Starting phenix.real_space_refine (version: dev) on Fri Apr 8 15:40:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln6_23450/04_2022/7ln6_23450_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln6_23450/04_2022/7ln6_23450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln6_23450/04_2022/7ln6_23450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln6_23450/04_2022/7ln6_23450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln6_23450/04_2022/7ln6_23450_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln6_23450/04_2022/7ln6_23450_updated.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 75": "OD1" <-> "OD2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A ASP 649": "OD1" <-> "OD2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ASP 450": "OD1" <-> "OD2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ASP 630": "OD1" <-> "OD2" Residue "C ASP 649": "OD1" <-> "OD2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C ASP 734": "OD1" <-> "OD2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "C PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "D ASP 484": "OD1" <-> "OD2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D ASP 564": "OD1" <-> "OD2" Residue "D PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 580": "OD1" <-> "OD2" Residue "D ASP 609": "OD1" <-> "OD2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D ASP 686": "OD1" <-> "OD2" Residue "D GLU 706": "OE1" <-> "OE2" Residue "D ASP 734": "OD1" <-> "OD2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E ASP 598": "OD1" <-> "OD2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E ASP 630": "OD1" <-> "OD2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E GLU 704": "OE1" <-> "OE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 751": "OD1" <-> "OD2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 204": "OD1" <-> "OD2" Residue "F GLU 221": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F ASP 373": "OD1" <-> "OD2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F ASP 428": "OD1" <-> "OD2" Residue "F GLU 477": "OE1" <-> "OE2" Residue "F ASP 478": "OD1" <-> "OD2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 580": "OD1" <-> "OD2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 35072 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5693 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 36, 'TRANS': 690, 'PCIS': 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5766 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 36, 'TRANS': 700, 'PCIS': 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5866 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 37, 'TRANS': 710, 'PCIS': 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5869 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 37, 'TRANS': 710, 'PCIS': 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5800 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 36, 'TRANS': 702, 'PCIS': 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5604 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 37, 'TRANS': 672, 'PCIS': 4} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 90 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.63, per 1000 atoms: 0.56 Number of scatterers: 35072 At special positions: 0 Unit cell: (166.891, 170.08, 147.757, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 31 15.00 Mg 7 11.99 O 6672 8.00 N 6222 7.00 C 21962 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.41 Conformation dependent library (CDL) restraints added in 5.2 seconds 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 201 helices and 33 sheets defined 43.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 130 through 138 removed outlier: 4.737A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.462A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.757A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 387 removed outlier: 3.653A pdb=" N LYS A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.780A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.193A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 547 No H-bonds generated for 'chain 'A' and resid 544 through 547' Processing helix chain 'A' and resid 554 through 568 Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 594 through 608 Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 713 removed outlier: 4.090A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 749 through 765 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 130 through 139 removed outlier: 4.450A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.531A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.162A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 271 through 274 No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.654A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 547 removed outlier: 4.015A pdb=" N LEU B 547 " --> pdb=" O GLY B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 547' Processing helix chain 'B' and resid 554 through 568 removed outlier: 3.668A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 582 No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 596 through 608 removed outlier: 3.557A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 650 through 662 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 713 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.733A pdb=" N GLU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 765 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 130 through 139 removed outlier: 4.692A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.302A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.806A pdb=" N VAL C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 554 through 568 Processing helix chain 'C' and resid 579 through 582 No H-bonds generated for 'chain 'C' and resid 579 through 582' Processing helix chain 'C' and resid 596 through 608 removed outlier: 3.756A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 713 removed outlier: 3.671A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.092A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 765 removed outlier: 3.698A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 130 through 139 removed outlier: 4.804A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.568A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.672A pdb=" N VAL D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 534 removed outlier: 3.578A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 547 No H-bonds generated for 'chain 'D' and resid 545 through 547' Processing helix chain 'D' and resid 554 through 568 removed outlier: 3.683A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 582 No H-bonds generated for 'chain 'D' and resid 579 through 582' Processing helix chain 'D' and resid 596 through 608 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 650 through 663 removed outlier: 5.165A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.703A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 713 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.709A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 764 removed outlier: 4.076A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 130 through 139 removed outlier: 4.693A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.906A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.103A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 271 through 274 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 338 removed outlier: 4.296A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 428 removed outlier: 4.081A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 483 through 498 removed outlier: 4.479A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.582A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 546 No H-bonds generated for 'chain 'E' and resid 544 through 546' Processing helix chain 'E' and resid 554 through 568 removed outlier: 3.632A pdb=" N VAL E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 582 No H-bonds generated for 'chain 'E' and resid 579 through 582' Processing helix chain 'E' and resid 596 through 610 Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 No H-bonds generated for 'chain 'E' and resid 631 through 634' Processing helix chain 'E' and resid 650 through 661 removed outlier: 3.584A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.595A pdb=" N ALA E 676 " --> pdb=" O LEU E 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 672 through 678' Processing helix chain 'E' and resid 684 through 713 Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.948A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 765 removed outlier: 3.766A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 759 " --> pdb=" O TYR E 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 130 through 138 removed outlier: 4.901A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.022A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 374 through 386 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 483 through 498 removed outlier: 4.209A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 547 No H-bonds generated for 'chain 'F' and resid 544 through 547' Processing helix chain 'F' and resid 554 through 568 Processing helix chain 'F' and resid 579 through 582 No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 600 through 613 removed outlier: 4.252A pdb=" N SER F 612 " --> pdb=" O MET F 608 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 634 No H-bonds generated for 'chain 'F' and resid 631 through 634' Processing helix chain 'F' and resid 650 through 663 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 713 Processing helix chain 'F' and resid 733 through 742 Processing helix chain 'F' and resid 749 through 761 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 83 removed outlier: 7.416A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.644A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.818A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.594A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 8.559A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= G, first strand: chain 'B' and resid 38 through 41 removed outlier: 8.207A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.604A pdb=" N ARG B 113 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.659A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.928A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 641 through 644 removed outlier: 8.270A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 27 through 29 Processing sheet with id= M, first strand: chain 'C' and resid 38 through 41 removed outlier: 7.811A pdb=" N VAL C 39 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.546A pdb=" N ILE C 114 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 113 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.809A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.425A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 641 through 645 removed outlier: 8.151A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 81 through 83 removed outlier: 7.687A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.605A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 144 through 147 removed outlier: 3.817A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.431A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 641 through 644 removed outlier: 8.246A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 27 through 29 Processing sheet with id= X, first strand: chain 'E' and resid 38 through 41 removed outlier: 7.341A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.537A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.775A pdb=" N ILE E 146 " --> pdb=" O CYS E 174 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS E 174 " --> pdb=" O ILE E 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.638A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 641 through 645 removed outlier: 8.418A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.603A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.562A pdb=" N HIS F 183 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL F 154 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 144 through 147 removed outlier: 3.991A pdb=" N ARG F 144 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 365 through 368 removed outlier: 6.953A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 346 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.674A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3576 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: 13.96 Time building geometry restraints manager: 15.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 35321 1.57 - 1.92: 333 1.92 - 2.27: 0 2.27 - 2.62: 0 2.62 - 2.96: 3 Bond restraints: 35657 Sorted by residual: bond pdb=" C LEU B 464 " pdb=" N ARG B 465 " ideal model delta sigma weight residual 1.332 2.953 -1.620 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 1.332 2.888 -1.556 1.40e-02 5.10e+03 1.24e+04 bond pdb=" C LEU D 464 " pdb=" N ARG D 465 " ideal model delta sigma weight residual 1.333 2.965 -1.632 1.73e-02 3.34e+03 8.90e+03 bond pdb=" CG PRO A 137 " pdb=" CD PRO A 137 " ideal model delta sigma weight residual 1.503 1.234 0.269 3.40e-02 8.65e+02 6.27e+01 bond pdb=" CB PRO A 137 " pdb=" CG PRO A 137 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.95e+00 ... (remaining 35652 not shown) Histogram of bond angle deviations from ideal: 55.14 - 72.09: 2 72.09 - 89.04: 2 89.04 - 105.99: 1055 105.99 - 122.94: 44444 122.94 - 139.89: 2716 Bond angle restraints: 48219 Sorted by residual: angle pdb=" O LEU E 464 " pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 122.12 55.14 66.98 1.06e+00 8.90e-01 3.99e+03 angle pdb=" O LEU B 464 " pdb=" C LEU B 464 " pdb=" N ARG B 465 " ideal model delta sigma weight residual 122.46 56.33 66.13 1.38e+00 5.25e-01 2.30e+03 angle pdb=" O LEU D 464 " pdb=" C LEU D 464 " pdb=" N ARG D 465 " ideal model delta sigma weight residual 122.34 85.90 36.44 1.80e+00 3.09e-01 4.10e+02 angle pdb=" C LEU D 464 " pdb=" N ARG D 465 " pdb=" CA ARG D 465 " ideal model delta sigma weight residual 122.55 91.47 31.08 2.03e+00 2.43e-01 2.34e+02 angle pdb=" N PRO A 137 " pdb=" CD PRO A 137 " pdb=" CG PRO A 137 " ideal model delta sigma weight residual 103.20 87.39 15.81 1.50e+00 4.44e-01 1.11e+02 ... (remaining 48214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.61: 21414 32.61 - 65.22: 513 65.22 - 97.83: 72 97.83 - 130.44: 5 130.44 - 163.06: 6 Dihedral angle restraints: 22010 sinusoidal: 9175 harmonic: 12835 Sorted by residual: dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 103.06 -163.06 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 96.01 -156.01 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 95.87 -155.87 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 22007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3875 0.040 - 0.080: 1036 0.080 - 0.119: 455 0.119 - 0.159: 55 0.159 - 0.199: 5 Chirality restraints: 5426 Sorted by residual: chirality pdb=" CB THR F 509 " pdb=" CA THR F 509 " pdb=" OG1 THR F 509 " pdb=" CG2 THR F 509 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CB ILE A 303 " pdb=" CA ILE A 303 " pdb=" CG1 ILE A 303 " pdb=" CG2 ILE A 303 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CB VAL A 235 " pdb=" CA VAL A 235 " pdb=" CG1 VAL A 235 " pdb=" CG2 VAL A 235 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 5423 not shown) Planarity restraints: 6314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 464 " 0.184 2.00e-02 2.50e+03 2.74e-01 7.48e+02 pdb=" C LEU E 464 " -0.441 2.00e-02 2.50e+03 pdb=" O LEU E 464 " 0.266 2.00e-02 2.50e+03 pdb=" N ARG E 465 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 464 " -0.187 2.00e-02 2.50e+03 2.73e-01 7.48e+02 pdb=" C LEU B 464 " 0.444 2.00e-02 2.50e+03 pdb=" O LEU B 464 " -0.258 2.00e-02 2.50e+03 pdb=" N ARG B 465 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 464 " 0.169 2.00e-02 2.50e+03 2.35e-01 5.51e+02 pdb=" C LEU D 464 " -0.396 2.00e-02 2.50e+03 pdb=" O LEU D 464 " 0.181 2.00e-02 2.50e+03 pdb=" N ARG D 465 " 0.045 2.00e-02 2.50e+03 ... (remaining 6311 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 281 2.57 - 3.15: 29005 3.15 - 3.74: 56267 3.74 - 4.32: 76768 4.32 - 4.90: 125688 Nonbonded interactions: 288009 Sorted by model distance: nonbonded pdb=" O3G ATP D 901 " pdb="MG MG D 904 " model vdw 1.989 2.170 nonbonded pdb=" O1G ATP D 902 " pdb="MG MG D 903 " model vdw 2.023 2.170 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 902 " model vdw 2.060 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 903 " model vdw 2.061 2.170 nonbonded pdb=" O3B ATP F 901 " pdb="MG MG F 903 " model vdw 2.073 2.170 ... (remaining 288004 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 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 388 or (resid 389 and (name N or name CA or name C or name O or name CB )) or r \ esid 390 through 533 or (resid 534 and (name N or name CA or name C or name O or \ name CB )) or resid 535 through 545 or (resid 546 through 549 and (name N or na \ me CA or name C or name O or name CB )) or resid 550 through 555 or (resid 556 t \ hrough 557 and (name N or name CA or name C or name O or name CB )) or resid 558 \ through 583 or resid 597 through 762)) selection = (chain 'B' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 441 or (resid 442 and (name N o \ r name CA or name C or name O or name CB )) or resid 443 through 461 or resid 47 \ 2 through 507 or (resid 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 through 545 or (resid 546 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB )) or resid 558 th \ rough 583 or resid 597 through 743 or (resid 744 and (name N or name CA or name \ C or name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 762)) selection = (chain 'C' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 335 or (resid 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 or (res \ id 338 through 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or (resid 546 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB )) or resid 558 th \ rough 583 or resid 597 through 743 or (resid 744 and (name N or name CA or name \ C or name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 762)) selection = (chain 'D' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 335 or (resid 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 or (res \ id 338 through 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or (resid 546 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB )) or resid 558 th \ rough 583 or resid 597 through 743 or (resid 744 and (name N or name CA or name \ C or name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 762)) selection = (chain 'E' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 335 or (resid 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 or (res \ id 338 through 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or (resid 546 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB )) or resid 558 th \ rough 583 or resid 597 through 743 or (resid 744 and (name N or name CA or name \ C or name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 762)) selection = (chain 'F' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 335 or (resid 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 or (res \ id 338 through 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 743 or (resid 744 and (name N or name CA or name C or \ name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or name \ CA or name C or name O or name CB )) or resid 756 through 762)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21962 2.51 5 N 6222 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.010 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.290 Process input model: 88.390 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 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 : 0.015 1.632 35657 Z= 1.075 Angle : 0.823 66.977 48219 Z= 0.526 Chirality : 0.044 0.199 5426 Planarity : 0.008 0.274 6314 Dihedral : 14.719 163.055 13678 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.64 % Favored : 97.34 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 0.78 (0.13), residues: 4393 helix: 0.85 (0.12), residues: 1936 sheet: 0.86 (0.21), residues: 671 loop : 0.18 (0.15), residues: 1786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 time to evaluate : 4.309 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 outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.5125 time to fit residues: 273.4805 Evaluate side-chains 181 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 4.300 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 20.0000 chunk 336 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 259 optimal weight: 0.3980 chunk 403 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN C 212 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 35657 Z= 0.216 Angle : 0.592 14.504 48219 Z= 0.297 Chirality : 0.044 0.164 5426 Planarity : 0.005 0.068 6314 Dihedral : 7.941 160.357 4914 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.61 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 1.07 (0.13), residues: 4399 helix: 1.25 (0.12), residues: 1932 sheet: 0.50 (0.20), residues: 711 loop : 0.37 (0.16), residues: 1756 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 200 time to evaluate : 4.209 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 outliers start: 29 outliers final: 14 residues processed: 215 average time/residue: 0.4474 time to fit residues: 161.7590 Evaluate side-chains 189 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 3.924 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3955 time to fit residues: 15.0789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 335 optimal weight: 0.5980 chunk 274 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 403 optimal weight: 5.9990 chunk 436 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 chunk 400 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 324 optimal weight: 2.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 GLN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 35657 Z= 0.338 Angle : 0.616 11.305 48219 Z= 0.308 Chirality : 0.044 0.158 5426 Planarity : 0.005 0.062 6314 Dihedral : 7.618 152.337 4914 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.64 % Favored : 97.34 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 1.07 (0.13), residues: 4399 helix: 1.36 (0.12), residues: 1927 sheet: 0.22 (0.19), residues: 731 loop : 0.37 (0.16), residues: 1741 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 8 residues processed: 204 average time/residue: 0.4581 time to fit residues: 159.5804 Evaluate side-chains 173 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 4.418 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3218 time to fit residues: 10.8036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.9980 chunk 303 optimal weight: 30.0000 chunk 209 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 405 optimal weight: 9.9990 chunk 429 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN E 348 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.110 35657 Z= 0.343 Angle : 0.615 14.223 48219 Z= 0.306 Chirality : 0.044 0.212 5426 Planarity : 0.005 0.058 6314 Dihedral : 7.426 144.507 4914 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4399 helix: 1.35 (0.12), residues: 1924 sheet: 0.12 (0.19), residues: 711 loop : 0.37 (0.16), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 4.317 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 outliers start: 44 outliers final: 17 residues processed: 203 average time/residue: 0.4451 time to fit residues: 156.1237 Evaluate side-chains 174 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 4.484 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3641 time to fit residues: 17.2332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.9990 chunk 243 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 366 optimal weight: 0.8980 chunk 296 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 385 optimal weight: 30.0000 chunk 108 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 568 GLN C 90 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 35657 Z= 0.180 Angle : 0.546 15.600 48219 Z= 0.266 Chirality : 0.043 0.176 5426 Planarity : 0.004 0.054 6314 Dihedral : 7.168 141.293 4914 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.43 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 1.21 (0.13), residues: 4399 helix: 1.51 (0.12), residues: 1925 sheet: 0.17 (0.19), residues: 712 loop : 0.45 (0.16), residues: 1762 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 192 average time/residue: 0.4551 time to fit residues: 150.9450 Evaluate side-chains 174 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 4.364 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3915 time to fit residues: 16.3280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 4.9990 chunk 386 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 429 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN C 90 ASN C 533 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.200 35657 Z= 0.297 Angle : 0.577 16.458 48219 Z= 0.286 Chirality : 0.043 0.168 5426 Planarity : 0.004 0.053 6314 Dihedral : 7.030 139.687 4914 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.14 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 1.24 (0.13), residues: 4399 helix: 1.55 (0.12), residues: 1919 sheet: 0.26 (0.20), residues: 691 loop : 0.42 (0.16), residues: 1789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 182 average time/residue: 0.4339 time to fit residues: 136.9216 Evaluate side-chains 166 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 4.235 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3049 time to fit residues: 12.2019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 244 optimal weight: 0.0670 chunk 313 optimal weight: 8.9990 chunk 243 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 427 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 260 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 568 GLN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.118 35657 Z= 0.200 Angle : 0.546 18.346 48219 Z= 0.266 Chirality : 0.042 0.170 5426 Planarity : 0.004 0.127 6314 Dihedral : 6.799 136.211 4914 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 1.32 (0.13), residues: 4399 helix: 1.64 (0.12), residues: 1912 sheet: 0.14 (0.19), residues: 733 loop : 0.51 (0.16), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 183 average time/residue: 0.4592 time to fit residues: 145.5887 Evaluate side-chains 166 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 4.501 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3363 time to fit residues: 10.7018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 291 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN C 90 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 35657 Z= 0.172 Angle : 0.531 15.909 48219 Z= 0.258 Chirality : 0.042 0.158 5426 Planarity : 0.004 0.094 6314 Dihedral : 6.596 132.811 4914 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 1.37 (0.13), residues: 4399 helix: 1.67 (0.12), residues: 1918 sheet: 0.23 (0.20), residues: 724 loop : 0.51 (0.16), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 4.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 167 average time/residue: 0.4489 time to fit residues: 130.7612 Evaluate side-chains 157 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 4.304 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3310 time to fit residues: 7.7413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 9.9990 chunk 409 optimal weight: 2.9990 chunk 374 optimal weight: 20.0000 chunk 398 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 360 optimal weight: 4.9990 chunk 377 optimal weight: 7.9990 chunk 397 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN D 296 ASN E 421 GLN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 760 GLN F 660 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.139 35657 Z= 0.471 Angle : 0.683 15.724 48219 Z= 0.337 Chirality : 0.046 0.158 5426 Planarity : 0.005 0.077 6314 Dihedral : 6.873 135.275 4914 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.48 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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 (0.13), residues: 4399 helix: 1.43 (0.12), residues: 1919 sheet: 0.28 (0.20), residues: 690 loop : 0.37 (0.16), residues: 1790 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 4.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 159 average time/residue: 0.4315 time to fit residues: 120.3787 Evaluate side-chains 154 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 4.190 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3061 time to fit residues: 9.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 2.9990 chunk 421 optimal weight: 20.0000 chunk 257 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 442 optimal weight: 10.0000 chunk 407 optimal weight: 0.0030 chunk 352 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 421 GLN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.166 35657 Z= 0.162 Angle : 0.561 16.694 48219 Z= 0.273 Chirality : 0.042 0.146 5426 Planarity : 0.004 0.078 6314 Dihedral : 6.516 130.459 4914 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 1.36 (0.13), residues: 4399 helix: 1.64 (0.12), residues: 1906 sheet: 0.29 (0.20), residues: 693 loop : 0.50 (0.16), residues: 1800 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 4.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.4487 time to fit residues: 127.2536 Evaluate side-chains 157 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 4.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 10.0000 chunk 375 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 362 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN E 348 ASN E 421 GLN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.076117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053212 restraints weight = 157606.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.053467 restraints weight = 90893.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053609 restraints weight = 62909.327| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.167 35657 Z= 0.362 Angle : 0.631 16.186 48219 Z= 0.310 Chirality : 0.044 0.174 5426 Planarity : 0.005 0.077 6314 Dihedral : 6.601 131.530 4914 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % 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: 1.28 (0.13), residues: 4399 helix: 1.58 (0.12), residues: 1910 sheet: 0.23 (0.20), residues: 696 loop : 0.48 (0.16), residues: 1793 =============================================================================== Job complete usr+sys time: 4947.95 seconds wall clock time: 92 minutes 46.40 seconds (5566.40 seconds total)