 626 ASP cc_start: 0.6753 (p0) cc_final: 0.6082 (t70) REVERT: F 666 GLN cc_start: 0.8036 (mp10) cc_final: 0.7640 (pm20) REVERT: F 682 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.7529 (mmm-85) REVERT: F 691 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8164 (tm-30) REVERT: G 428 TYR cc_start: 0.8121 (t80) cc_final: 0.7884 (t80) REVERT: G 456 VAL cc_start: 0.8341 (m) cc_final: 0.8076 (t) REVERT: G 559 ASP cc_start: 0.7467 (t0) cc_final: 0.6686 (t0) REVERT: G 574 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8247 (tt) REVERT: G 663 GLU cc_start: 0.7041 (pm20) cc_final: 0.6781 (pm20) REVERT: G 693 ARG cc_start: 0.7359 (mtt90) cc_final: 0.7154 (mtt90) REVERT: H 442 ILE cc_start: 0.8275 (mt) cc_final: 0.8072 (tp) REVERT: H 469 SER cc_start: 0.7957 (p) cc_final: 0.7728 (t) REVERT: H 539 ASP cc_start: 0.7578 (t0) cc_final: 0.7096 (t0) REVERT: H 551 GLU cc_start: 0.6483 (tm-30) cc_final: 0.6217 (tm-30) REVERT: H 637 MET cc_start: 0.7486 (ppp) cc_final: 0.7090 (ppp) REVERT: H 647 LEU cc_start: 0.7784 (mp) cc_final: 0.7530 (mm) REVERT: H 686 MET cc_start: 0.7685 (mmp) cc_final: 0.7072 (mmp) outliers start: 55 outliers final: 34 residues processed: 613 average time/residue: 0.3198 time to fit residues: 284.3734 Evaluate side-chains 617 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 579 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 645 MET Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 574 LEU Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 626 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 467 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 HIS ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS E 657 HIS ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS H 644 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3735 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= 0.205 Angle : 0.686 13.739 25400 Z= 0.334 Chirality : 0.041 0.147 2910 Planarity : 0.004 0.050 3248 Dihedral : 4.287 20.191 2498 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.22 % Allowed : 20.59 % Favored : 76.19 % 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: -1.14 (0.18), residues: 2296 helix: -0.25 (0.13), residues: 1614 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 448 HIS 0.010 0.001 HIS H 644 PHE 0.052 0.002 PHE C 516 TYR 0.015 0.001 TYR H 504 ARG 0.007 0.000 ARG H 464 *********************** 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 646 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 581 time to evaluate : 2.010 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: A 440 GLN cc_start: 0.8118 (mt0) cc_final: 0.7677 (mt0) REVERT: A 484 ARG cc_start: 0.6577 (pmt-80) cc_final: 0.5974 (pmt-80) REVERT: A 486 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8071 (mmmt) REVERT: A 491 ASN cc_start: 0.7520 (m-40) cc_final: 0.7222 (m-40) REVERT: A 526 MET cc_start: 0.7722 (tpp) cc_final: 0.7386 (tpp) REVERT: A 629 LYS cc_start: 0.7409 (ptmm) cc_final: 0.7184 (ptmm) REVERT: A 670 ASP cc_start: 0.7872 (p0) cc_final: 0.7514 (p0) REVERT: A 695 GLU cc_start: 0.7290 (tp30) cc_final: 0.5722 (tp30) REVERT: A 698 ARG cc_start: 0.7374 (mtm110) cc_final: 0.6114 (mtm180) REVERT: A 700 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7101 (mm-30) REVERT: B 419 LYS cc_start: 0.7513 (tppt) cc_final: 0.7014 (tppt) REVERT: B 460 LYS cc_start: 0.8115 (mttt) cc_final: 0.7817 (mttp) REVERT: B 508 LYS cc_start: 0.8284 (tttp) cc_final: 0.7937 (ttpp) REVERT: B 524 GLU cc_start: 0.7981 (mp0) cc_final: 0.7762 (mp0) REVERT: B 527 ASN cc_start: 0.8065 (p0) cc_final: 0.7714 (p0) REVERT: B 536 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6610 (tm-30) REVERT: B 539 ASP cc_start: 0.8072 (t0) cc_final: 0.7781 (t0) REVERT: B 682 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: B 691 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 692 LEU cc_start: 0.8750 (tp) cc_final: 0.8527 (tt) REVERT: C 428 TYR cc_start: 0.8024 (t80) cc_final: 0.7795 (t80) REVERT: C 474 ASP cc_start: 0.7814 (t70) cc_final: 0.7604 (t0) REVERT: C 574 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8005 (tt) REVERT: D 464 ARG cc_start: 0.7324 (ttp80) cc_final: 0.6794 (ttp80) REVERT: D 469 SER cc_start: 0.7998 (p) cc_final: 0.7798 (t) REVERT: D 536 GLN cc_start: 0.6898 (tm-30) cc_final: 0.6448 (tm-30) REVERT: D 637 MET cc_start: 0.7583 (ppp) cc_final: 0.6974 (ppp) REVERT: D 663 GLU cc_start: 0.7705 (pm20) cc_final: 0.7295 (pm20) REVERT: D 667 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: D 686 MET cc_start: 0.7731 (mmp) cc_final: 0.7478 (mmp) REVERT: D 687 ASP cc_start: 0.7927 (t70) cc_final: 0.7572 (t0) REVERT: E 419 LYS cc_start: 0.7980 (tppt) cc_final: 0.7682 (tppt) REVERT: E 438 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7518 (mtt90) REVERT: E 440 GLN cc_start: 0.8113 (mt0) cc_final: 0.7682 (mt0) REVERT: E 460 LYS cc_start: 0.8359 (mttt) cc_final: 0.7888 (mtmm) REVERT: E 491 ASN cc_start: 0.7495 (m-40) cc_final: 0.7179 (m-40) REVERT: E 524 GLU cc_start: 0.7883 (mp0) cc_final: 0.7568 (mp0) REVERT: E 526 MET cc_start: 0.7815 (tpp) cc_final: 0.7575 (tpp) REVERT: E 629 LYS cc_start: 0.7323 (ptmm) cc_final: 0.6916 (ptmm) REVERT: E 666 GLN cc_start: 0.8253 (tp40) cc_final: 0.7954 (tp40) REVERT: E 670 ASP cc_start: 0.7855 (p0) cc_final: 0.7468 (p0) REVERT: E 693 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7823 (ttm-80) REVERT: E 695 GLU cc_start: 0.7342 (tp30) cc_final: 0.6411 (tp30) REVERT: E 698 ARG cc_start: 0.7337 (mtm110) cc_final: 0.6430 (mtm180) REVERT: E 700 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7056 (mm-30) REVERT: E 710 MET cc_start: 0.7541 (mmm) cc_final: 0.7314 (mmm) REVERT: E 715 GLU cc_start: 0.7872 (mp0) cc_final: 0.7197 (mp0) REVERT: F 419 LYS cc_start: 0.7609 (tppt) cc_final: 0.7159 (tppt) REVERT: F 460 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7978 (mttp) REVERT: F 515 GLU cc_start: 0.6793 (pt0) cc_final: 0.6494 (pt0) REVERT: F 527 ASN cc_start: 0.8171 (p0) cc_final: 0.7885 (p0) REVERT: F 536 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6717 (tm-30) REVERT: F 626 ASP cc_start: 0.6679 (p0) cc_final: 0.5947 (t70) REVERT: F 691 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8227 (tm-30) REVERT: G 539 ASP cc_start: 0.7856 (t0) cc_final: 0.7163 (m-30) REVERT: G 663 GLU cc_start: 0.7117 (pm20) cc_final: 0.6767 (pm20) REVERT: H 460 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7898 (mtpp) REVERT: H 539 ASP cc_start: 0.7538 (t0) cc_final: 0.6872 (t0) REVERT: H 551 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6100 (tm-30) REVERT: H 560 GLN cc_start: 0.7963 (tt0) cc_final: 0.7729 (tt0) REVERT: H 572 LEU cc_start: 0.8806 (mt) cc_final: 0.8533 (mm) REVERT: H 637 MET cc_start: 0.7441 (ppp) cc_final: 0.7033 (ppp) REVERT: H 645 MET cc_start: 0.8053 (mtt) cc_final: 0.7742 (mtp) REVERT: H 647 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7484 (mm) REVERT: H 667 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: H 686 MET cc_start: 0.7746 (mmp) cc_final: 0.7543 (mmp) REVERT: H 691 GLN cc_start: 0.8252 (mt0) cc_final: 0.8017 (mt0) outliers start: 65 outliers final: 40 residues processed: 605 average time/residue: 0.3203 time to fit residues: 282.1607 Evaluate side-chains 615 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 571 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 HIS Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 645 MET Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 594 THR Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 188 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 HIS A 649 ASN ** D 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS H 636 HIS H 644 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18794 Z= 0.224 Angle : 0.689 15.038 25400 Z= 0.334 Chirality : 0.041 0.144 2910 Planarity : 0.004 0.048 3248 Dihedral : 4.270 22.350 2498 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.37 % Allowed : 21.09 % Favored : 75.54 % 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: -0.97 (0.18), residues: 2296 helix: -0.10 (0.13), residues: 1626 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 448 HIS 0.009 0.001 HIS D 644 PHE 0.029 0.002 PHE C 516 TYR 0.015 0.001 TYR H 504 ARG 0.006 0.000 ARG H 464 *********************** 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 664 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 596 time to evaluate : 1.930 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: A 440 GLN cc_start: 0.8092 (mt0) cc_final: 0.7663 (mt0) REVERT: A 484 ARG cc_start: 0.6651 (pmt-80) cc_final: 0.6038 (pmt-80) REVERT: A 486 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8069 (mmmt) REVERT: A 491 ASN cc_start: 0.7518 (m-40) cc_final: 0.7173 (m-40) REVERT: A 629 LYS cc_start: 0.7452 (ptmm) cc_final: 0.7232 (ptmm) REVERT: A 670 ASP cc_start: 0.7858 (p0) cc_final: 0.7503 (p0) REVERT: A 675 GLU cc_start: 0.7175 (tt0) cc_final: 0.6891 (tt0) REVERT: A 695 GLU cc_start: 0.7315 (tp30) cc_final: 0.5881 (tp30) REVERT: A 698 ARG cc_start: 0.7448 (mtm110) cc_final: 0.6216 (mtm180) REVERT: A 700 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 419 LYS cc_start: 0.7416 (tppt) cc_final: 0.6857 (tppt) REVERT: B 427 ASP cc_start: 0.8155 (t0) cc_final: 0.7455 (m-30) REVERT: B 508 LYS cc_start: 0.8316 (tttp) cc_final: 0.8015 (ttmt) REVERT: B 527 ASN cc_start: 0.8066 (p0) cc_final: 0.7708 (p0) REVERT: B 536 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6606 (tm-30) REVERT: B 539 ASP cc_start: 0.8098 (t0) cc_final: 0.7786 (t0) REVERT: B 553 GLU cc_start: 0.6646 (pt0) cc_final: 0.5911 (pt0) REVERT: B 682 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7572 (mmm-85) REVERT: B 691 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8276 (tm-30) REVERT: B 692 LEU cc_start: 0.8750 (tp) cc_final: 0.8547 (tp) REVERT: B 693 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6885 (ptt-90) REVERT: C 428 TYR cc_start: 0.8032 (t80) cc_final: 0.7820 (t80) REVERT: C 474 ASP cc_start: 0.7822 (t70) cc_final: 0.7603 (t0) REVERT: C 574 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8085 (tt) REVERT: D 464 ARG cc_start: 0.7332 (ttp80) cc_final: 0.6790 (ttp80) REVERT: D 637 MET cc_start: 0.7498 (ppp) cc_final: 0.6979 (ppp) REVERT: D 663 GLU cc_start: 0.7714 (pm20) cc_final: 0.7353 (pm20) REVERT: D 667 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: D 686 MET cc_start: 0.7781 (mmp) cc_final: 0.7538 (mmp) REVERT: D 687 ASP cc_start: 0.7971 (t70) cc_final: 0.7594 (t0) REVERT: E 419 LYS cc_start: 0.7926 (tppt) cc_final: 0.7622 (tppt) REVERT: E 440 GLN cc_start: 0.8079 (mt0) cc_final: 0.7644 (mt0) REVERT: E 460 LYS cc_start: 0.8353 (mttt) cc_final: 0.7888 (mtmm) REVERT: E 486 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8097 (mmmt) REVERT: E 491 ASN cc_start: 0.7538 (m-40) cc_final: 0.7196 (m-40) REVERT: E 522 VAL cc_start: 0.7184 (m) cc_final: 0.6979 (m) REVERT: E 524 GLU cc_start: 0.7877 (mp0) cc_final: 0.7537 (mp0) REVERT: E 629 LYS cc_start: 0.7420 (ptmm) cc_final: 0.7020 (ptmm) REVERT: E 666 GLN cc_start: 0.8266 (tp40) cc_final: 0.7916 (tp-100) REVERT: E 670 ASP cc_start: 0.7844 (p0) cc_final: 0.7355 (p0) REVERT: E 695 GLU cc_start: 0.7427 (tp30) cc_final: 0.6385 (tp30) REVERT: E 698 ARG cc_start: 0.7422 (mtm110) cc_final: 0.6448 (mtm180) REVERT: E 700 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7033 (mm-30) REVERT: E 710 MET cc_start: 0.7587 (mmm) cc_final: 0.7305 (mmm) REVERT: E 715 GLU cc_start: 0.7925 (mp0) cc_final: 0.7221 (mp0) REVERT: F 419 LYS cc_start: 0.7591 (tppt) cc_final: 0.7101 (tppt) REVERT: F 460 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7991 (mttp) REVERT: F 508 LYS cc_start: 0.8445 (tttp) cc_final: 0.8125 (ttmt) REVERT: F 524 GLU cc_start: 0.7927 (mp0) cc_final: 0.7726 (mp0) REVERT: F 527 ASN cc_start: 0.8178 (p0) cc_final: 0.7889 (p0) REVERT: F 529 ILE cc_start: 0.7828 (mm) cc_final: 0.7536 (mt) REVERT: F 536 GLN cc_start: 0.7245 (tm-30) cc_final: 0.6713 (tm-30) REVERT: F 553 GLU cc_start: 0.6462 (pt0) cc_final: 0.6130 (pt0) REVERT: F 626 ASP cc_start: 0.6561 (p0) cc_final: 0.5886 (t70) REVERT: F 666 GLN cc_start: 0.8059 (mp10) cc_final: 0.7849 (pm20) REVERT: F 691 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8181 (tm-30) REVERT: F 692 LEU cc_start: 0.8761 (tp) cc_final: 0.8512 (tt) REVERT: G 558 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7536 (tp) REVERT: G 602 GLN cc_start: 0.6730 (mt0) cc_final: 0.6312 (mt0) REVERT: H 442 ILE cc_start: 0.8495 (mm) cc_final: 0.8284 (tp) REVERT: H 539 ASP cc_start: 0.7370 (t0) cc_final: 0.6662 (t0) REVERT: H 551 GLU cc_start: 0.6447 (tm-30) cc_final: 0.6157 (tm-30) REVERT: H 560 GLN cc_start: 0.8002 (tt0) cc_final: 0.7795 (tt0) REVERT: H 572 LEU cc_start: 0.8789 (mt) cc_final: 0.8478 (mm) REVERT: H 637 MET cc_start: 0.7410 (ppp) cc_final: 0.7012 (ppp) REVERT: H 645 MET cc_start: 0.8019 (mtt) cc_final: 0.7751 (mtp) REVERT: H 647 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7381 (mm) REVERT: H 667 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8091 (m-80) outliers start: 68 outliers final: 45 residues processed: 621 average time/residue: 0.3322 time to fit residues: 299.6031 Evaluate side-chains 638 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 587 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 HIS Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 645 MET Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 594 THR Chi-restraints excluded: chain G residue 637 MET Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 129 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 657 HIS ** D 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS E 649 ASN F 534 GLN H 636 HIS H 644 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4280 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= 0.186 Angle : 0.669 15.857 25400 Z= 0.322 Chirality : 0.039 0.135 2910 Planarity : 0.004 0.051 3248 Dihedral : 4.125 22.419 2498 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.22 % Allowed : 22.48 % Favored : 74.31 % 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: -0.59 (0.18), residues: 2296 helix: 0.20 (0.14), residues: 1608 sheet: None (None), residues: 0 loop : -1.64 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 448 HIS 0.009 0.001 HIS H 644 PHE 0.024 0.002 PHE C 516 TYR 0.011 0.001 TYR H 544 ARG 0.008 0.000 ARG E 693 *********************** 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 654 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 589 time to evaluate : 1.891 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: A 440 GLN cc_start: 0.8034 (mt0) cc_final: 0.7596 (mt0) REVERT: A 484 ARG cc_start: 0.6726 (pmt-80) cc_final: 0.6183 (pmt-80) REVERT: A 486 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8196 (mmmt) REVERT: A 491 ASN cc_start: 0.7528 (m-40) cc_final: 0.7181 (m-40) REVERT: A 534 GLN cc_start: 0.6826 (tt0) cc_final: 0.6377 (tt0) REVERT: A 590 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7885 (mm) REVERT: A 629 LYS cc_start: 0.7394 (ptmm) cc_final: 0.7015 (ptmm) REVERT: A 670 ASP cc_start: 0.7810 (p0) cc_final: 0.7442 (p0) REVERT: A 675 GLU cc_start: 0.7123 (tt0) cc_final: 0.6835 (tt0) REVERT: A 695 GLU cc_start: 0.7310 (tp30) cc_final: 0.5588 (tp30) REVERT: A 698 ARG cc_start: 0.7462 (mtm110) cc_final: 0.6186 (mtm180) REVERT: A 700 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 419 LYS cc_start: 0.7408 (tppt) cc_final: 0.6913 (tppt) REVERT: B 508 LYS cc_start: 0.8363 (tttp) cc_final: 0.8025 (ttmt) REVERT: B 527 ASN cc_start: 0.7998 (p0) cc_final: 0.7661 (p0) REVERT: B 536 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6592 (tm-30) REVERT: B 539 ASP cc_start: 0.8088 (t0) cc_final: 0.7769 (t0) REVERT: B 601 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7364 (t80) REVERT: B 682 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: B 691 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 693 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6968 (ptt-90) REVERT: C 428 TYR cc_start: 0.8052 (t80) cc_final: 0.7785 (t80) REVERT: C 474 ASP cc_start: 0.7801 (t70) cc_final: 0.7575 (t0) REVERT: C 574 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8019 (tt) REVERT: D 464 ARG cc_start: 0.7320 (ttp80) cc_final: 0.6770 (ttp80) REVERT: D 466 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7560 (tp) REVERT: D 637 MET cc_start: 0.7449 (ppp) cc_final: 0.6941 (ppp) REVERT: D 686 MET cc_start: 0.7762 (mmp) cc_final: 0.7494 (mmp) REVERT: D 687 ASP cc_start: 0.7996 (t70) cc_final: 0.7621 (t0) REVERT: E 440 GLN cc_start: 0.8071 (mt0) cc_final: 0.7618 (mt0) REVERT: E 460 LYS cc_start: 0.8330 (mttt) cc_final: 0.7859 (mtmm) REVERT: E 486 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8139 (mmmt) REVERT: E 491 ASN cc_start: 0.7540 (m-40) cc_final: 0.7166 (m-40) REVERT: E 522 VAL cc_start: 0.7159 (m) cc_final: 0.6940 (m) REVERT: E 524 GLU cc_start: 0.7817 (mp0) cc_final: 0.7526 (mp0) REVERT: E 629 LYS cc_start: 0.7375 (ptmm) cc_final: 0.7010 (ptmm) REVERT: E 666 GLN cc_start: 0.8230 (tp40) cc_final: 0.7878 (tp-100) REVERT: E 670 ASP cc_start: 0.7793 (p0) cc_final: 0.7303 (p0) REVERT: E 695 GLU cc_start: 0.7385 (tp30) cc_final: 0.6610 (tp30) REVERT: E 696 ILE cc_start: 0.8593 (tp) cc_final: 0.8360 (tp) REVERT: E 698 ARG cc_start: 0.7369 (mtm110) cc_final: 0.6500 (mtm180) REVERT: E 700 GLU cc_start: 0.7253 (mm-30) cc_final: 0.7001 (mm-30) REVERT: E 715 GLU cc_start: 0.7951 (mp0) cc_final: 0.7299 (mp0) REVERT: F 419 LYS cc_start: 0.7533 (tppt) cc_final: 0.7054 (tppt) REVERT: F 508 LYS cc_start: 0.8439 (tttp) cc_final: 0.8087 (ttmt) REVERT: F 527 ASN cc_start: 0.8137 (p0) cc_final: 0.7860 (p0) REVERT: F 536 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6722 (tm-30) REVERT: F 553 GLU cc_start: 0.6495 (pt0) cc_final: 0.6133 (pt0) REVERT: F 626 ASP cc_start: 0.6525 (p0) cc_final: 0.5851 (t70) REVERT: F 691 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8120 (tm-30) REVERT: F 692 LEU cc_start: 0.8747 (tp) cc_final: 0.8499 (tt) REVERT: F 693 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6926 (ptt-90) REVERT: G 558 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7605 (tp) REVERT: G 602 GLN cc_start: 0.6714 (mt0) cc_final: 0.6429 (mt0) REVERT: H 466 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.6862 (mt) REVERT: H 551 GLU cc_start: 0.6362 (tm-30) cc_final: 0.6097 (tm-30) REVERT: H 560 GLN cc_start: 0.7990 (tt0) cc_final: 0.7772 (tt0) REVERT: H 572 LEU cc_start: 0.8713 (mt) cc_final: 0.8440 (mm) REVERT: H 637 MET cc_start: 0.7373 (ppp) cc_final: 0.6987 (ppp) REVERT: H 645 MET cc_start: 0.7999 (mtt) cc_final: 0.7740 (mtp) REVERT: H 647 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7334 (mm) REVERT: H 667 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8076 (m-80) outliers start: 65 outliers final: 38 residues processed: 615 average time/residue: 0.3174 time to fit residues: 285.1441 Evaluate side-chains 620 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 572 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 693 ARG Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 219 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 ASN B 649 ASN D 545 ASN ** D 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS H 636 HIS H 644 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18794 Z= 0.217 Angle : 0.687 16.439 25400 Z= 0.332 Chirality : 0.040 0.173 2910 Planarity : 0.004 0.054 3248 Dihedral : 4.167 22.682 2498 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.61 % Allowed : 22.43 % Favored : 73.96 % 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: -0.65 (0.18), residues: 2296 helix: 0.20 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 630 HIS 0.008 0.001 HIS H 644 PHE 0.041 0.002 PHE G 667 TYR 0.015 0.001 TYR H 504 ARG 0.007 0.000 ARG E 438 *********************** 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 661 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 588 time to evaluate : 2.161 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: A 438 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7351 (mtt90) REVERT: A 440 GLN cc_start: 0.8058 (mt0) cc_final: 0.7630 (mt0) REVERT: A 484 ARG cc_start: 0.6727 (pmt-80) cc_final: 0.6232 (pmt-80) REVERT: A 491 ASN cc_start: 0.7531 (m-40) cc_final: 0.7163 (m-40) REVERT: A 534 GLN cc_start: 0.6855 (tt0) cc_final: 0.6357 (tt0) REVERT: A 629 LYS cc_start: 0.7475 (ptmm) cc_final: 0.7047 (ptmm) REVERT: A 670 ASP cc_start: 0.7818 (p0) cc_final: 0.7461 (p0) REVERT: A 675 GLU cc_start: 0.7143 (tt0) cc_final: 0.6846 (tt0) REVERT: A 695 GLU cc_start: 0.7382 (tp30) cc_final: 0.6847 (tp30) REVERT: A 700 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7088 (mm-30) REVERT: B 419 LYS cc_start: 0.7454 (tppt) cc_final: 0.6953 (tppt) REVERT: B 508 LYS cc_start: 0.8361 (tttp) cc_final: 0.8003 (ttmt) REVERT: B 527 ASN cc_start: 0.8075 (p0) cc_final: 0.7743 (p0) REVERT: B 536 GLN cc_start: 0.7186 (tm-30) cc_final: 0.6606 (tm-30) REVERT: B 539 ASP cc_start: 0.8107 (t0) cc_final: 0.7806 (t0) REVERT: B 601 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7370 (t80) REVERT: B 666 GLN cc_start: 0.8038 (mp10) cc_final: 0.7794 (pm20) REVERT: B 682 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.7685 (mmm-85) REVERT: B 691 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8247 (tm-30) REVERT: B 693 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7140 (ptt-90) REVERT: C 428 TYR cc_start: 0.8042 (t80) cc_final: 0.7784 (t80) REVERT: C 574 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8009 (tt) REVERT: C 665 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8588 (mtpp) REVERT: D 464 ARG cc_start: 0.7335 (ttp80) cc_final: 0.6788 (ttp80) REVERT: D 466 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7577 (tp) REVERT: D 637 MET cc_start: 0.7426 (ppp) cc_final: 0.6922 (ppp) REVERT: D 663 GLU cc_start: 0.7755 (pm20) cc_final: 0.7301 (pm20) REVERT: D 667 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: D 686 MET cc_start: 0.7797 (mmp) cc_final: 0.7543 (mmp) REVERT: D 687 ASP cc_start: 0.8031 (t70) cc_final: 0.7653 (t0) REVERT: E 440 GLN cc_start: 0.8052 (mt0) cc_final: 0.7599 (mt0) REVERT: E 486 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8104 (mmmt) REVERT: E 491 ASN cc_start: 0.7568 (m-40) cc_final: 0.7203 (m-40) REVERT: E 629 LYS cc_start: 0.7415 (ptmm) cc_final: 0.6974 (ptmm) REVERT: E 666 GLN cc_start: 0.8272 (tp40) cc_final: 0.7889 (tp-100) REVERT: E 670 ASP cc_start: 0.7772 (p0) cc_final: 0.7278 (p0) REVERT: E 695 GLU cc_start: 0.7397 (tp30) cc_final: 0.6535 (tp30) REVERT: E 696 ILE cc_start: 0.8564 (tp) cc_final: 0.8303 (tp) REVERT: E 698 ARG cc_start: 0.7431 (mtm110) cc_final: 0.6463 (mtm180) REVERT: E 700 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6970 (mm-30) REVERT: E 715 GLU cc_start: 0.7962 (mp0) cc_final: 0.7291 (mp0) REVERT: F 419 LYS cc_start: 0.7506 (tppt) cc_final: 0.6992 (tppt) REVERT: F 508 LYS cc_start: 0.8455 (tttp) cc_final: 0.8110 (ttmt) REVERT: F 515 GLU cc_start: 0.6816 (pt0) cc_final: 0.6587 (pt0) REVERT: F 527 ASN cc_start: 0.8222 (p0) cc_final: 0.7935 (p0) REVERT: F 529 ILE cc_start: 0.7759 (mm) cc_final: 0.7470 (mt) REVERT: F 536 GLN cc_start: 0.7241 (tm-30) cc_final: 0.6650 (tm-30) REVERT: F 691 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8132 (tm-30) REVERT: F 692 LEU cc_start: 0.8765 (tp) cc_final: 0.8517 (tt) REVERT: F 693 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6955 (ptt-90) REVERT: G 558 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7628 (tp) REVERT: G 602 GLN cc_start: 0.6765 (mt0) cc_final: 0.6450 (mt0) REVERT: H 466 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.6791 (mt) REVERT: H 470 SER cc_start: 0.8770 (m) cc_final: 0.8160 (p) REVERT: H 514 MET cc_start: 0.6446 (tpp) cc_final: 0.6196 (tpp) REVERT: H 551 GLU cc_start: 0.6427 (tm-30) cc_final: 0.6153 (tm-30) REVERT: H 560 GLN cc_start: 0.8012 (tt0) cc_final: 0.7809 (tt0) REVERT: H 572 LEU cc_start: 0.8725 (mt) cc_final: 0.8469 (mm) REVERT: H 637 MET cc_start: 0.7368 (ppp) cc_final: 0.6937 (ppp) REVERT: H 645 MET cc_start: 0.8009 (mtt) cc_final: 0.7741 (mtp) REVERT: H 647 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7358 (mm) REVERT: H 667 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8125 (m-80) outliers start: 73 outliers final: 47 residues processed: 616 average time/residue: 0.3094 time to fit residues: 279.1426 Evaluate side-chains 638 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 581 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 HIS Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 693 ARG Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 607 TYR Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 149 optimal weight: 0.0970 chunk 108 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 ASN A 664 GLN D 636 HIS D 666 GLN E 644 HIS E 649 ASN F 467 HIS F 534 GLN H 602 GLN ** H 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 644 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4699 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= 0.172 Angle : 0.678 17.146 25400 Z= 0.321 Chirality : 0.039 0.173 2910 Planarity : 0.004 0.053 3248 Dihedral : 4.021 22.488 2498 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.62 % Allowed : 23.47 % Favored : 73.91 % 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: -0.40 (0.18), residues: 2296 helix: 0.38 (0.14), residues: 1618 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 448 HIS 0.008 0.001 HIS H 644 PHE 0.030 0.002 PHE G 667 TYR 0.010 0.001 TYR D 554 ARG 0.008 0.000 ARG E 438 *********************** 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 643 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 590 time to evaluate : 2.003 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: A 438 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7357 (mtt90) REVERT: A 440 GLN cc_start: 0.8007 (mt0) cc_final: 0.7589 (mt0) REVERT: A 484 ARG cc_start: 0.6741 (pmt-80) cc_final: 0.6231 (pmt-80) REVERT: A 491 ASN cc_start: 0.7541 (m-40) cc_final: 0.7171 (m-40) REVERT: A 515 GLU cc_start: 0.7695 (tp30) cc_final: 0.7424 (tp30) REVERT: A 629 LYS cc_start: 0.7386 (ptmm) cc_final: 0.7032 (ptmm) REVERT: A 670 ASP cc_start: 0.7776 (p0) cc_final: 0.7448 (p0) REVERT: A 675 GLU cc_start: 0.7120 (tt0) cc_final: 0.6838 (tt0) REVERT: A 695 GLU cc_start: 0.7396 (tp30) cc_final: 0.5450 (tp30) REVERT: A 698 ARG cc_start: 0.7497 (mtm110) cc_final: 0.6213 (mtm180) REVERT: A 700 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 419 LYS cc_start: 0.7438 (tppt) cc_final: 0.6886 (tppt) REVERT: B 508 LYS cc_start: 0.8366 (tttp) cc_final: 0.8012 (ttmt) REVERT: B 514 MET cc_start: 0.7345 (ttm) cc_final: 0.7098 (ttm) REVERT: B 527 ASN cc_start: 0.8016 (p0) cc_final: 0.7689 (p0) REVERT: B 536 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6578 (tm-30) REVERT: B 539 ASP cc_start: 0.8071 (t0) cc_final: 0.7757 (t0) REVERT: B 682 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7660 (mmm-85) REVERT: B 691 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 693 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7130 (ptt-90) REVERT: C 428 TYR cc_start: 0.8056 (t80) cc_final: 0.7751 (t80) REVERT: C 514 MET cc_start: 0.7258 (ttm) cc_final: 0.7017 (ttm) REVERT: C 574 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7671 (tt) REVERT: C 663 GLU cc_start: 0.7103 (pm20) cc_final: 0.6761 (pm20) REVERT: C 711 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7846 (mmt180) REVERT: D 464 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6679 (ttp80) REVERT: D 466 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7317 (mt) REVERT: D 470 SER cc_start: 0.8822 (m) cc_final: 0.8162 (p) REVERT: D 637 MET cc_start: 0.7381 (ppp) cc_final: 0.6821 (ppp) REVERT: D 666 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6100 (pm20) REVERT: D 667 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: D 687 ASP cc_start: 0.8020 (t70) cc_final: 0.7645 (t0) REVERT: E 440 GLN cc_start: 0.7984 (mt0) cc_final: 0.7564 (mt0) REVERT: E 491 ASN cc_start: 0.7580 (m-40) cc_final: 0.7201 (m-40) REVERT: E 629 LYS cc_start: 0.7364 (ptmm) cc_final: 0.7012 (ptmm) REVERT: E 666 GLN cc_start: 0.8200 (tp40) cc_final: 0.7838 (tp40) REVERT: E 670 ASP cc_start: 0.7713 (p0) cc_final: 0.7342 (p0) REVERT: E 693 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7893 (tpp80) REVERT: E 695 GLU cc_start: 0.7411 (tp30) cc_final: 0.6310 (tp30) REVERT: E 696 ILE cc_start: 0.8503 (tp) cc_final: 0.8255 (tp) REVERT: E 698 ARG cc_start: 0.7391 (mtm110) cc_final: 0.6374 (mtm180) REVERT: E 700 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6960 (mm-30) REVERT: E 715 GLU cc_start: 0.7901 (mp0) cc_final: 0.7234 (mp0) REVERT: F 515 GLU cc_start: 0.6758 (pt0) cc_final: 0.6524 (pt0) REVERT: F 527 ASN cc_start: 0.8197 (p0) cc_final: 0.7935 (p0) REVERT: F 536 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6597 (tm-30) REVERT: F 643 SER cc_start: 0.7461 (m) cc_final: 0.6898 (p) REVERT: F 691 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8097 (tm-30) REVERT: F 692 LEU cc_start: 0.8743 (tp) cc_final: 0.8486 (tt) REVERT: F 693 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6952 (ptt-90) REVERT: G 558 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7615 (tp) REVERT: G 602 GLN cc_start: 0.6717 (mt0) cc_final: 0.6515 (mt0) REVERT: H 466 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.6736 (mt) REVERT: H 470 SER cc_start: 0.8738 (m) cc_final: 0.8085 (p) REVERT: H 525 VAL cc_start: 0.7360 (t) cc_final: 0.7123 (p) REVERT: H 551 GLU cc_start: 0.6294 (tm-30) cc_final: 0.6063 (tm-30) REVERT: H 560 GLN cc_start: 0.7954 (tt0) cc_final: 0.7745 (tt0) REVERT: H 572 LEU cc_start: 0.8686 (mt) cc_final: 0.8434 (mm) REVERT: H 637 MET cc_start: 0.7264 (ppp) cc_final: 0.6921 (ppp) REVERT: H 645 MET cc_start: 0.7995 (mtt) cc_final: 0.7732 (mtp) REVERT: H 647 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7306 (mm) REVERT: H 667 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: H 685 MET cc_start: 0.7069 (tpt) cc_final: 0.6613 (mmm) outliers start: 53 outliers final: 31 residues processed: 608 average time/residue: 0.3179 time to fit residues: 283.9589 Evaluate side-chains 616 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 575 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 693 ARG Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 607 TYR Chi-restraints excluded: chain G residue 637 MET Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.2980 chunk 210 optimal weight: 0.4980 chunk 192 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 193 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS F 534 GLN F 649 ASN H 545 ASN H 636 HIS H 644 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18794 Z= 0.197 Angle : 0.709 17.357 25400 Z= 0.336 Chirality : 0.040 0.262 2910 Planarity : 0.004 0.052 3248 Dihedral : 4.018 22.192 2498 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.57 % Allowed : 24.75 % Favored : 72.67 % 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: -0.38 (0.18), residues: 2296 helix: 0.40 (0.13), residues: 1618 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 448 HIS 0.007 0.001 HIS H 644 PHE 0.026 0.002 PHE G 667 TYR 0.011 0.001 TYR H 554 ARG 0.008 0.000 ARG E 438 *********************** 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 634 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 582 time to evaluate : 2.023 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: A 438 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7383 (mtt90) REVERT: A 440 GLN cc_start: 0.8017 (mt0) cc_final: 0.7603 (mt0) REVERT: A 484 ARG cc_start: 0.6723 (pmt-80) cc_final: 0.6239 (pmt-80) REVERT: A 486 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8187 (mmmt) REVERT: A 491 ASN cc_start: 0.7529 (m-40) cc_final: 0.7156 (m-40) REVERT: A 515 GLU cc_start: 0.7720 (tp30) cc_final: 0.7448 (tp30) REVERT: A 534 GLN cc_start: 0.6868 (tt0) cc_final: 0.6339 (tt0) REVERT: A 629 LYS cc_start: 0.7387 (ptmm) cc_final: 0.7014 (ptmm) REVERT: A 670 ASP cc_start: 0.7805 (p0) cc_final: 0.7453 (p0) REVERT: A 675 GLU cc_start: 0.7138 (tt0) cc_final: 0.6845 (tt0) REVERT: A 695 GLU cc_start: 0.7428 (tp30) cc_final: 0.6920 (tp30) REVERT: A 700 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 419 LYS cc_start: 0.7449 (tppt) cc_final: 0.6960 (tppt) REVERT: B 508 LYS cc_start: 0.8362 (tttp) cc_final: 0.8017 (ttmt) REVERT: B 514 MET cc_start: 0.7435 (ttm) cc_final: 0.7027 (ttp) REVERT: B 527 ASN cc_start: 0.8011 (p0) cc_final: 0.7712 (p0) REVERT: B 536 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6625 (tm-30) REVERT: B 539 ASP cc_start: 0.8094 (t0) cc_final: 0.7777 (t0) REVERT: B 601 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.7328 (t80) REVERT: B 666 GLN cc_start: 0.7996 (mp10) cc_final: 0.7791 (pm20) REVERT: B 691 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 693 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7115 (ptt-90) REVERT: C 428 TYR cc_start: 0.8055 (t80) cc_final: 0.7802 (t80) REVERT: C 539 ASP cc_start: 0.7503 (t70) cc_final: 0.7249 (m-30) REVERT: C 559 ASP cc_start: 0.7576 (t0) cc_final: 0.7368 (t0) REVERT: C 574 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7686 (tt) REVERT: D 464 ARG cc_start: 0.7304 (ttp80) cc_final: 0.6732 (ttp80) REVERT: D 466 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7392 (mt) REVERT: D 573 LEU cc_start: 0.8810 (mm) cc_final: 0.8512 (mm) REVERT: D 637 MET cc_start: 0.7283 (ppp) cc_final: 0.6784 (ppp) REVERT: D 663 GLU cc_start: 0.7681 (pm20) cc_final: 0.7213 (pm20) REVERT: D 667 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: D 687 ASP cc_start: 0.8018 (t70) cc_final: 0.7654 (t0) REVERT: E 438 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7122 (mtt90) REVERT: E 440 GLN cc_start: 0.7987 (mt0) cc_final: 0.7594 (mt0) REVERT: E 491 ASN cc_start: 0.7569 (m-40) cc_final: 0.7200 (m-40) REVERT: E 629 LYS cc_start: 0.7370 (ptmm) cc_final: 0.6984 (ptmm) REVERT: E 666 GLN cc_start: 0.8176 (tp40) cc_final: 0.7828 (tp40) REVERT: E 670 ASP cc_start: 0.7729 (p0) cc_final: 0.7346 (p0) REVERT: E 695 GLU cc_start: 0.7453 (tp30) cc_final: 0.6390 (tp30) REVERT: E 696 ILE cc_start: 0.8513 (tp) cc_final: 0.8250 (tp) REVERT: E 698 ARG cc_start: 0.7386 (mtm110) cc_final: 0.6422 (mtm180) REVERT: E 700 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6967 (mm-30) REVERT: E 715 GLU cc_start: 0.7925 (mp0) cc_final: 0.7270 (mp0) REVERT: F 515 GLU cc_start: 0.6771 (pt0) cc_final: 0.6562 (pt0) REVERT: F 527 ASN cc_start: 0.8178 (p0) cc_final: 0.7937 (p0) REVERT: F 529 ILE cc_start: 0.7640 (mm) cc_final: 0.7362 (mt) REVERT: F 536 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6600 (tm-30) REVERT: F 691 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8089 (tm-30) REVERT: F 692 LEU cc_start: 0.8742 (tp) cc_final: 0.8495 (tt) REVERT: F 693 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6960 (ptt-90) REVERT: G 558 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7628 (tp) REVERT: H 466 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.6706 (mt) REVERT: H 470 SER cc_start: 0.8728 (m) cc_final: 0.8114 (p) REVERT: H 551 GLU cc_start: 0.6378 (tm-30) cc_final: 0.6132 (tm-30) REVERT: H 572 LEU cc_start: 0.8714 (mt) cc_final: 0.8473 (mm) REVERT: H 637 MET cc_start: 0.7315 (ppp) cc_final: 0.6955 (ppp) REVERT: H 645 MET cc_start: 0.8009 (mtt) cc_final: 0.7745 (mtp) REVERT: H 647 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7332 (mm) REVERT: H 667 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8112 (m-80) outliers start: 52 outliers final: 34 residues processed: 603 average time/residue: 0.3070 time to fit residues: 271.5617 Evaluate side-chains 620 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 576 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 693 ARG Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 607 TYR Chi-restraints excluded: chain G residue 637 MET Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 227 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 0.2980 chunk 143 optimal weight: 0.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS F 468 ASN G 602 GLN G 707 ASN H 636 HIS H 644 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4808 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= 0.196 Angle : 0.717 17.595 25400 Z= 0.338 Chirality : 0.040 0.262 2910 Planarity : 0.004 0.052 3248 Dihedral : 4.025 22.160 2498 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.38 % Allowed : 25.10 % Favored : 72.52 % 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: -0.31 (0.18), residues: 2296 helix: 0.45 (0.14), residues: 1618 sheet: None (None), residues: 0 loop : -1.68 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 448 HIS 0.007 0.001 HIS H 644 PHE 0.026 0.002 PHE F 441 TYR 0.011 0.001 TYR H 554 ARG 0.009 0.000 ARG C 655 ********************** 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 627 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 579 time to evaluate : 2.015 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: A 438 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7380 (mtt90) REVERT: A 440 GLN cc_start: 0.8040 (mt0) cc_final: 0.7621 (mt0) REVERT: A 484 ARG cc_start: 0.6740 (pmt-80) cc_final: 0.6281 (pmt-80) REVERT: A 486 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8244 (mmmt) REVERT: A 491 ASN cc_start: 0.7520 (m-40) cc_final: 0.7163 (m-40) REVERT: A 515 GLU cc_start: 0.7710 (tp30) cc_final: 0.7436 (tp30) REVERT: A 534 GLN cc_start: 0.6867 (tt0) cc_final: 0.6329 (tt0) REVERT: A 629 LYS cc_start: 0.7386 (ptmm) cc_final: 0.7025 (ptmm) REVERT: A 670 ASP cc_start: 0.7803 (p0) cc_final: 0.7450 (p0) REVERT: A 675 GLU cc_start: 0.7131 (tt0) cc_final: 0.6835 (tt0) REVERT: A 695 GLU cc_start: 0.7426 (tp30) cc_final: 0.5562 (tp30) REVERT: A 698 ARG cc_start: 0.7526 (mtm110) cc_final: 0.6227 (mtm180) REVERT: A 700 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7043 (mm-30) REVERT: A 715 GLU cc_start: 0.7896 (mp0) cc_final: 0.7360 (mp0) REVERT: B 419 LYS cc_start: 0.7443 (tppt) cc_final: 0.6962 (tppt) REVERT: B 508 LYS cc_start: 0.8366 (tttp) cc_final: 0.8021 (ttmt) REVERT: B 514 MET cc_start: 0.7561 (ttm) cc_final: 0.7254 (ttp) REVERT: B 527 ASN cc_start: 0.8031 (p0) cc_final: 0.7754 (p0) REVERT: B 536 GLN cc_start: 0.7168 (tm-30) cc_final: 0.6600 (tm-30) REVERT: B 539 ASP cc_start: 0.8079 (t0) cc_final: 0.7762 (t0) REVERT: B 601 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7300 (t80) REVERT: B 666 GLN cc_start: 0.7992 (mp10) cc_final: 0.7791 (pm20) REVERT: B 691 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 693 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7083 (ptt-90) REVERT: C 428 TYR cc_start: 0.8058 (t80) cc_final: 0.7745 (t80) REVERT: C 539 ASP cc_start: 0.7482 (t70) cc_final: 0.7230 (m-30) REVERT: C 559 ASP cc_start: 0.7586 (t0) cc_final: 0.7381 (t0) REVERT: C 574 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7673 (tt) REVERT: C 711 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7802 (mmt180) REVERT: D 464 ARG cc_start: 0.7301 (ttp80) cc_final: 0.6731 (ttp80) REVERT: D 466 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7160 (mt) REVERT: D 573 LEU cc_start: 0.8813 (mm) cc_final: 0.8521 (mm) REVERT: D 637 MET cc_start: 0.7280 (ppp) cc_final: 0.6784 (ppp) REVERT: D 687 ASP cc_start: 0.8011 (t70) cc_final: 0.7654 (t0) REVERT: E 438 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7115 (mtt90) REVERT: E 440 GLN cc_start: 0.7978 (mt0) cc_final: 0.7582 (mt0) REVERT: E 491 ASN cc_start: 0.7569 (m-40) cc_final: 0.7195 (m-40) REVERT: E 629 LYS cc_start: 0.7346 (ptmm) cc_final: 0.6981 (ptmm) REVERT: E 666 GLN cc_start: 0.8175 (tp40) cc_final: 0.7827 (tp40) REVERT: E 670 ASP cc_start: 0.7730 (p0) cc_final: 0.7331 (p0) REVERT: E 695 GLU cc_start: 0.7450 (tp30) cc_final: 0.6378 (tp30) REVERT: E 696 ILE cc_start: 0.8512 (tp) cc_final: 0.8248 (tp) REVERT: E 698 ARG cc_start: 0.7381 (mtm110) cc_final: 0.6422 (mtm180) REVERT: E 700 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6960 (mm-30) REVERT: E 715 GLU cc_start: 0.7917 (mp0) cc_final: 0.7265 (mp0) REVERT: F 515 GLU cc_start: 0.6771 (pt0) cc_final: 0.6555 (pt0) REVERT: F 527 ASN cc_start: 0.8170 (p0) cc_final: 0.7918 (p0) REVERT: F 529 ILE cc_start: 0.7608 (mm) cc_final: 0.7330 (mt) REVERT: F 536 GLN cc_start: 0.7143 (tm-30) cc_final: 0.6595 (tm-30) REVERT: F 691 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8073 (tm-30) REVERT: F 692 LEU cc_start: 0.8722 (tp) cc_final: 0.8485 (tt) REVERT: F 693 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6971 (ptt-90) REVERT: G 558 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7497 (tp) REVERT: G 602 GLN cc_start: 0.6593 (mt0) cc_final: 0.6071 (mt0) REVERT: H 441 PHE cc_start: 0.8268 (t80) cc_final: 0.7928 (t80) REVERT: H 466 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.6702 (mt) REVERT: H 470 SER cc_start: 0.8724 (m) cc_final: 0.8112 (p) REVERT: H 551 GLU cc_start: 0.6351 (tm-30) cc_final: 0.6117 (tm-30) REVERT: H 572 LEU cc_start: 0.8700 (mt) cc_final: 0.8475 (mm) REVERT: H 637 MET cc_start: 0.7259 (ppp) cc_final: 0.6896 (ppp) REVERT: H 645 MET cc_start: 0.8013 (mtt) cc_final: 0.7743 (mtp) REVERT: H 647 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7377 (mp) REVERT: H 667 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: H 685 MET cc_start: 0.7004 (tpt) cc_final: 0.6542 (mmm) outliers start: 48 outliers final: 33 residues processed: 601 average time/residue: 0.3094 time to fit residues: 272.7389 Evaluate side-chains 616 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 574 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 693 ARG Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 607 TYR Chi-restraints excluded: chain G residue 637 MET Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 0.0670 chunk 159 optimal weight: 0.0040 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS F 468 ASN F 534 GLN G 689 HIS H 644 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.158831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125482 restraints weight = 51438.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132865 restraints weight = 24014.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136347 restraints weight = 12370.131| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18794 Z= 0.190 Angle : 0.704 17.652 25400 Z= 0.334 Chirality : 0.040 0.244 2910 Planarity : 0.004 0.053 3248 Dihedral : 3.999 21.599 2498 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.43 % Allowed : 25.25 % Favored : 72.33 % 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: -0.21 (0.18), residues: 2296 helix: 0.50 (0.14), residues: 1620 sheet: None (None), residues: 0 loop : -1.60 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 542 HIS 0.006 0.001 HIS D 644 PHE 0.051 0.002 PHE G 667 TYR 0.011 0.001 TYR H 554 ARG 0.007 0.000 ARG G 693 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5222.27 seconds wall clock time: 93 minutes 36.23 seconds (5616.23 seconds total)